Biology subjects

Shek, K. L.

Publications and source records attributed to Shek, K. L..

4 recordsLinked to original sources

bioRxiv2025

Consistent microorganisms respond during aerobic thaw of Alaskan permafrost soils

Arctic systems are experiencing warming at four times the rate of the global average, causing permafrost--permanently frozen soil, ice, organic matter, and bedrock--to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition--a process mediated by microbes--which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well-established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. Here, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska and assessed their abiotic soil properties and microbiome characteristics during a 3-month laboratory microcosm incubation. In all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number and absolute abundance. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We assessed the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, which likely reflects the increased dominance of specific thaw-responsive taxa, which may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and allows for better predictions of how Arctic ecosystem structure and function respond to change.

microbiology↗

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↗

bioRxiv2020

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4 flux are not well understood. To address this knowledge gap, we measured soil CH4 flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4 uptake at modest rates, while pasture soils exhibited CH4 emission at high but variable rates. Secondary forest soils exhibited low rates of CH4 uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4 sink-to-source trend. While few environmental variables were significantly associated with CH4 flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4 flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4 fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4 flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4 fluxes, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4 flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4 cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

ecology↗