Biology subjects

Shapleigh, J. P.

Publications and source records attributed to Shapleigh, J. P..

3 recordsLinked to original sources

bioRxiv2020

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Denitrifier community phenotypes often result in transient accumulation of denitrification (NO3-[->]NO2-[->]NO[->]N2O[->]N2) intermediates. Consequently, anoxic spells drive NO-, N2O- and possibly HONO-emissions to the atmosphere, affecting both climate and tropospheric chemistry. Soil pH is a key controller of intermediate levels, and while there is a clear negative correlation between pH and emission of N2O, NO2- concentrations instead increase with pH. These divergent trends are probably a combination of direct effects of pH on the expression/activity of denitrification enzymes, and an indirect effect via altered community composition. This was studied by analyzing metagenomics/transcriptomics and phenomics of two soil denitrifier communities, one of pH 3.8 (Soil3.8) and the other 6.8 (Soil6.8). Soil3.8 had severely delayed N2O reduction despite early transcription of nosZ, encoding N2O reductase, by diverse denitrifiers, and of several nosZ accessory genes. This lends support to a post-transcriptional, pH-dependent mechanism acting on the NosZ apo-protein or on enzymes involved in its maturation. Metagenome/metatranscriptome reads of nosZ were almost exclusively clade I in Soil3.8 while clade II dominated in Soil6.8. Reads of genes and transcripts for NO2--reductase were dominated by nirK over nirS in both soils, while qPCR-based determinations showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK community. The -omics results suggested that low NO2- concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to enzymatic activity. The NO reductase gene qnor was strongly expressed in Soil3.8, suggesting an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2- accumulating soil, was estimated to be ten times higher from Soil3.8 than from Soil6.8. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

microbiology↗

bioRxiv2020

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Plant-derived phenolic acids are metabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria would enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (PHB). We further investigated whether PHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. The activity of Paraburkholderia and Caballeronia dominated PHB degradation in all soils regardless of tree species or soil type. We isolated the principal PHB-degrading phylotype (Paraburkholderia madseniana RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, aryl-alcohol oxidase and DyP-type peroxidase, and confirmed its ability to degrade phenolics. The addition of PHB to soil led to significant enrichment (23-fold) of the RP11T phylotype (RP11ASV), as well as enrichment of other phylotypes of Paraburkholderia and Caballeronia. Metabolism of PHB primed significant loss of SOC (3 to 13 {micro}mols C g-1 dry wt soil over 7 days). In contrast, glucose addition reduced SOC mineralization (-3 to -8 {micro}mols C g-1 dry wt soil over 7 days). RP11ASV abundance and the expression of PHB monooxygenase (pobA) correlated with PHB respiration and were inversely proportional to SOC content in the field. We propose that plant-derived phenolics stimulate the activity of phenolic acid-degrading bacteria thereby causing soil priming and SOC loss. We show that Burkholderiaceae dominate soil priming in diverse forest soils and this observation counters the prevailing view that priming phenomena are a generalized non-specific response of community metabolism.

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↗