M. Kleiner

Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen

The paper identifies nitrogen fixation genes in deep-sea Ca. Thiodiazotropha symbionts of Lucinoma kazani but finds no expression of these genes, while highlighting high expression of carbon fixation and sulfur oxidation genes.

Dietary protein source alters gut microbiota composition and function

This study shows that different dietary protein sources alter gut microbiota composition and function in mice, affecting amino acid and mucus degradation processes.

Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella

This study identifies pseudo-pac site sequences in Salmonella genomes that enable P22 phage to initiate generalized transduction, using bioinformatics analysis of sequencing data.

Diverse bacteriohemerythrin genes of Methylomonas denitrificans FJG1 provide insight into the survival and activity of methanotrophs in low oxygen ecosystems

This study identifies a methanotroph-specific bacteriohemerythrin homolog in Methylomonas denitrificans FJG1 that likely facilitates oxygen delivery to methane monooxygenase under low oxygen conditions.

Effective seed sterilization methods require optimization across maize genotypes

This study evaluates seed sterilization protocols for two maize varieties, finding that different protocols are needed for different genotypes and seed sources to prevent fungal contamination.

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

This study identifies microbial DNA and protein in casein-based diets, showing they contribute to microbiome measurements and are absent in other protein sources.

Mechanism of high energy efficiency of carbon fixation by sulfur-oxidizing symbionts revealed by single-cell analyses and metabolic modeling

The paper investigates carbon fixation efficiency in sulfur-oxidizing symbionts using single-cell analyses and metabolic modeling, finding that stored sulfur and polyhydroxyalkanoate contribute to energy and reducing equivalents for carbon fixation.

An intranuclear bacterial parasite of deep-sea musselsexpresses apoptosis inhibitors acquired from its host

This study identifies apoptosis inhibitors in an intranuclear bacterial parasite of deep-sea mussels, showing they acquired these genes via horizontal transfer from their hosts.

Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization

This study evaluates frozen SynCom stocks for maize root colonization, finding they are as effective as fresh SynComs in reproducibility and colonization ability.

Environmental legacy effects impact maize growth and microbiome assembly under drought stress

The paper shows that historical soil moisture conditions influence maize growth and root microbiome composition under drought, with wetter soils improving drought tolerance.

Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

This study restores a lost AM symbiosis trait in Arabidopsis by expressing IPD3, revealing gene expression changes related to immunity and metabolism in non-host plants.

Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

The paper investigates metabolic interactions among symbionts in deep-sea mussels, identifying their roles in nutrient cycling and environmental adaptation.

De novo phytosterol synthesis in animals

The paper shows marine annelids synthesize sitosterol, a phytosterol, challenging the assumption that phytosterol synthesis is exclusive to plants.

Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants

This paper introduces a synthetic carbon fixation cycle in plants that fixes CO2 without RuBisCO, showing increased photosynthetic capacity in transgenic Camelina sativa.

Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses

This study evaluates RNAlater as a field-compatible preservation method for metaproteomics, finding it preserves proteins as effectively as flash freezing and remains stable for up to 4 weeks at room temperature.

Evaluation of sample preservation and storage methods for metaproteomics analysis of intestinal microbiomes

This study evaluates preservation methods for fecal microbiome samples used in metaproteomics, finding that RNAlater or RNAlater-like solutions perform as well as flash-freezing.

Repeated losses and gains of bacterial symbionts in gutless marine annelids over 150 million years

This study investigates the evolutionary dynamics of bacterial symbionts in gutless marine annelids over 150 million years, showing host-driven stability and convergent gains of symbionts.

Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes

This paper introduces Protein-SIP, an ultra-sensitive method for quantifying isotope incorporation in microbiomes, showing higher sensitivity and accuracy than existing approaches.

Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

CAMPI evaluates metaproteomic workflows across labs, finding sample processing drives peptide variability while workflows yield similar functional profiles.

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

The paper examines fidelity variation in a gutless marine worm's symbiosis with multiple microbial symbionts, finding strict fidelity for key symbionts and variable fidelity for others.

Microbe-dependent heterosis in maize

This study shows that maize heterosis for root biomass and germination depends on soil microbes, as inbred lines perform as well as F1 hybrids under sterile conditions but not when microbes are present.

Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila

The paper identifies metabolic differences between symbiont subpopulations in Riftia pachyptila, showing small symbionts focus on division and host interaction while large ones specialize in carbon fixation and biosynthesis.

Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities

This paper introduces a sequencing-based method called transductomics to detect and analyze ongoing horizontal gene transfer in microbial communities and pure cultures.

A shared core microbiome in soda lakes separated by large distances

The paper identifies a shared core microbiome across distant soda lakes and suggests common design principles for high productivity.

The Trichoplax microbiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria

The paper identifies two intracellular bacteria in Trichoplax H2, showing they live in symbiosis with the host and have distinct metabolic roles.

Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation

This study identifies Kentron, sulfur-oxidizing symbionts lacking canonical autotrophic CO2 fixation genes, instead relying on organic carbon for heterotrophic growth.

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

The paper identifies a horizontally acquired Calvin cycle in Campylobacterota symbionts and free-living members, challenging assumptions about carbon fixation pathway distribution.

Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle

The paper identifies a cultured bacterium with both Calvin-Benson-Bassham and reverse tricarboxylic acid carbon fixation pathways, suggesting coexistence in symbiotic and free-living sulfur-oxidizing bacteria.

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

This paper introduces a metaproteomics method called direct Protein-SIF and software to measure carbon isotope ratios in microbial communities, confirming its accuracy and utility in studying microbial metabolism.

Assessing species biomass contributions in microbial communities via metaproteomics

The paper develops metaproteomics methods to assess microbial community composition by measuring biomass contributions through protein abundance, validated using artificial communities and applied to environmental and saliva samples.