Biology subjects

Bohannan, B.

Publications and source records attributed to Bohannan, B..

7 recordsLinked to original sources

bioRxiv2022

Local and regional scale mycorrhizal network assembly in an experimental prairie-pasture system

Arbuscular mycorrhizal (AM) symbioses between plants and fungi are essential to the functioning of terrestrial ecosystems through maintaining soil stability, controlling nutrient cycles (e.g. C, N, P and K), and influencing competitive dynamics in plant communities. Despite the importance of AM symbioses, the ecological coassembly patterns of AM fungi-plant partners are not well characterized across environmental gradients. Further, it is unclear whether fungi forming associations with several plants of the same or different species - forming common mycorrhizal networks (CMNs) - preferentially allocate limiting resources within natural plant communities at the local-scale. We used an experimental prairie-pasture grassland system in three sites along a latitudinal gradient ranging from cool/wet to warm/dry climates to investigate how environmental conditions, local plant diversity and drought shift AM fungal composition and plant-fungal coassembly patterns across spatial scales. We show that plant-AM fungal assembly patterns are hierarchically structured, with environmental variables driving differences in AM fungal communities at the largest spatial scale (across sites), and plant host identity and diversity governing AM assembly at the local scale (within plot). Bipartite interaction networks revealed evidence for preferential partner selection between plants and fungi, while there was no evidence for nested assembly of plant-fungal partners. At the plot-level, we applied stable isotopes (13C and 15N) to illustrate CMN assembly and nutritional function. There was no significant correlation between increased resource transfer among plants in a plot that shared more AM fungal partners; however, we identified specific AM fungi that were indicator taxa for increased plant isotope enrichment. Further research integrating stable isotope probing of fungal DNA in plant roots is necessary to more clearly illustrate the form and function of CMNs in grasslands under different environmental and plant diversity conditions.

ecology↗

bioRxiv2022

Agnostic fungi: plant traits and tissue stoichiometry explain nutrient transfer in common arbuscular mycorrhizal networks of temperate grasslands

Plants and mycorrhizal fungi form mutualistic relationships that affect how resources flow between organisms and within ecosystems. Common mycorrhizal networks (CMNs) could facilitate preferential transfer of carbon and limiting nutrients, but this remains difficult to predict. Do CMNs favor fungal resource acquisition at the expense of plant resource demands (a fungi-centric view), or are they passive channels through which plants regulate resource fluxes (a plant-centric view)? We used stable isotope tracers (13CO2 and 15NH3), plant traits, and mycorrhizal DNA to quantify above- and belowground carbon and nitrogen transfer between 18 plant species along a 520-km latitudinal gradient in the Pacific Northwest, USA. Plant functional type and tissue stoichiometry were the most important predictors of interspecific resource transfer. Of "donor" plants, 98% were 13C-enriched, but we detected transfer in only 2% of "receiver" plants. However, all donors were 15N-enriched and we detected transfer in 81% of receivers. Nitrogen was preferentially transferred to annuals (0.26 {+/-} 0.50 mg N per g leaf mass) compared to perennials (0.13 {+/-} 0.30 mg N per g leaf mass). This corresponded with tissue stoichiometry differences. Our findings suggest that plants and fungi that are located closer together in space and with stronger demand for resources over time are more likely to receive larger amounts of those limiting resources.

ecology↗

bioRxiv2022

Quantifying climate change impacts on plant functional composition and soil nitrogen fixation in Mediterranean grasslands

