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Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica -enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica -enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B , a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica -enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica -enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica -enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops. Rice coordinates recruitment of the root microbiota to optimize nitrogen acquisition from soil.

Aims High-yielding maize-based crop systems require maize to take up large quantities of nitrogen over short periods of time. Nitrogen management in conventional crop systems assumes that soil N mineralization alone cannot meet rapid rates of crop N uptake, and thus large pools of inorganic N, typically supplied as fertilizer, are required to meet crop N demand. Net soil N mineralization data support this assumption; net N mineralization rates are typically lower than maize N uptake rates. However, net N mineralization does not fully capture the flux of N from organic to inorganic forms. Gross ammonification may better represent the absolute flux of inorganic N produced by soil N mineralization. Methods Here we utilize a long-term cropping systems experiment in Iowa, USA to compare the peak rate of N accumulation in maize biomass to the rate of inorganic N production through gross ammonification of soil organic N. Results Peak maize N uptake rates averaged 4.4 kg N ha⁻¹ d⁻¹, while gross ammonification rates over the 0–80 cm depth averaged 23 kg N ha⁻¹ d⁻¹. Gross ammonification was highly stratified, with 63% occurring in the 0–20 cm depth and 37% in the 20–80 cm depth. Neither peak maize N uptake rate nor gross ammonification rate differed significantly among three cropping systems with varied rotation lengths and fertilizer inputs. Conclusions Gross ammonification rate was 3.4 to 4.5 times greater than peak maize N uptake across the cropping systems, indicating that inorganic N mineralized from soil organic matter may be able to satisfy a large portion of crop N demand, and that explicit consideration of gross N mineralization may contribute to development of strategies that reduce crop reliance on large soil inorganic N pools that are easily lost to the environment.

Lime application (liming) has historically been used to ameliorate soil acidity in grasslands. Liming effectively improves soil pH, plant productivity, and soil physicochemical properties, but the long-term impact of acidity control by liming on key microbial nitrogen (N)-cycling genes in semi-natural grasslands is unknown. We investigated the effect of 65 years of liming on N-cycling processes in the limed and control plots of the Ossekampen long-term grassland experiment in the Netherlands. These plots have not received any other fertilizers for 65 years. Soil sampling and nitrous oxide (N 2 O) emission measurements were conducted three times in spring and four times in summer, and quantitative real-time PCR was performed to determine the absolute abundances of N-cycling genes, including ammonia-oxidation ( amoA -AOB, amoA -AOA, amoA -comammox), denitrification ( nirS , nirK , nosZ ), nitrate ammonification ( nrfA ), and N-fixation ( nifH ) genes. Long-term liming increased the absolute abundances of nitrifiers, denitrifiers, and nitrate ammonifiers. Soil N 2 O emissions did not differ significantly between liming and control treatments. Additionally, liming had a buffering effect that maintained the population of N-cycling microbes against seasonal variations in abundance. Our results indicate that improving soil acidity through liming potentially facilitates microbial N-cycling processes without increasing N 2 O emissions.

Microplastics (MPs) have emerged as a pervasive environmental pollutant, posing significant threats to both aquatic and terrestrial ecosystems. Despite the growing concern, research on the impacts of MPs on soil ecosystems, particularly on crucial processes like nitrogen cycling, remains limited compared to aquatic environments. This study aimed to fill this knowledge gap by conducting a 60-day incubation experiment to investigate the effects of polypropylene (PP), polyethylene (PE), and polyethylene terephthalate (PET) microplastics on soil nitrogen transformation processes. The findings revealed that microplastic contamination influenced soil nitrogen dynamics, with PP having the most detrimental impact. Specifically, the ammonification rate was consistently lower than the nitrification potential, and although the nitrification potential was not negatively affected by the presence of MPs, the availability of soil nitrogen, particularly in the form of nitrate, was predominantly maintained. However, at the end of the incubation period, soils contaminated with PP showed a significant reduction in available nitrogen concentrations. Generally, it was found that PP had the most negative effect on soil nitrogen processes. These results underscore the varying effects of different types of microplastics on soil nitrogen processes, highlighting the critical need for further investigation into their long-term environmental impacts.

