Biology subjects

Hahnke, R. L.

Publications and source records attributed to Hahnke, R. L..

3 recordsLinked to original sources

bioRxiv2026

TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions

Understanding the molecular mechanisms underlying plant-microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the complexity of natural microbial communities remains challenging. Such challenges can be addressed by employing synthetic microbial communities (SynComs) derived from well characterized microbial culture collections. Despite their importance, plant-associated microbial collections from major agricultural crops remain scarce. To bridge this gap, we established TriMic, a taxonomically and functionally representative culture collection of wheat root-associated bacteria. Complementing this collection, we include high quality genome sequences and an overview of genes involved in plant colonization, nutrient cycling, and plant growth promotion. Furthermore, we expanded this experimental toolkit by designing a reduced complexity SynCom that enables controlled dissection of plant-microbe interactions. Together, these resources lay the groundwork for mechanistic studies of plant-microbe interactions to accelerate biostimulant development aimed at enhancing agricultural productivity and sustainability. The TriMic collection and whole genomes are publicly available at the DSMZ (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/trimic) and NCBI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/740170v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@91bda0org.highwire.dtl.DTLVardef@386c49org.highwire.dtl.DTLVardef@4d455aorg.highwire.dtl.DTLVardef@1043ccb_HPS_FORMAT_FIGEXP M_FIG C_FIG Overview of the workflow for development of the wheat root bacterial collection and SynCom. (a) Bacterial isolates were recovered from roots of wheat grown in natural soil using two strategies after a root slurry was prepared: directly plating or host-mediated, which involved producing a secondary root slurry from wheat roots inoculated with the original root slurry (Ben Niu et al. 2017). Both root slurries were diluted and then plated onto four different types of media (1/10 R2A, 1/20 R2A, 1/100 R2A, and VxylG). Colonies were picked based on morphology and time of appearance. (b) Non-redundant strains of 88 purified isolates were made publicly available at the German Collection of Microorganisms and Cell cultures GmbH (DSMZ). (c) A 15-species synthetic community (SynCom) was developed after evaluating community dynamics in wheat roots inoculated with a 27-member consortium selected across genera in the collection. (d) Isolate genomes were sequenced using either short-read or hybrid assemblies with long-reads. Following functional annotation, genomes were screened for traits associated with plant-microbe interactions and secondary metabolite production.

microbiology↗

bioRxiv2026

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

microbiology↗

bioRxiv2025

Viral infection collapses intracytoplasmic membrane integrity and autotrophic metabolism in ammonia-oxidizing Nitrosomonas europaea

Ammonia-oxidizing bacteria (AOB) catalyze the first and rate-limiting step of nitrification. They are essential for nitrogen cycling in engineered and natural environments, yet little is known about their viruses or the consequences of phage infection for host physiology. Here, we report the isolation and characterization of a novel lytic bacteriophage, vB_NeuP-Nir1 (Nir1), infecting the model AOB Nitrosomonas europaea. Phage Nir1 was highly virulent, ceased ammonia oxidation within hours, and caused complete lysis of host populations even at multiplicities of infection as low as 10-6. Electron microscopy revealed drastic host cell remodeling during infection, including pronounced cell bloating and large-scale disintegration of intracytoplasmic membranes. Integrated transcriptomic and metabolomic analyses showed that loss of these ATP and reducing equivalent generating membrane systems was accompanied by signatures of compromised lipid homeostasis and collapse of autotrophic CO2 fixation. In parallel, Nir1 infection induced metabolic rewiring of the host, including upregulation of uptake systems for nucleic acids, amino acids, and small organic compounds, increased expression of iron acquisition and putative iron-dependent respiratory components, as well as accumulation of metabolites associated with membrane breakdown and stabilization of viral DNA. Together, these results provide the first detailed mechanistic insight into phage-induced host modulation in a chemolithoautotrophic nitrifier. Our study establishes the Nir1-N. europaea system as a model for investigating virus-host interactions in AOB and lays the foundation for assessing the role of phages in shaping nitrification and nitrogen cycling in engineered and natural ecosystems.

microbiology↗