The projected increase in warming and drought severity (i.e., hotter and drier summers) in the U.S. Pacific Northwest (PNW) may negatively impact grassland plant composition and ecosystem function, with further implications for sustainable land management in the region. To test the vulnerability of Mediterranean grassland function to climate change, we quantified the response of grassland communities to multiannual warming (+2.5{degrees}C) and drought (-40% precipitation) by quantifying plant species diversity, legume cover, and biogeochemical controls on and patterns of soil asymbiotic nitrogen fixation (ANF). We hypothesized that the effects of warming on plant functional diversity would increase soil ANF inputs by decreasing legume cover and soil nitrogen availability. Given that asymbiotic N fixers can increase soil organic carbon (C) and nitrogen (N) availability under drought, we hypothesized that the effect of drought on grassland plant cover correlated with increased soil ANF. We surveyed the vegetation and collected composite soil samples from five co-located plots under control (ambient), drought and warming conditions during the fall and spring seasons. In control and drought plots, we quantified the moderator effect of plant composition by comparing low-diversity (unmanipulated plant composition) and high-diversity (manipulated composition) grassland plots. We used a point intercept technique to survey plot-level plant community composition and calculate Shannons diversity index and percent cover of legumes (members of Fabaceae according to the Integrated Taxonomic Information System). We measured ANF by incubating collected soils with N-labeled dinitrogen (15N2), and quantified total soil C, total and available N, available phosphorus (P) and iron (Fe) pools, pH, and soil water holding capacity. Plant species diversity decreased significantly with warming and along the drought severity gradient. ANF response to warming varied by season and site, with rates increasing along the drought severity gradient in the fall but decreasing in the spring. Total soil inorganic N was the strongest predictor of ANF response to warming in the spring but not in the fall. Soil ANF response to drought increased with drought intensity; while soil ANF increased nearly twofold in the southernmost (warm and dry) site, ANF decreased in the northernmost (cool and wet) site. ANF response to drought also varied depending on plant diversity, where low-diversity grasslands had more predictable response to drought than high-diversity grasslands. Soil P availability and pH were the most important variables explaining ANF variability across vegetation types and sites. Our study highlights the importance of using soil-plant-atmosphere interactions to assess grassland ecosystem resilience to drought and warming in the PNW.

ecology↗

bioRxiv2020

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change

Despite the global importance in ecological processes, the Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. In this study, we used a combination of deep shotgun metagenomics and a machine learning approach to compare physiological strategies of microbial communities between contrasting forest and pasture soils. We showed that microbial communities (bacteria, archaea and viruses), and the composition of protein-coding genes are distinct in each ecosystem. The diversities of these metagenomic datasets are strongly correlated, indicating that the protein-coding genes found in any given sample of these soil types are predictable from their taxonomic lineages. Shifts in metagenome profiles reflected potential physiological differences caused by forest-to-pasture conversion with alterations in gene abundances related to carbohydrate and energy metabolisms. These variations in these gene contents are associated with several soil factors including C/N, temperature and H++Al3+ (exchangeable acidity). These data underscore that microbial community taxa and protein-coding genes co-vary. Differences in gene abundances for carbohydrate utilization, energy, amino acid, and xenobiotic metabolisms indicate alterations of physiological strategy with forest-to-pasture conversion, with potential consequences to C and N cycles. Our analysis also indicated that soil virome was altered and shifts in the viral community provide insights into increased health risks to human and animal populations.

microbiology↗

bioRxiv2020

Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica

Active volcanoes in Antarctica, in contrast to the rest of the icy landscape, have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers (<0 {degrees}C) and active fumaroles (up to 100 {degrees}C). Steep gradients in temperature, salinity and geochemistry over very short distances have been reported for Deception Island, and have been shown to effect microbial community structure and diversity. However, little is known regarding how these gradients affect ecosystem functioning, for example due to inhibition of key metabolic enzymes or pathways. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore how microbial functional diversity is shaped by extreme geochemical, salinity and temperature gradients in fumarole and glacier sediments. We observed that microbial communities from a 98 {degrees}C fumarole harbor specific hyperthermophilic molecular strategies, as well as reductive and autotrophic pathways, while those from <80 {degrees}C fumaroles possess more diverse metabolic and survival strategies capable of responding to fluctuating redox and temperature conditions. In contrast, glacier communities showed less diverse metabolic potentials, comprising mainly heterotrophic and carbon pathways. Through the reconstruction of genomes, we were able to clarify putative novel lifestyles of underrepresented taxonomic groups, especially those related to Nanoarchaeota and thermophilic ammonia-oxidizing archaeal lineages. Our results enhance understanding of the metabolic and survival capabilities of different extremophilic lineages of Bacteria and Archaea.

