I’ve started a Microbial Ecology Reading group at UC Riverside. Here are the papers we read each week in case you want to follow along!
Spring 2024:
Week 1: Arunrat et al. Short-term response of soil bacterial and fungal communities to fire in rotational shifting cultivation, northern Thailand. Applied Soil Ecology. 2024.
Week 2: Barreiro et al Long-term response of soil microbial communities to fire and fire-fighting chemicals. Biol Fertil. Soils. 2016.
Week 3: Hopkins et al Fire season and time since fire determine arbuscular mycorrhizal fungal trait responses to fire. Plant and Soil. 2024
Winter 2024:
Week 1: Schloss P “Waste not, want not: revisiting the analysis that called into question the practice of rarefaction” mSphere 2023.
Week 2: Fox et all “Fire-excluded and frequently burned longleaf pine forests have contrasting soil microbial communities” FEM 2024
Week 3:Zhang et al “Drivers and mechanisms that contribute to microbial βdiversity patterns and range sizes in mountains across a climatic variability gradient”. Ecography. 2023.
Week 4: Smith et al “Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi” FEMS Microbiology Ecology 2023.
Week 5: Zhang et al The temporal and spatial response of soil fungal community composition and potential function to wildfire in a permafrost region in Canada Functional Ecology 2023
Week 6: Hopkins et alDrought legacy interacts with wildfire to alter soil microbial communities in a Mediterranean climate-type forest. Science of the total environment. 2024
Week 7: Zeba et alSoil carbon mineralization and microbial community dynamics in response to pyrogenic organic matter addition. SBB. 2024
Fall 2023:
Week 1: Barbour et al Testing the contribution of dispersal to microbial succession following a wildfire mSystems 2023
Week 2: Greenwood et al Fire shapes fungal guild diversity and composition through direct and indirect pathways Molecular Ecology 2023.
Week 3: Wang et al“A core microbiome in the hyphosphere of arbuscular mycorrhizal fungi has functional significance in organic phosphorus mineralization” New Phytologist 2022
Week 4: Johnson et al “Experimentally determined traits shape bacterial community composition one and five years following wildfire” Nature Ecology Evolution 2023
Week 5: Rai et al “Short-term prescribed fire-induced changes in soil microbial communities and nutrients in native rangelands of Florida” Applied Soil Ecology 2023
Spring 2023:
Week 1: Finks and Martiny Plasmid-Encoded Traits Vary across Environments. mBio. 2023.
Week 2: Guest speaker Dr. Luke Hillary teaches us about viromics!
Week 3: Hopkins et al Spore traits mediate disturbance effects on arbuscular mycorrhizal fungal community composition and mutualisms. Ecology. 2023.
Week 4: Martiny et al. Investigating the eco-evolutionary response of microbiomes to environmental change. Ecology Letters. 2023
Week 5: Allsup et al Shifting microbial communities can enhance tree tolerance to changing climates. Science. 2023
Afkhami M Past microbial stress benefits tree resilience. Science. 2023
Week 6: Horsch et alTrait-based assembly of arbuscular mycorrhizal fungal communities determines soil carbon formation and retention New Phytologist 2023.
Winter 2023:
Week 1: Chaudhary et al Fungal Dispersal Across Spatial Scales. Annual Review of Ecology, Evolution, and Systematics. 2022.
Week 2: Vourlitis et al Fire and post-fire management alters soil microbial abundance and activity: A case study in semi-arid shrubland soils. Applied Soil Ecology. 2022.
Week 3: Mujic et al Co‐invasive ectomycorrhizal fungi alter native soil fungal communities. Plant Soil. 2023.
Week 4: Shemesh et al Changing balance between dormancy and mortalitydetermines the trajectory ofectomycorrhizal fungal sporelongevity over a 15-yr burialexperiment. New Phytologist. 2022.
Week 5: Dao et al Substrate and low intensity fires influence bacterial communities in longleaf pine savanna Scientific Reports 2022
Week 6: Hiltunen et al The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades. Genome Biology and Evolution. 2021.
Fall 2022:
Week 1: Cahanovitc et al Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks. ISME. 2022
Week 2: Hestrin et al Plant-associated fungi support bacterial resilience following water limitation. ISME. 2022.
Week 3: Van Goethem et al Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Communications Biology. 2021.
Week 4: practice presentation for Arik quals
Week 5: Martinovi ́c et al Microbial utilization of simple and complex carbon compounds in a
temperate forest soil. SBB. 2022.
Summer 2022:
Week 1: Raudabaugh et al In Vitro Observations of the Interactions between Pholiota carbonaria and Polytrichum commune and Its Potential Environmental Relevance. Life 2021, 11, 518. https://doi.org/10.3390/ life11060518.
