A. J. Probst

Metaproteogenomics resolution of a high-CO2 aquifer community suggests an active symbiotic lifestyle of groundwater Gracilibacteria

The paper investigates Gracilibacteria activity in a high-CO2 aquifer using metaproteogenomics, suggesting they may function as microbial predators.

Differential expression of core metabolic functions in Candidatus Altiarchaeum inhabiting distinct subsurface ecosystems

This study compares the metatranscriptomes of two Candidatus Altiarchaeum populations in different subsurface ecosystems, identifying gene expression differences related to metabolism and defense mechanisms.

Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

This study evaluates using lower DNA quantities for Nanopore sequencing in metagenomics, showing that high-quality MAGs can be recovered from as little as 35 ng of input DNA.

Virus-host dynamics in archaeal groundwater biofilms and the associated bacterial community composition

The paper studies virus-host dynamics in archaeal groundwater biofilms over three years, finding a steady increase in viral infections and a stable bacterial community dominated by Desulfobacterota.

Functional prediction of proteins from the human gut archaeome

The paper predicts and characterizes protein functions in Methanobrevibacter smithii using sequence and structure data, identifying gut-specific proteins and potential horizontal gene transfer events.

Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism

The paper identifies CPR bacteria in sulfide-rich biofilms, linking them to sulfur and hydrogen metabolism through genomic and spectroscopic analyses.

Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities

This paper introduces eABPP, a proteomics-based method to identify active enzymes in microbial communities, and demonstrates its application in discovering thermostable serine hydrolases from hot springs.

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

The paper shows marine viruses disperse bidirectionally between air-sea interface ecosystems and rainwater, with genetic evidence of virus-host interactions and implications for atmospheric processes.

Host-associated phages disperse across the extraterrestrial analogue Antarctica

The paper tracks host-associated phages across Antarctica using metagenomic data, finding long-distance dispersal of Ralstonia phages with implications for Astrobiology and Planetary Protection.

Rates of primary production in groundwater rival those in oligotrophic marine systems

The paper measures carbon fixation rates in groundwater and finds they rival those in oligotrophic marine systems.

Label-free Raman microspectroscopy for identifying virocells

This paper uses Raman microspectroscopy to identify virocells by analyzing biochemical changes in bacterial and archaeal cells during viral infection.

Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling

The paper identifies genomic remnants in Archaea that reveal ancestral hydrogen and methane metabolism, showing their role in anaerobic carbon cycling.

The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

This study investigates Patescibacteria in groundwater, finding they have minimal metabolic pathways and show little adaptation to environmental drivers, suggesting an economical lifestyle with broad host interactions.

Virus-associated organosulfur metabolism in human and environmental systems

This study identifies 39 viral gene families involved in organosulfur metabolism across diverse ecosystems, showing their role in sulfide production and viral fitness.

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

The paper identifies diverse viruses in Atacama Desert soils that carry genes for microbial extremotolerance, suggesting a mutualistic role in host survival under extreme conditions.

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

This study uses stable isotope-informed genome-resolved metagenomics to trace carbon flow in rhizosphere soil and identify microbial interactions with plants and phages.

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth's crust

The paper uses genome-informed microscopy to show lytic viruses infect uncultivated carbon-fixing archaea in Earth's crust, challenging previous assumptions about viral lifestyles in subsurface ecosystems.

Geological degassing enhances microbial metabolism in the continental subsurface

This study investigates how mantle degassing affects microbial metabolism in deep subsurface environments, finding that gas-rich sites show increased microbial activity compared to non-impacted sites.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

An archaeal symbiont-host association from the deep terrestrial subsurface

The paper identifies a host-symbiont relationship between two uncultivated archaea in a deep aquifer, showing co-occurrence and metabolic interdependence.

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

The paper analyzes lipid composition in CO2-rich subsurface aquifers to infer microbial carbon cycling and lipid sources, finding CPR bacteria may rely on lysolipids from other community members.

Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism

The paper reconstructs a complete genome from a deep subsurface archaeon, revealing that homologous recombination and transposon propagation shape its population structure.

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon

The paper identifies a Saccharibacteria genome in rhizosphere soil that relies on externally-derived nucleotides and utilizes plant-derived carbon through fermentation and potential aerobic respiration.

Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy

This paper introduces DAS Tool, a metagenomic binning method that improves genome recovery accuracy and completeness across diverse samples.