Alexander L. Jaffe

Deeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean

The paper presents deeply-sequenced metagenomes and over 1000 draft genomes from the deep ocean to study microbial communities across depth gradients.

Microbial autotrophy is widespread across soils and most prevalent in deep and saturated environments

The paper analyzes microbial autotrophy in soils using metagenomic and metatranscriptomic data, finding widespread RuBisCO genes and prevalence in deep, saturated soils.

Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers

This study identifies widespread and diverse deep-sea chemoautotrophs beyond nitrifiers, revealing their genetic potential for carbon fixation and impact on the carbon cycle.

Fifteen-year microbiome survey of endangered killer whales (Orcinus orca) reveals declining diversity and population differences

This study analyzes 15-year fecal microbiome data from endangered killer whales to show declining diversity and population-specific differences.

Diversity-driven biochemical survey reveals dimeric structural origin of rubisco

The paper characterizes the structural and functional diversity of rubisco by synthesizing and analyzing diverse sequences, revealing a dimeric origin and a novel large rubisco structure.

Abundant and metabolically flexible lineages within the SAR324 and gammaproteobacteria dominate the potential for rubisco-mediated carbon fixation in the dark ocean

The paper analyzes metagenomic data to show that rubisco-encoding organisms, particularly from SAR324 and gammaproteobacteria, dominate carbon fixation potential in the dark ocean.

Prevalence of the Calvin-Benson-Bassham cycle in chemolithoautotrophic psychrophiles and the potential for cold-adapted Rubisco

This paper identifies the Calvin-Benson-Bassham cycle as the dominant chemolithoautotrophic pathway in subzero environments and explores cold-adapted Rubisco variants in psychrophilic bacteria.

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos

The paper identifies a Prochlorococcus lineage in oxygen deficient zones that expresses both form I and form II rubiscos, suggesting an adaptation to low oxygen environments.

Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean

This study shows urea is a major nitrogen source for deep-sea microbes and supports nitrification, fueling chemoautotrophy in the dark ocean.