K. T. Konstantinidis

Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

The paper defines rare biosphere and generalists using metagenomic and macroecological metrics, showing their roles in microbial resilience to disturbances like tropical cyclones and warming.

An ANI gap within bacterial species that advances the definitions of intra-species units

The paper identifies an ANI gap within bacterial species, proposing a more precise definition for intra-species diversity units.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

This study investigates N2O reduction in acidic tropical soils, finding distinct microbial communities and novel taxa associated with N2O reduction at low pH.

Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O-Antigen Expression

The paper investigates phage resistance in E. coli due to O-antigen expression and finds that most E. coli in the gut are resistant, limiting phage impact on bacterial composition.

Sustained bacterial (N2O) reduction at acidic pH

The paper identifies a bacterial culture from acidic soil that reduces N2O to N2 at pH 4.5, challenging the assumption that microbial N2O reduction is limited to circumneutral pH.

Low-troposphere microbial communities differ between dry-air and rainfall but do not show strong seasonal patterns in Metro Atlanta, Southeast USA

The paper compares microbial communities in dry air and rainfall in Metro Atlanta, finding dry air has more human pathogens and allergens, but no strong seasonal patterns.

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of a salt marsh foundation plant species

This study shows sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of Spartina alterniflora, with a novel symbiosis involving Candidatus Thiodiazotropha.

Towards estimating the number of strains that make up a natural bacterial population

The paper estimates the number of strains in a natural bacterial population using genomic and metagenomic data, finding up to 5,500 to 11,000 genomovars in one pond.

Novel municipal sewage-associated bacterial genomes and their potential in source tracking

This study identifies sewage-specific bacterial genomes from wastewater treatment plants and shows their utility in tracking sewage contamination in waterbodies.

Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking

This study tracks cow, pig, and human fecal pollution in lake water over time using metagenomics and benchmarks novel protocols against standard culture-based and qPCR tests for water quality monitoring.

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling

This study characterizes soil microbial communities in the Luquillo Experimental Forest using metagenomics, revealing differences in nitrogen cycling genes compared to temperate soils.

Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions

This study compares survival strategies of environmental and enteric E. faecalis isolates under freshwater conditions, finding similar decay rates but distinct rRNA:rDNA ratios and limited evidence of habitat adaptation.

High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

This study shows high arsenic levels increase transcriptional activity of arsenic metabolism genes in paddy soils without significantly affecting their diversity or abundance.

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

The paper investigates how bacterial pangenomes adapt to environmental changes by analyzing gene abundance in Salinibacter ruber under manipulated salinity and light conditions.

Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs

The paper analyzes metagenomic data from geothermal springs over time, finding stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs.

A Novel Droplet Digital PCR Human mtDNA Assay for Global Fecal Source Tracking

This paper develops a ddPCR assay for human mtDNA to track fecal sources, finding it more sensitive than a common bacterial marker in human feces from three regions.

Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming

This study shows that microbial adaptation reduces soil carbon loss under long-term warming by decreasing temperature sensitivity of respiration.

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

The paper characterizes microbial communities in creek sediments from an agricultural region using metagenomics, finding low public health risk and high antibiotic resistance gene levels.

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

This study compiles 1,635 metagenome-assembled genomes from 134 biogas reactor datasets to explore microbial diversity and functional traits in anaerobic digestion.