R. R. Malmstrom

Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis

This study uses spatial transcriptomics to analyze the molecular stages of arbuscular mycorrhizal symbiosis in plant roots.

A standardized quantitative analysis strategy for stable isotope probing metagenomics

This paper introduces a standardized analysis framework and R package for quantifying isotopic enrichment in SIP metagenomics to identify active microbial genomes.

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

This study examines viral infection dynamics in green sulfur bacteria, finding that multiple viruses, including lysogenic ones, co-infect host populations and that host diversity may influence the lytic/lysogenic switch.

Measurement error and resolution in quantitative stable isotope probing: implications for experimental design

This paper evaluates measurement error and resolution in qSIP, finding that variance decreases with taxon abundance and that nine density fractions balance cost and precision.

Niche differentiation is spatially and temporally regulated in the rhizosphere

This study identifies four microbial guilds in the rhizosphere and detritusphere of Avena fatua, showing niche differentiation drives carbohydrate depolymerization and soil carbon cycling.

Oxidative pathways of deoxyribose and deoxyribonate catabolism

The paper identifies novel oxidative pathways for deoxyribose and deoxyribonate catabolism in bacteria using genome-wide mutant fitness assays and genetic evidence.

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes

This study recovers 19 Verrucomicrobia draft genomes from freshwater metagenomes to explore their ecophysiology and role in carbon cycling.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

The paper examines genetic and ecological differentiation in freshwater bacterial populations using single-cell genomes and metagenomic data, finding ecologically distinct populations within some lineages but not others.

Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI