The Flavohemoglobin Hmp and Nitric Oxide Reductase Restrict Initial nir Expression in the Bet-Hedging Denitrifier Paracoccus denitrificans by Curtailing Hypoxic NO Signalling.

In denitrifying bacteria, nitric oxide (NO) is an electron acceptor and a free intermediate produced during anaerobic respiration. NO is also a signal for transcriptional regulation of the genes encoding nitrite (Nir), nitric oxide (Nor) and nitrous oxide reductases (NOR). We hypothesise that the timing and strength of the NO signal necessary for full nir expression are key factors in the bet-hedging strategy of Paracoccus denitrificans, and that systems scavenging NO under hypoxia reduce the probability of nir induction.

Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.

Unlabelled: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs).

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals.

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs.

Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and NO emissions.

Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas NO - is intricately controlled by O. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox).

Hydroxylamine production by challenges the paradigm of heterotrophic nitrification.

Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification.

Unlocking bacterial potential to reduce farmland NO emissions.

Farmed soils contribute substantially to global warming by emitting NO (ref. ), and mitigation has proved difficult. Several microbial nitrogen transformations produce NO, but the only biological sink for NO is the enzyme NosZ, catalysing the reduction of NO to N (ref.

Suggested role of NosZ in preventing NO inhibition of dissimilatory nitrite reduction to ammonium.

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO and/or NO to NH . Interestingly, DNRA-catalyzing microorganisms possessing genes are occasionally found harboring genes encoding nitrous oxide reductases, i.e.

Using adaptive and aggressive NO-reducing bacteria to augment digestate fertilizer for mitigating NO emissions from agricultural soils.

Nitrous oxide (NO) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying NO-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of NO, ability to grow in organic waste, and ability to survive in farmland soil.

Denitrification by Bradyrhizobia under Feast and Famine and the Role of the bc1 Complex in Securing Electrons for NO Reduction.

Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also must survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O tension using -oxides as electron acceptors. The cellular machinery regulating this transition is relatively well known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms.

A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture.

Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among NO-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the NO-reduction capacity of soils.

Regulation of the Emissions of the Greenhouse Gas Nitrous Oxide by the Soybean Endosymbiont .

The greenhouse gas nitrous oxide (NO) has strong potential to drive climate change. Soils are a major source of NO, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont is a model microorganism to study denitrification, a process that depends on a set of reductases, encoded by the , , , and genes, which sequentially reduce nitrate (NO) to nitrite (NO), nitric oxide (NO), NO, and dinitrogen (N).

Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers.

Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO , but it often entails accumulation of the cytotoxic intermediate NO and the greenhouse gas N O. To explore if these high NO and N O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO , NO, N O, N and O as they depleted O and transitioned to denitrification with NO as the only electron acceptor and hydrogen as the electron donor.

Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions.

Inoculating agricultural soils with nitrous oxide respiring bacteria (NRB) can reduce NO-emission, 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 NO.

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of NO emissions and nitrite accumulation in soil.

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.

Competition for electrons favours N O reduction in denitrifying Bradyrhizobium isolates.

Bradyrhizobia are common members of soil microbiomes and known as N -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N O. Inoculation with compatible rhizobia is often needed for optimal N -fixation, but the choice of inoculant may have consequences for N O emission.

NO and N O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains.

Fungal denitrification is claimed to produce non-negligible amounts of N O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N O-kinetics for abiotic NO- and N O-production (sterile controls).

Scientists' warning to humanity: microorganisms and climate change.

In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'.

Abating N in Nordic agriculture - Policy, measures and way forward.

During the past twenty years, the Nordic countries (Denmark, Sweden, Finland and Norway) have introduced a range of measures to reduce losses of nitrogen (N) to air and to aquatic environment by leaching and runoff. However, the agricultural sector is still an important N source to the environment, and projections indicate relatively small emission reductions in the coming years. The four Nordic countries have different priorities and strategies regarding agricultural N flows and mitigation measures, and therefore they are facing different challenges and barriers.

Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell.

Denitrification allows sustained respiratory metabolism during periods of anoxia, an advantage in soils with frequent anoxic spells. However, the gains may be more than evened out by the energy cost of producing the denitrification machinery, particularly if the anoxic spell is short. This dilemma could explain the evolution of different regulatory phenotypes observed in model strains, such as sequential expression of the four denitrification genes needed for a complete reduction of nitrate to N, or a "bet hedging" strategy where all four genes are expressed only in a fraction of the cells.

Denitrification as an NO sink.

The strong greenhouse gas nitrous oxide (NO) can be emitted from wastewater treatment systems as a byproduct of ammonium oxidation and as the last intermediate in the stepwise reduction of nitrate to N by denitrifying organisms. A potential strategy to reduce NO emissions would be to enhance the activity of NO reductase (NOS) in the denitrifying microbial community. A survey of existing literature on denitrification in wastewater treatment systems showed that the NO reducing capacity (V) exceeded the capacity to produce NO (V) by a factor of 2-10.

A bet-hedging strategy for denitrifying bacteria curtails their release of NO.

When oxygen becomes limiting, denitrifying bacteria must prepare for anaerobic respiration by synthesizing the reductases NAR (NO → NO), NIR (NO → NO), NOR (2NO → NO), and NOS (NO → N), either or sequentially, to avoid entrapment in anoxia without energy. Minimizing the metabolic burden of this precaution is a plausible fitness trait, and we show that the model denitrifier achieves this by synthesizing NOS in all cells, while only a minority synthesize NIR. Phenotypic diversification with regards to NIR is ascribed to stochastic initiation of gene transcription, which becomes autocatalytic via NO production.

Author Correction: Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil.

A correction has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.