Impact of nitrification inhibitors, phosphorus application, and microbial interactions on enhancing nutrient efficiency and crop performance - bacterial sequences
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PROVIDER: PRJEB80700 | ENA |
REPOSITORIES: ENA
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Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
2019-03-15 | PXD013103 | Pride
Project description:The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
2023-10-24 | PXD039573 | Pride
Project description:BackgroundUnderstanding diversity of arbuscular mycorrhizal fungi (AMF) is important for optimizing their role for phosphorus (P) nutrition of soybeans (Glycine max (L.) Merr.) in P-limited soils. However, it is not clear how soybean growth and P nutrition is related to AMF colonization and diversity of AMF communities in a continuous P-unfertilized cover cropping system. Thus, we investigated the impact of P-application and cover cropping on the interaction among AMF colonization, AMF diversity in soybean roots, soybean growth and P nutrition under a five-year P-unfertilized crop rotation.MethodsIn this study, we established three cover crop systems (wheat, red clover and oilseed rape) or bare fallow in rotation with soybean. The P-application rates before the seeding of soybeans were 52.5 and 157.5 kg ha-1 in 2014 and 2015, respectively. We measured AMF colonization in soybean roots, soybean growth parameters such as aboveground plant biomass, P uptake at the flowering stage and grain yields at the maturity stage in both years. AMF community structure in soybean roots was characterized by specific amplification of small subunit rDNA.ResultsThe increase in the root colonization at the flowering stage was small as a result of P-application. Cover cropping did not affect the aboveground biomass and P uptake of soybean in both years, but the P-application had positive effects on the soybean performance such as plant P uptake, biomass and grain yield in 2015. AMF communities colonizing soybean roots were also significantly influenced by P-application throughout the two years. Moreover, the diversity of AMF communities in roots was significantly influenced by P-application and cover cropping in both years, and was positively correlated with the soybean biomass, P uptake and grain yield throughout the two years.DiscussionOur results indicated that P-application rather than cover cropping may be a key factor for improving soybean growth performance with respect to AMF diversity in P-limited cover cropping systems. Additionally, AMF diversity in roots can potentially contribute to soybean P nutrition even in the P-fertilized cover crop rotational system. Therefore, further investigation into the interaction of AMF diversity, P-application and cover cropping is required for the development of more effective P management practices on soybean growth performance.
| S-EPMC5910793 | biostudies-literature
Project description:nitrification microbe Metagenome
| PRJNA360661 | ENA
Project description:Increased recycling of nutrient-rich organic waste to meet crop nutrient needs is an essential component of a more sustainable food system. However, agricultural specialization continues to pose a significant challenge to balancing crop nutrient needs and the nutrient supply from animal manure and human excreta locally. For Sweden, this study found that recycling all excreta (in 2007) could meet up to 75% of crop nitrogen and 81% of phosphorus needs, but that this would exceed crop potassium needs by 51%. Recycling excreta within municipalities could meet 63% of crop P nutrient needs, but large regional differences and imbalances need to be corrected to avoid over or under fertilizing. Over 50% of the total nitrogen and phosphorus in excreta is contained in just 40% of municipalities, and those have a surplus of excreta nutrients compared to crop needs. Reallocation of surpluses (nationally optimized for phosphorus) towards deficit municipalities, would cost 192 million USD (for 24 079 km of truck travel). This is 3.7 times more than the total NPK fertilizer value being transported. These results indicate that Sweden could reduce its dependence on synthetic fertilizers through investments in excreta recycling, but this would likely require valuing also other recycling benefits.
| S-EPMC6635506 | biostudies-literature
Project description:Majority of Pakistani soils are deficient in phosphorus. Phosphorus is usually applied in form of synthetic fertilizer. However integrated use of P from synthetic and organic sources can be more profitable and beneficial on sustainable basis. Field trials were conducted at research farm University of Poonch, Rawalakot, AJK, Pakistan for two consecutive years to check the comparative effects of synthetic fertilizer and organic manures applied alone and in combinations on the phosphorus use efficiency (PUE), wheat yield and yield components. Shafaq-06 cultivar of wheat was used as test cultivar. Ten treatments were included: (I) Control (P0) without application of fertilizer; (II) SSP @ 60 kg/ha (P60SSP); (III) SSP @ 90 kg/ha (P90SSP); (IV) SSP @ 120 kg/ha (P120SSP); (V) PM @60 kg/ha (P60PM); (VI) PM @90 kg/ha (P90PM); (VII) PM @120 kg/ha (P120PM); (VIII) SSP @30 kg/ha + PM @30 kg/ha (P30SSP+30PM); (IX) SSP @45 kg/ha + PM @45 kg/ha (P45SSP+45PM); (X) SSP @60 kg/ha + PM @60 kg/ha (P60SSP+60PM) which were laid out under the Randomized Complete Block Design. Significantly higher values for yield of grain (2397 kg/ha) was recorded with PM + SSP @ 60 kg P2O5 ha-1 each. Likewise, FPUE, PIR of wheat and AFPUE was quite higher with combined use of PM and SSP i.e. P60SSP+60PM treatment. Additionally, increase in PUE, wheat yield and yield components associated with combined treated plot would help to minimize the use of high cost synthetic mineral fertilizers and represents an environmentally and agronomically sound management strategy.
| S-EPMC8494362 | biostudies-literature
Project description:partial-nitrification & anammox Raw sequence reads
| PRJNA665601 | ENA
Project description:Effect of nitrification inhibitors, rock phosphate and beneficial microbes on maize fitness
| PRJEB73342 | ENA
Project description:Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi.We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi. Production and consumption of NOx increased and production of N2O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable.
2016-10-05 | GSE84969 | GEO
Project description:A field experiment was conducted during the wet seasons of 2013 and 2014 to evaluate the effect of three rice establishment methods: viz. puddled transplanted rice (PTR), system of rice intensification (SRI) and aerobic rice system (ARS), two cyanobacteria based inoculants, viz. Anabaena sp (CR1) + Providencia sp (PR3) consortium and Anabaena-Pseudomonas (An-Ps) biofilm formulation, and zinc (Zn) fertilization on the rice yield, water productivity, and nutrient use efficiency. The yields of rough, brown and milled rice were highest in SRI, which was on par with PTR and both methods proved significantly superior to ARS in both years. The total water productivity of rough and brown rice in the first year was significantly higher in SRI. The SRI method saved 21.9% and 27.4% irrigation water over PTR, and savings in ARS were 37.4% and 50.8% in first and second year respectively, over PTR. The use of An-Ps biofilm formulation along with 75% RDN improved the agronomic use efficiency of both nitrogenous and phosphatic fertilizers applied. On the basis of the present study, it can be concluded that SRI improved rice yields and water productivity; while involvement of An-Ps biofilm formulation can be recommended for improved nutrient use efficiency.
| S-EPMC6777210 | biostudies-literature