Week 2:Ward et al The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests. New Phytologist. 2022.
Week 3: practice presentations for MSA
Week 4: practice presentations for MSA
Week 5: Kakouridis et al “Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants” New Phytologist. 2022.
Week 6: Steindorff et al Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance
and sexual development. New Phytologist. 2022
Week 7: Tedersoo et al Best practices in metabarcoding of fungi: From experimental design to results. Molecular Ecology. 2021.
Week 8: Tedersoo et al Global patterns in endemicity and vulnerability of soil fungi. Global Change Biology. 2022
Spring 2022:
Week1: Manriquez, B. et al “Experimental Evolution in Plant-Microbe Systems: A tool for deciphering the functioning and evolution of plant-associated microbial communities” Frontiers in Microbiology. 2022.
Week2: Kobziar et al “Wildland fire smoke alters the composition, diversity, and potential atmospheric function of microbial life in the aerobiome” ISME. 2022.
Week3: Fox et al “Fire as a driver of fungal diversity — A synthesis of current knowledge” Mycologia. 2022.
Week4: Marro et al “The effects of arbuscular mycorrhizal fungal species and taxonomic groups on stressed and unstressed plants: a global meta-analysis” New Phytologist. 2022.
Week5: Dove et al “Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential” ISME 2022.
Week6: Fischer_Biorxiv_April_2022. Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest.
Week 7: Aldossari and Ishii “Fungal denitrification revisited – Recent advancements and future opportunities” SBB 2021.
Week 8: Liu et al “Phylotype diversity within soil fungal functional groups drives ecosystem stability” Nature Ecology and Evolution. 2022.
Week 9. van de Pepp et al Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces. Current Biology. 2022.
Fall 2021:
Week 1:Filialuna and Cripps“Evidence that pyrophilous fungi aggregate soil after forest fire”. Forest Ecology and Management. 2021.
Week 2: Nelson et al “Playing with FiRE: A genome resolved view of the soil microbiome responses to high high severity wildfire.” biorxiv. 2021.
Week 3: Querejeta et al “Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition” New Phytologist. 2021
Week 4: Wang et al “Arbuscular mycorrhizal fungi and plant diversity drive
restoration of nitrogen-cycling microbial communities”. Molecular Ecology. 2021.
Week 5: Koziol et al 2021 “Manipulating plant microbiomes in the field: Native
mycorrhizae advance plant succession and improve native plant restoration”Journal of Applied Ecology. 2021
Week 6: Lindahl et al “A group of ectomycorrhizal fungi restricts organic matter
accumulation in boreal forest.” Ecology Letters 2021.
Week 7: Revillini et al“Microbiome-mediated response to pulse fire disturbance
outweighs the effects of fire legacy on plant performance”. New Phytologist 2021.
Week 8: Harrower, JT and GS Gilbert. “Parasitism to mutualism continuum for Joshua trees inoculated with different communities of arbuscular mycorrhizal fungi from a desert elevation gradient” Plos ONE 2021.
Spring 2021:
Week 1: Fischer et al “Pyrolyzed substrates induce aromatic compound metabolism in the post-fire fungus, Pyronema domesticum” biorxiv. 2021.
Week 2: Padje et al “Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies” ISME 2021.
Week 3: Li et al “A genome-scale phylogeny of the kingdom Fungi”. Current Biology. 2021.
Week 4: Terrer et al “A trade-off between plant and soil carbon storage under elevated CO2″ Nature. 2021
Week 5: Averill et al“Soil microbiome predictability increases with spatial and taxonomic scale” Nature Ecology and Evolution 2021
Week 6: Yuan et al “Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches” mBio 2021
Week 7: Certini et al “The impact of fire on soil-dwelling biota: A review” Forest Ecology and Management 2021
Week 8: Adkins and Miesel “Post-fire effects of soil heating intensity and pyrogenic organic matter on microbial anabolism” Biogeochemistry 2021
Week 9: Woolet and Whitman. “Pyrogenic organic matter effects on soil bacterial community composition” SBB 2020.
Winter 2021:
Week 1: Smith et al Contrasting fungal responses to wildfire across different ecosystem type. Molecular Ecology. 2020.
Week 2: Moore et al Wildland fire as an atmospheric source of viable microbial aerosols and biological ice nucleating particles. ISME J. 2020.
Week 3: Carrara et al “Differences in microbial community response to nitrogen fertilization result in unique enzyme shifts between arbuscular and ectomycorrhizal dominated soils” Global Change Biology. 2021
Week 4: Li et al. Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem. FEMS Microbiology Ecology. 2020.