Background The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments. Results Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status. Conclusions Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. CBzZNC2FEDswGcHctbDosa Video Abstract

In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium, which is directly reusable by primary producers. We combined multiple parallel long-term incubations of marine microbial nitrate-respiring communities with isotope labeling and metagenomics to unravel how specific environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate, and the carbon/nitrogen ratio were identified as key environmental controls that determine whether nitrite will be reduced to nitrogenous gas or ammonium. Our results define the microbial ecophysiology of a biogeochemical feedback loop that is key to global change, eutrophication, and wastewater treatment.

Biodeposition of minerals is a widespread phenomenon in the biological world and is mediated by bacteria, fungi, protists, and plants. Calcium carbonate is one of those minerals that naturally precipitate as a by-product of microbial metabolic activities. Over recent years, microbially induced calcium carbonate precipitation (MICP) has been proposed as a potent solution to address many environmental and engineering issues. However, for being a viable alternative to conventional techniques as well as being financially and industrially competitive, various challenges need to be overcome. In this review, the detailed metabolic pathways, including ammonification of amino acids, dissimilatory reduction of nitrate, and urea degradation (ureolysis), along with the potent bacteria and the favorable conditions for precipitation of calcium carbonate, are explained. Moreover, this review highlights the potential environmental and engineering applications of MICP, including restoration of stones and concrete, improvement of soil properties, sand consolidation, bioremediation of contaminants, and carbon dioxide sequestration. The key research and development questions necessary for near future large-scale applications of this innovative technology are also discussed.

The paradigm that permafrost-affected soils show restricted mineral nitrogen (N) cycling in favor of organic N compounds is based on the observation that net N mineralization rates in these cold climates are negligible. However, we find here that this perception is wrong. By synthesizing published data on N cycling in the plant-soil-microbe system of permafrost ecosystems we show that gross ammonification and nitrification rates in active layers were of similar magnitude and showed a similar dependence on soil organic carbon (C) and total N concentrations as observed in temperate and tropical systems. Moreover, high protein depolymerization rates and only marginal effects of C:N stoichiometry on gross N turnover provided little evidence for N limitation. Instead, the rather short period when soils are not frozen is the single main factor limiting N turnover. High gross rates of mineral N cycling are thus facilitated by released protection of organic matter in active layers with nitrification gaining particular importance in N-rich soils, such as organic soils without vegetation. Our finding that permafrost-affected soils show vigorous N cycling activity is confirmed by the rich functional microbial community which can be found both in active and permafrost layers. The high rates of N cycling and soil N availability are supported by biological N fixation, while atmospheric N deposition in the Arctic still is marginal except for fire-affected areas. In line with high soil mineral N production, recent plant physiological research indicates a higher importance of mineral plant N nutrition than previously thought. Our synthesis shows that mineral N production and turnover rates in active layers of permafrost-affected soils do not generally differ from those observed in temperate or tropical soils. We therefore suggest to adjust the permafrost N cycle paradigm, assigning a generally important role to mineral N cycling. This new paradigm suggests larger permafrost N climate feedbacks than assumed previously.

The cycling of essential nutrients is central to mangrove productivity. A mass balance shows that mangroves rely on soil ammonification, nitrification, and dissimilatory reduction to ammonium for available nitrogen. Mangroves are often nutrient limited and show tight coupling between nutrient availability and tree photosynthesis. This relationship and, thus, forest productivity can be disrupted by various disturbances such as deforestation, changes in hydrology due to impoundments, land-use change, increasing frequency and intensity of storms, increasing temperatures, increasing atmospheric CO2 concentrations, and a rising sea-level. Deforestation and hydrological changes are the most devastating to soil nutrient-plant relations and mangrove productivity. Land-use changes can result in positive and negative impacts on mangroves and can also results in increasing frequency of storms and intensity of storms. Increasing temperatures and atmospheric CO2 levels have an initially enhanced effect on mangroves and microbial transformation rates of nitrogen and phosphorus. The effects of rising seas are complex and depend on the local rate of sea-level rise, the soil accretion rate, the subsidence or uplift rate, and the tidal position. If mangroves cannot keep pace with a sea-level rise, seaward mangroves will likely drown but landward mangroves will expand and show enhanced growth and more rapid nutrient cycling if space permits.

Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.