Biology subjects

Lycus, P.

Publications and source records attributed to Lycus, P..

3 recordsLinked to original sources

bioRxiv2023

Meta-omics analyses of dual substrate enrichment culturing of nitrous oxide respiring bacteria suggest that attachment and complex polysaccharide utilisation contributed to the ability of Cloacibacterium strains to reach dominance

Bioengineering soil metabolism by inoculation is an emerging approach to enhance plant growth and strengthen specific functions such as N2O reduction in order to reduce climate forcing. The use of organic wastes as substrates and carriers of microbial biomass has proven to be a viable approach to improving effectiveness and economic viability. A key factor in the success of this approach lies in selection of microbes capable of growth and survival in both organic wastes as well as soils, and which are tolerant of the rapid environmental fluctuations such fertilisations involve. A dual substrate, N2O-enrichment experiment, switching between soil and organic waste as substrates has yielded Cloacibacterium isolates which grow well in organic wastes and retain significant N2O reduction capacity when applied to soils. However, an understanding of the genetic and phenotypic characteristics utilised by these enrichment winners to dominate under such conditions remains unexplored. Here we have performed a multi-omics examination of the enrichment cultures, using both metagenomics and metaproteomics to probe the genetic basis and expressed proteins which may contribute to the success of Cloacibacterium in the enrichments, and their survival in soil. These omics results show an increase in complex carbohydrate metabolism, chemotaxis and motility genes throughout the enrichment as well as the expression of gliding motility proteins and polysaccharide utilization loci proteins by Cloacibacterium organisms. Taken together this suggests that attachment and complex polysaccharide utilisation may be key processes allowing Cloacibacterium to tolerate the stresses of a changing environment during transfers between digestate and soil.

microbiology↗

bioRxiv2020

Bacteria in biogas digestates for reduced climate forcing

Inoculating agricultural soils with N2O-respiring bacteria (NRB) can reduce N2O-emissions, but would be impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production are suitable substrates and vectors for NRB. We show that indigenous NRB in digestates grew to high abundance during anaerobic enrichment under N2O. Gas-kinetics and meta-omic analyses showed that these NRB's, recovered as metagenome-assembled genomes (MAGs), grew by harvesting fermentation intermediates of the methanogenic consortium. Three NRB's were isolated, one of which matched the recovered MAG of a Dechloromonas, deemed by proteomics to be the dominant producer of N2O-reductase in the enrichment. While the isolates harbored genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O sinks in soil, which was confirmed experimentally. The isolates were grown by aerobic respiration in digestates, and fertilization with these NRB-enriched digestates reduced N2O emissions from soil. Our use of digestates for low-cost and large-scale inoculation with NRB in soil can be taken as a blueprint for future applications of this powerful instrument to engineer the soil microbiome, be it for enhancing plant growth, bioremediation, or any other desirable function.

microbiology↗

bioRxiv2020

Competition for electrons favors N2O reduction in denitrifying Bradyrhizobium isolates

Bradyrhizobia are common members of soil microbiomes and known as N2-fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2O. Inoculation with compatible rhizobia is often needed for optimal N2-fixation, but the choice of inoculant may also have consequences for N2O emission. Here, we analyzed the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. All were dinitrifiers, but only ~1/3 could reduce N2O while most others were net N2O producers. The N2O-reducing isolates showed strong preference for N2O- over NO3--reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3- reductase) and Nos (N2O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3- reductase (Nar), reduced N2O and NO3- simultaneously. We propose that the control at the metabolic level, favoring N2O reduction over NO3- reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar. Originality-Significance StatementThis study extends the current knowledge on denitrification in bradyrhizobia, which mostly originates from studies of one model strain, by investigating the denitrification phenotypes of a diverse collection of Bradyrhizobium isolates. Only 1/3 of them could reduce N2O while the others were net sources for this potent greenhouse gas. All N2O-reducers showed strong preference for N2O over NO3-. We revealed by proteomics that this was not explained by differences in the abundances of Nap (periplasmic nitrate reductase) and Nos (N2O reductase), which strengthens our hypothesis (Mania et al., 2020) of a metabolic control mechanism by which Nos competes efficiently with Nap for electrons, making these organisms strong sinks for N2O. The findings highlight the potential importance of these organisms as N2O sinks in natural and agricultural ecosystems and pinpoint the need to take N2O reduction into account, along with N2-fixation effectiveness, when searching for strains suitable for production of inoculants.

microbiology↗