A. P. Arkin

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

This paper uses high-throughput genetics to identify nutrient utilization and accessory energy metabolism genes in the methanogen Methanococcus maripaludis.

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

This study investigates how genomic and environmental factors influence the distribution of Castellaniella species in a contaminated subsurface, identifying genetic mechanisms underlying their adaptation to stress.

Niche exclusion of a lung pathogen in mice with designed probiotic communities

This study shows that probiotic communities can prevent Burkholderia thailandensis infection in mice by reducing niche overlap with the pathogen.

Geochemical constraints on bacteriophage infectivity in terrestrial environments

This study measures ion thresholds for phage infection and shows that phage impact on terrestrial microbiomes is strongest in high-ion environments with simple carbon sources.

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

The paper analyzes MGEs from heavy metal contaminated and unimpacted subsurface regions, finding enriched HMRGs in contaminated areas associated with specific bacterial hosts.

Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages {lambda} and P1

The paper uses CRISPRi to identify essential genes in coliphages λ and P1, revealing insights into gene essentiality and highlighting potential false positives in less studied phages.

Many Families of Lids for TonB-dependent Transporters in Bacteroides

The paper identifies six families of putative lids for non-SusC TonB-dependent transporters in Bacteroides, showing their role in receptor function.

Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance

The paper identifies new gene functions in gut Bacteroidales using a barcoded overexpression screen, revealing roles in carbon utilization and stress resistance.

Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis

This paper develops a genetic toolkit for Arthrospira platensis and demonstrates acetaminophen production as a proof-of-concept for small molecule synthesis in an edible cyanobacterium.

Charting a narrow course for direct electron uptake-facilitated electromicrobial production

This study evaluates the feasibility of direct electron uptake-based electromicrobial production by analyzing performance limits and reactor conditions required for competitiveness with alternative methods.

Quantifying the Local Adaptive Landscape of a Nascent Bacterial Community

The paper quantifies the adaptive potential of a bacterial community by measuring gene knockout fitness effects across different genetic backgrounds and ecological conditions.

Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins

The paper identifies host suppressors of phage-encoded single gene lysis proteins, revealing convergent evolution and common mechanisms across diverse phages.

The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella

This study identifies 301 host factors in Salmonella involved in phage resistance, reveals cross-resistance mechanisms between RpoS and RpoN, and shows additional constraints define phage host range.

GapMind for Carbon Sources: Automatedannotations of catabolic pathways

GapMind for carbon sources annotates catabolic pathways in bacterial and archaeal genomes using genetic data and curated information, improving coverage and confidence in pathway predictions.

Mapping the genetic landscape of biomineralization in Magnetospirillum magneticum AMB-1 with RB-Tnseq

This study uses RB-TnSeq to identify genetic requirements for magnetosome formation in Magnetospirillum magneticum AMB-1 under different growth conditions, revealing condition-specific gene functions.

Biofilm Interaction Mapping and Analysis (BIMA): A tool for deconstructing interspecific interactions in co-culture biofilms

The paper introduces BIMA, a method to analyze interspecific interactions in biofilm co-cultures by examining colony morphology, inhibition, invasion, and associated genes/metabolites.

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

The paper identifies 41 viral clusters in groundwater plasmidomes, links them to bacterial hosts, and detects novel phage genera and host-specific genes.

Evaluating the cost of pharmaceutical purification for a long-duration space exploration medical foundry

This study evaluates pharmaceutical purification costs for space missions using the ESM metric, comparing biotic and abiotic methods for monoclonal antibody purification.

Sustained ability of a natural microbial community to remove nitrate from groundwater

This study demonstrates that a natural microbial community can sustain nitrate removal from groundwater even after prolonged absence of an electron donor.

A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis

This paper introduces a direct PCR method for bacterial community analysis that is cheaper, faster, and more scalable than traditional DNA extraction methods.

Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins

This study identifies genetic factors in pseudomonads that influence sensitivity to tailocins using transposon libraries and genomics.

Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium

This study characterizes the genetic essentiality and conditional phenotypes of Desulfovibrio vulgaris Hildenborough using a transposon mutant library under various metabolic and stress conditions.

Systems-informed genome mining for electroautotrophic microbial production

This study develops a multiphysics model to identify microbes capable of electroautotrophic CO2 fixation and determines the practical limits of microbial electrosynthesis.

High-throughput mapping of the phage resistance landscape in E. coli

This study maps host genetic determinants of phage resistance in E. coli using high-throughput genetic screens, identifying both known and novel resistance factors across 14 phages.

Four Families of Folate-independent Methionine Synthases

The paper identifies four families of folate-independent methionine synthases and characterizes their methyl donor requirements and distribution across different organisms.

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.

The paper demonstrates that microbial communities in in-field bioreactors shift dynamically in response to geochemical perturbations, with significant changes in taxa composition and similarity to contaminated well communities.

Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi

This study uses CRISPRi to systematically analyze coding and non-coding elements in E. coli, revealing conditional essentiality and novel insights into promoter and TFBS targeting.

A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming

The paper introduces a framework to quantify microbial community assembly mechanisms in grassland soils under warming, finding homogeneous selection and drift dominate, with warming altering their relative contributions.

Selective carbon sources influence the end-products of microbial nitrate respiration

The paper investigates how different carbon sources affect the end-products of nitrate respiration in microbial communities from diverse environments.

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

This paper uses RB-TnSeq to identify novel enzymes in Pseudomonas putida lysine metabolism, revealing new biochemical pathways and functions for DUF1338 proteins.