Fall 2020:
Week 1: Day et al Identifying functional impacts of heat-resistant fungi on boreal forest recovery after wildfire. Frontiers in Forests and Global Change. 2020.
Week 2: Benucci et al Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? Plos One. 2020.
Week 3: Perez-Valera et al “Soil microbiome drives the recovery of ecosystem function after fire” SBB 2020
Week 4: Steindorff et al“Comparative genomics of pyrophilous fungi reveals a link between fireevents and developmental genes” AEM. 2020.
Week 5: Miyauchi et al. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nature Communications. 2020
Week 6: Perez Izquierdo et al Crown-fire severity is more important than ground-fire severity in determining soil fungal community development in the boreal forest. Journal of Ecology 2020.
Week 7: Nayfach et al A genomic catalog of Earth’s microbiomes Nature Biotechnology 2020.
Week 8: Mitchison-Field et al “Unconventional cell division cycles from marine-derived yeasts” Current Biology 2019.
Week 9: Mushinski et al Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests. Global Change Biology 2020.
Summer 2020:
Week 1: Yang et al Distinct fungal successional trajectories following wildfire between soil horizons in a cold‐temperate forest. New Phytologist. 2020.
Week 2: Lustenhouwer et al. A trait-based understanding of wood decomposition by fungi. PNAS. 2020.
Week 3: Cavicchioli et al . Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology. 2020.
Hallin and Bodelier et al. Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry. Frontiers in Microbiology. 2020
Week 4: Chagnon et al“A trait-based framework to understand life history of mycorrhizal fungi” Trends in Plant Science 2013
Week 5: Soudzilovskaia et al “FungalRoot: Global online database of plant mycorrhizal associations” New Phytologist 2020.
Week 6: Kokkoris et al Review of nuclear behavior in AMF. Trends in Plant Science 2020.
Week 7: Hoeksema et al Ectomycorrhizal Plant-Fungal Co-invasions as Natural Experiments for Connecting Plant and Fungal Traits to Their Ecosystem Consequences. Front. For. Glob. Change 2020.
Week 8: Lopez Mondejar et al Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil Soil Biology and Biogeochemistry 2020.
Week 9: Naylor et al Deconstructing the Soil Microbiome into Reduced-Complexity Functional Module Mbio 2020
Week 10: Hopkins et al Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem. Oecologia 2020.
Spring 2020:
Week 1: Tedersoo et al “How mycorrhizal associations drive plant population and community biology” Science 2020.
Week 2: Whiteside et al et al “Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks” Current Biology 2019.
Week 3: Averill et al “Global imprint of mycorrhizal fungi on whole-plant nutrient economics” PNAS 2020.
Week 4: Egidi et al “A few Ascomycota taxa dominate soil fungal communities worldwide” Nature Communications 2019.
Week 5: Diamond et al “Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms” Nature Microbiology 2019
Week 6: Chapter 1 Mike Allen new Mycorrhizal Ecology Book
Week 7: Chapter 2 Mike Allen new Mycorrhizal Ecology Book
Week 8: Frey, S. Mycorrhizal Fungi as Mediators of Soil Organic Matter Dynamics. AREES. 2019.
Week 9: Chapter 3 Mike Allen new Mycorrhizal Ecology Book
Week 10: Chapter 4 Mike Allen new Mycorrhizal Ecology Book
Week 11: Afkhami et al “Tripartite mutualisms as models for understanding plant–microbial interactions” Current Opinion in Plant Biology 2020
Winter 2020:
Week 1: Raudabaugh et al Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. Fungal Ecology. 2020.
Week 2: Zanne et al “Fungal functional ecology: bringing a trait-based approach to plant-associated fungi” Biological Reviews. 2019.
Week 3: Varga et al “Megaphylogeny resolves global patterns of mushroom evolution” Nature Ecology and Evolution 2019
Week 4: Bargett and Caruso“Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states” Philosophical Transactions B 2020
Week 5: Nuccio et al “Niche differentiation is spatially and temporally regulated in the rhizosphere” ISME J 2020.
Week 6: Farrer et al Soil Microbial Networks Shift Across a High-Elevation Successional Gradient. Frontiers in Microbiology 2019.
Fall 2019:
Week 1: Perez_Valera_et_al Resilience to fire of phylogenetic diversity across biological domains. Molecular Ecology. 2018
Week 2: Dylan Enright presents his NSF GRFP proposal
Week 3: Semenova-Nelsen et al “Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape” New Phytologist 2019
Week 4: Delavaux et al “Mycorrhizal fungi influence global plant biogeography”. Nature Ecology and Evolution 2019
Week 5: Crowther et al “The global soil community and its influence on biogeochemistry” Science 2019
Week 6: Delgado-Baquerizo et al“A global atlas of the dominant bacteria found in soil”. Science. 2018.
