Microbial Ecology Reading Group

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 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 alWildfire 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