Biology subjects

Kemner, K. M.

Publications and source records attributed to Kemner, K. M..

5 recordsLinked to original sources

bioRxiv2026

A network perspective on the role of c-di-GMP-associated protein complexes in biofilm formation.

1.The secondary messenger cyclic di-GMP is a ubiquitous bacterial signal that regulates the switch from a free-swimming to a sessile biofilm-forming lifestyle. Many biofilm-forming Pseudomonas species possess numerous c-di-GMP-binding proteins (CDGs) which regulate gene expression, protein activity, and protein complexes. However, the mechanisms by which numerous CDG effectors form a coherent signaling network to coordinate lifestyle changes remain poorly understood. We addressed this knowledge gap by focusing on ten CDG proteins involved in biofilm development in P. fluorescens SBW25. We used an integrated approach combining a protein interaction network from genome-wide yeast two-hybrid (Y2H) screens with large-scale biofilm and motility phenotype analyses via CRISPR interference (CRISPRi). Our network associated c-di-GMP signaling with processes such as signal transduction, solute transport, secretion, virulence, transcriptional regulation, DNA repair, and cell division. We discovered unknown functions of two CDG proteins in DNA repair and cell division, supporting the significance of our network. Notably, the phosphodiesterase DipA interacts with numerous CDG proteins through GGDEF domains. Phenotypic analyses revealed that CDG partners were highly correlated or strongly anticorrelated with DipA. These findings suggest that DipA is a central hub for CDG interactions that integrates opposing modules. These findings support the hub-based model of c-di-GMP signaling, which is crucial for localized control and rapid adaptation to environmental changes.

microbiology↗

bioRxiv2023

Groundwater redox dynamics across the terrestrial-aquatic interface of Lake Erie coastal ecosystems

Groundwater biogeochemistry in coastal areas is spatially and temporally dynamic because fluctuations in groundwater level may cause alternate redox between distinct hydrological conditions. Recent studies have proposed connections between biogeochemistry and large-scale hydrological processes, specifically focusing on the role of redox-active compounds in changing the oxidation state during flooding and draining events. While water saturation generally results in a shift of redox-active compounds from electron donors to acceptors, the specific mechanisms underlying the transition of groundwater between oxidizing and reducing conditions in response to water level fluctuations are uncertain. To determine the effects of groundwater levels on redox dynamics, we monitored groundwater redox potential across the terrestrial-aquatic interface in Lake Erie coastal areas throughout the high and low-water seasons. In contrast to previously observed responses to flooding in soils, our results revealed patterns of oxidizing redox potentials during high-water and reducing during low-water periods. Furthermore, short-term fluctuations in water table levels significantly impacted the redox potential of groundwater when dissolved oxygen increased, and redox dynamics displayed voltage hysteresis in most events. Based on these findings, we propose that for improved predictions of microbial functions and biogeochemical cycles, redox-informed models should incorporate the antagonistic changes in groundwater redox balance compared to soils and consider the time lags in redox fluctuations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/544684v1_figu1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4d7a19org.highwire.dtl.DTLVardef@8b2b92org.highwire.dtl.DTLVardef@d9bc11org.highwire.dtl.DTLVardef@ca3e13_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractConceptual diagram of groundwater redox fluctuations in coastal ecosystems. Large redox fluctuations are derived by dissolved oxygen inputs and smaller more frequent redox fluctuations are led by redox sensitive species leaching from topsoil. C_FIG

ecology↗

bioRxiv2020

Wetland plant evolutionary history influences soil and endophyte microbial community composition

Methane is a microbially derived greenhouse gas whose emissions are highly variable throughout wetland ecosystems. Differences in plant community composition account for some of this variability, suggesting an influence of plant species on microbial community structure and function in these ecosystems. Given that closely related plant species have similar morphological and biochemical features, we hypothesize that plant evolutionary history is related to differences in microbial community composition. To examine species-specific patterns in microbiomes, we selected five monoculture-forming wetland plant species based on the evolutionary distances among them. We detected significant differences in microbial communities between sample types (unvegetated soil, bulk soil, rhizosphere soil, internal root tissues, and internal leaf tissues) associated with these plant species based on 16S relative abundances. We additionally found that differences in plant evolutionary history were correlated with variation in microbial communities across plant species within each sample type. Using qPCR, we observed substantial differences in overall methanogen and methanotroph population sizes between plant species and sample types. Methanogens tended to be most abundant in rhizosphere soils while methanotrophs were the most abundant in roots. Given that microbes influence methane flux and that plants affect methanogen and methanotroph populations, plant species contribute to variable degrees of methane emissions. Incorporating the influence of plant evolutionary history into future modeling efforts may improve predictions of wetland methane emission since microbial community differences correlate with differences in plant evolutionary history.

ecology↗

bioRxiv2018

RMI-chip: a microfluidics setup for functional imaging of microbial interactions with tree roots

Coupling microfludics with microscopy has emerged as a powerful approach to study at cellular resolution the dynamics in plant physiology and root-microbe interactions. Most devices have been designed to study the model plant Arabidopsis thaliana at higher throughput than conventional methods. However, there is a need for microfluidic devices which enable in vivo studies of root development and root-microbe interactions in woody plants. Here, we developed the RMI-chip, a simple microfluidic setup in which Populus tremuloides (aspen tree) seedlings can grow for over a month, allowing continuous microscopic observation of interactions between live roots and rhizobacteria. We find that the colonization of growing aspen roots by Pseudomonas fluorescens in the RMI-chip involves dynamic biofilm formation and dispersal, in keeping with previous observations in a different experimental set-up. Also, we find that whole-cell biosensors based on the rhizobacterium Bacillus subtilis can be used to monitor compositional changes in the rhizosphere but that the application of these biosensors is limited by their efficiency at colonizing aspen roots and persisting. These results indicate that functional imaging of dynamic root-bacteria interactions in the RMI-chip requires careful matching between the host plant and the bacterial root colonizer.

physiology↗

bioRxiv2017

Community dynamics in parallelized, aerobic, single carbon-source enrichments

Here we seek to test the extent to which laboratory enrichments mimic natural community processes and the degree to which the initial structure of a community determines its response to a press disturbance via the addition of environmentally-relevant carbon compounds. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from 6 different classes of organic compound (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 hours, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still is strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g. Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g. Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Niche selection therefore seems to play a strong role in shaping the communities in the substrate arrays, although some stochasticity is seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to a changing environment.

microbiology↗