Week 7: Wagg et al “Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning” Nature Communications 2019
Week 8: Yang et al “Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning” Global Change Biology 2019.
Week 9: Fabi Pulido-Chavez Ford Fellowship Proposal
Week 10: Rillig et al “The role of multiple global change factors in driving soil functions and microbial biodiversity” Science 2019
Spring 2019:
Week 1: Koziol et al The Plant Microbiome and Native Plant Restoration: The Example of Native Mycorrhizal Fungi. Biocience. 2019.
Week 2: Sydney gives the Botany and Plant Sciences seminar
Week 3: Repas et al “Growing plants on oily, nutrient-poor soil using a native symbiotic fungus” Plos One 2017.
Week 4: Dove and Hart “Fire reduces fungal species richness and in situ mycorrhizal colonization: a meta-analysis” Fire Ecology 2017.
Week 5: Nicholas Dove seminar
Week 6: Mushinksi RM et al “Microbial mechanisms and ecosystem flux estimation for aerobic NOy emissions from deciduous forest soils” PNAS 2019
Week 7: Ladau and Eloe-Fadrosh. “Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology” Trends in Microbiology 2019.
Week 8: Martiny A“High proportions of bacteria are culturable across major biomes”. ISME J 2019.
Carini P “A “Cultural” Renaissance: Genomics Breathes New Life into an Old Craft”. mSystems. 2019.
Week 9: Day et al“Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada” Global Change Biology. 2019.
Week 10: Wubs et al“Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly” Ecology Letters 2019.
Winter 2019:
Week 1: Nilsson H et al “Mycobiome diversity: high-throughput sequencing and identification of fungi.” Nature Microbiology Reviews 2018.
Week 2: Pollock J et al “The Madness of Microbiome: Attempting to Find Consensus “Best Practice” for 16S Microbiome Studies.” AEM 208.
Week 3: Bruns T “The developing relationship between the study of fungal communities and community ecology theory” Fungal Ecology 2019.
Week 4: Delgado-Baquerizo_et_al “Effects of climate legacies on above- and belowground community assembly.” Global Change Biology 2018
Week 5: Zhang et al “Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.” Nature Communications 2018.
Week 6: Carini et al “Relic DNA is abundant in soil and obscures estimates of soil microbial diversity” Nature Microbiology 2016.
Lennon et al “How, when, and where relic DNA affects microbial diversity” mBio 2018.
Week 7: Bonfante P “The future has roots in the past: the ideas and scientists that shaped mycorrhizal research” New Phytologist 2018.
Brundrett and Tedersoo “Evolutionary history of mycorrhizal symbioses and global host plant diversity” New Phytologist 2018.
Week 8: Roo Vandegrift Seminar
Week 9: Tipton et al “A developing symbiosis: Enabling cross-talk between ecologists and microbiome scientists” Frontiers in Microbiology 2019
Costello et al “The Application of Ecological Theory Toward an Understanding of the Human Microbiome.” Science 2012
week 10: Taylor et al “Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing” AEM 2016
Tedersoo and Lindahl “Fungal identification biases in microbiome projects” Environmental Microbiology Reports 2016
Fall 2018:
Week one: Bahram et al “Structure and function of the global topsoil microbiome” Nature 2018
Week two: Carini et al “Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities” bioRxiv 2018
Week three: Hall et al “Understanding how microbiomes influence the systems they inhabit” Nature Microbiology 2018
week four: Pressler_et_al “Belowground community responses to fire: meta-analysis reveals contrasting responses of soil microorganisms and mesofauna” Oikos 2018
Week five: Averill_et_al “Continental-scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks” Global Change Biology 2018
week six: Ahrendt et al “Leveraging single-cell genomics to expand the fungal tree of life” Nature Microbiology 2018
week seven: Sulman_et_al “Multiple models and experiments underescore large uncertainty in soil carbon dynamics” Biogeochemistry 2018
week eight: de Vries_et_al “Soil bacterial networks are less stable under drought than fungal networks” Nature Communications 2018
week nine: Wilhelm_et_al_ “Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing” ISME J 2018
week ten: Jansson and Hofmoeckel “The soil microbiome- from metagenomics to metaphenomics” Current Opinion in Microbiology 2018
week eleven: Schimel J “Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes” Annual Reviews of Ecology, Evolution and Systematics 2018
Sydney I. Glassman 