Biology subjects

Fansler, S. J.

Publications and source records attributed to Fansler, S. J..

8 recordsLinked to original sources

bioRxiv2026

Drought duration does not impact soil microbiome resilience

Increasing global droughts exert large but poorly understood effects on the microbial communities and ecology of soil. Microbial communities generally show resilience and return to pre-drought conditions when short-term droughted soils are rewet; soils exposed to long-term drought, however, often show a lag upon rewetting, after which microbial communities may or may not return to their pre-stressed conditions. Though short-term droughts have been widely studied, long-term drought manipulation experiments remain rare, especially those that compare microbial response to short-term and long-term drought in tandem. We conducted a 1000-day drought simulation in controlled laboratory conditions with soil cores collected from a tidal freshwater ecosystem in Washington state, USA, and subsequently exposed them to rewetting for two weeks. We also included short-term (30-day and 90-day) drought and rewet treatments to directly compare microbial community and organic matter responses across drought durations. We found distinct microbial taxa belonging to Firmicutes and Actinobacteria enriched after the 1000-day drought, but not after the short-term droughts. While we hypothesized that the microbial community would recover from a short-term drought after rewetting to resemble pre-drought conditions, our results revealed community dissimilarities between rewet and pre-drought conditions across all drought durations. These findings suggest unique microbial life history strategies within certain microbial phyla that make them successful colonizers during an extended drought period, and the influence of environmental and physiological context on microbial responses to rewetting. ImportanceDroughts are increasing in frequency and intensity globally with severe implications for ecosystem services and soil functions. It is important to understand how long-term drought impacts soil microbial communities and organic matter chemistry to better predict future ecosystem responses to sustained moisture deficit conditions. We subjected soils to short-term (30 and 90 days) and long-term (1000 days) drought treatments and subsequently rewetted them to understand microbiome recovery to pre-drought conditions. Our results showed that prolonged drought drastically changes the microbial community and soil organic matter profile compared to short-term drought. While we expected the soil microbiome to recover upon rewetting after short-term drought, our results showed an altered microbiome composition, compared to pre-drought conditions, for both short-and long-term drought, suggesting microbial responses to soil rewetting was independent of drought duration imposed. These results provide important insights into soil biological and chemical functions that remain sensitive to change under fluctuating soil moisture conditions and future drought scenarios.

ecology↗

bioRxiv2020

Disturbance Triggers Non-Linear Microbe-Environment Feedbacks

Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community--but not the whole community--responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter became less favorable for oxidation (an environmental component) and respiration decreased (a microbial process). While these responses were step functions of desiccation, we observed continuous monotonic relationships among community assembly, respiration, and organic matter thermodynamics. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance, mediated by thermodynamics, and that cause the impacts of disturbance to be dependent on the history of disturbance.

ecology↗

bioRxiv2020

Unification of Environmental Metabolomics with Metacommunity Ecology

Environmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis meta-metabolome ecology and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed -diversity and {beta}-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and {beta}NTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.

ecology↗

bioRxiv2019

Temporal dynamics of nitrogen cycle gene diversity in a hyporheic microbiome

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-- defined as the number of unique within-gene phylotypes--across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that (1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and (2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

ecology↗

bioRxiv2019

Selection, succession and stabilization of soil microbial consortia

Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. Here we investigated the successional dynamics of a soil microbiome during 21-weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a highly mixed liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain relatively constant community structure over time. We also hypothesized that long term, substrate-driven growth would result in consortia with reduced species richness as compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil compared to liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix compared to liquid environments. IMPORTANCEThe soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. Here we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

microbiology↗

bioRxiv2018

A broad-host-range event detector: expanding and quantifying performance across bacterial species

Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli. It is clear that new applications - such as chemical sensing and event logging in complex environments - will benefit from new host chassis. This study quantitatively compared how a chemical event logger performed across multiple microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads - Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two bench-mark Escherichia coli chassis including the probiotic Nissle 1917 and common cloning strain DH5. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and down-stream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5 in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

synthetic biology↗

bioRxiv2018

Forfeiting the founder effect: turnover defines biofilm community succession

Microbial community succession is a fundamental process that effects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the roles of founder species? We performed a succession experiment within a hypersaline microbial mat ecosystem to investigate how ecological processes contributed to the turnover of founder species. Bacterial and micro-eukaryotic founder species were identified from primary succession and tracked through a defined maturation period using 16S and 18S rRNA gene amplicon sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate basic functional capabilities. The majority of the founder species did not maintain high relative abundances in later stages of succession. Turnover (versus nestedness) was the dominant process shaping the final community structure. We also asked if different ecological processes acted on bacteria versus eukaryotes during successional stages and found that deterministic and stochastic forces corresponded more with eukaryote and bacterial colonization, respectively. Our results show that taxa from different kingdoms, that share habitat in the tight spatial confines of a biofilm, were influenced by different ecological forces and time scales of succession.

ecology↗

bioRxiv2018

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

ecology↗