microbiology↗

bioRxiv2019

Moving microbes: the dynamics of transient microbial residence on human skin

The human skin microbiome interacts intimately with human health, yet the drivers of skin microbiome composition and diversity are not well-understood. The composition of the skin microbiome has been characterized as both highly variable and relatively stable, depending on the time scale under consideration, and it is not clear what role contact with environmental sources of microbes plays in this variability. We experimentally mimicked human skin contact with two common environmental sources of microorganisms -- soils and plant leaves -- and characterized the dynamics of microbial acquisition and persistence on skin on very short time scales. Repeatable changes in skin community composition following encounters with environmental sources were observed, and these trajectories largely depend on donor community biomass distributions. Changes in composition persisted for at least 24 hours and through a soap and water wash following exposures to relatively high biomass soil communities. In contrast, exposures to lower biomass leaf communities were undetectable after a 24 hour period. Absolute abundances of bacterial taxa in source communities predicted transmission probabilities and residence times, independent of phylogenetic considerations. Our results suggest that variability in the composition of the skin microbiome can be driven by transient encounters with common environmental sources, and that these relatively transient effects can persist when the source is of sufficient biomass.\n\nImportanceHumans come into contact with environmental sources of microbes, such as soil or plants, constantly. Those microbial exposures have been linked to health through training and modulation of the immune system. While much is known about the human skin microbiome, the short term dynamics after a contact event, such as touching soil, have not been well characterized. In this study, we examine what happens after such a contact event, describing trends in microbial transmission to and persistence on the skin. Additionally, we use computational sampling model simulations to interrogate null expectations for these kinds of experiments. This work has broad implications for infection control strategies and therapeutic techniques that rely on modification of the microbiome, such as probiotics and faecal transplantation.

microbiology↗

bioRxiv2018

Use of RNA and DNA to Identify Mechanisms of Microbial Community Homogenization

Biotic homogenization is a commonly observed response following conversion of native ecosystems to agriculture, but our mechanistic understanding of this process is limited for microbial communities. In the case of rapid environmental changes, inference of homogenization mechanisms may be confounded by the fact that only a minority of taxa is active at any given point. RNA- and DNA-based community inference may help to distinguish the active fraction of a community from inactive taxa. Using these two community inference methods, we asked how soil prokaryotic communities respond to land use change following transition from rainforest to agriculture in the Congo Basin. Our results indicate that the magnitude of community homogenization is larger in the RNA-inferred community than the DNA-inferred perspective. We show that as the soil environment changes, the RNA-inferred community structure tracks environmental variation and loses spatial structure. The DNA-inferred community loses its association with environmental variability. Homogenization of the DNA-inferred community appears to instead be driven by the range expansion of a minority of taxa shared between the forest and conversion sites, which is also seen in the RNA-inferred community. Our results suggest that complementing DNA-based surveys with RNA can provide unique perspectives on community responses to environmental change.\n\nIMPORTANCETwo primary mechanisms by which community homogenization occurs are: 1) the loss of environmental heterogeneity driving community convergence, and 2) increased rates of biotic mixing, driven by exotic invasions or range expansions. Better identifying these mechanisms could help inform future mitigation strategies. Only a minority of soil taxa tends to be active at any time, which makes identifying these mechanisms difficult. To circumvent this problem, we measured prokaryotic community structure in two ways: RNA-based inference (which should enrich for active taxa), and DNA-based inference (which includes active and inactive taxa) along a gradient of land use change. Our results suggest that changes to soil heterogeneity impact the RNA-inferred community, while range expansions contribute to the homogenization of both DNA- and RNA-inferred communities. Thus, RNA-based community inference may be a more sensitive indicator of environmentally driven homogenization, and researchers interested in microbial responses to rapid environmental change should consider this method.

ecology↗