Biology subjects

Klimek, D.

Publications and source records attributed to Klimek, D..

3 recordsLinked to original sources

bioRxiv2025

Phylum-wide propionate degradation and its potential connection to poly- γ-glutamate biosynthesis in Candidatus Cloacimonadota

The candidate phylum Cloacimonadota is frequently detected in anaerobic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood due to the lack of cultured representatives. Metagenomic evidence suggests capacities for amino acid fermentation, cellulose degradation, and production of carbohydrate-active enzymes, with particular interest in their presumed role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from a lab-scale anaerobic baffled reactor fed with sugar beet pulp, where a sharp increase in an uncultured Cloacimonadota OTU coincided with recovery of methanogenesis and enhanced methane production. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of this OTU, complemented by a curated database of 47 genome-resolved Cloacimonadota species. Comparative genomics revealed conserved protein clusters indicative of an alternative mmc pathway, suggesting that this variant of the SPO pathway is a widespread, phylum-specific trait potentially linked to protein degradation and poly-{gamma}-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a primary syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

microbiology↗

bioRxiv2024

Comparative genomic analysis of Planctomycetota potential towards complex polysaccharide degradation identifies phylogenetically distinct groups of biotechnologically relevant microbes

The outstanding hydrolytic potential of the Planctomycetota phylum for complex polysaccharide degradation has recently been acknowledged based on the numerous carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Our in-depth characterisation of the available planctomycetotal genomic resources increased our knowledge of the carbohydrolytic capacities of Planctomycetota. We showed that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families, and that many members are characterised by a high versatility towards complex carbohydrate degradation, including lignocellulose. We also highlighted members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to Phycisphaerales were identified as an interesting source of novel, lytic polysaccharide monooxygenases that could boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors were shown to encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes. Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.

microbiology↗

bioRxiv2020

Targeted biomass degradation by the higher termite gut system - integrative omics applied to host and its gut microbiome

Miscanthus sp. is regarded as suitable biomass for different biorefinery value chains. However, due to high recalcitrance, its wide use is yet untapped. Termite is the most efficient lignocellulose degrading insect, and its success results from synergistic cooperation with its gut microbiome. Here, we investigated at holobiont level the dynamic adaptation of a higher termite Cortaritermes sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose recalcitrance. We used an integrative omics approach, comprising amplicon sequencing, metagenomics and metatranscriptomics that we combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Adaptation to the new diet was evidenced by reduced gut bacterial diversity and modified gene expression profiles, further suggesting a shift towards utilisation of cellulose and arabinoxylan, two main components of Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to microbes from closely related termite species, supported the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. Application-wise, this makes each termite gut system an endless source of enzymes that are potentially industrially relevant. This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.

systems biology↗