Determination of N-species in soil extracts using microplate techniques

Climate risk analysis of low-altitude tea gardens in central Taiwan using a Bayesian network

Tea is a vital agricultural product in Taiwan. Due to global warming, the increasing extreme weather events have disrupted tea garden conditions and caused economic losses in agriculture. To address these challenges, a comprehensive tea garden risk assessment model, a Bayesian network (BN), was developed by considering various factors, including meteorological data, disaster events, tea garden environment (location, altitude, tea tree age, and soil characteristics), farming practices, and farmer interviews, and constructed risk assessment indicators for tea gardens based on the climate change risk analysis concept from the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5). The results demonstrated an accuracy of over 92% in both validating and testing the model for tea tree damage and yield reduction. Sensitivity analysis revealed that tea tree damage and yield reduction were mutually influential, with weather, fertilization, and irrigation also impacting tea garden risk. Risk analysis under climate change scenarios from various global climate models (GCMs) indicated that droughts may pose the highest risk with up to 41% and 40% of serious tea tree growth damage and tea yield reduction, respectively, followed by cold events that most tea gardens may have less than 20% chances of serious impacts on tea tree growth and tea yield reduction. The impacts of heavy rains get the least concern because all five tea gardens may not be affected in terms of tea tree growth and tea yield with large chances of 67 to 85%. Comparing farming methods, natural farming showed lower disaster risk than conventional and organic approaches. The tea plantation risk assessment model can serve as a valuable resource for analyzing and offering recommendations for tea garden disaster management and is used to assess the impact of meteorological disasters on tea plantations in the future.

Rapid anaerobic culture and reaction kinetic study of anammox bacteria on microfluidic chip

Anammox bacteria are being increasingly investigated as part of an emerging nitrogen removal technology. However, due to the difficulty in culturing, current understanding of their behavior is limited. In this study, anaerobic microfluidic chips were used to study anammox bacteria, showing great advantages over reactors. On-chip fluorescence in situ hybridization (FISH) showed the relative abundance of free form anammox bacteria increased by 56.1 % after one week's culture, an increase that is three times higher than that of bioreactor (17.1 %). For granular form cultures, the nitrogen removal load reached 2.34 ∼ 2.51 kg-N/(m3·d), which was also substantially higher than the bioreactor (∼1.22 kg-N/(m3·d)). Furthermore, studying the kinetics of nitrite inhibition of granular sludge with different particle sizes (100-900 μm) showed that the maximum ammonia load and the nitrite semi-saturation coefficient noticeably decreased for smaller particle sizes. These results illustrate the usefulness of the microfluidic method for in-depth understanding anammox process and its implementation.

Benefits of biological nitrification inhibition of Leymus chinensis under alkaline stress: the regulatory function of ammonium-N exceeds its nutritional function

Introduction

The production of root exudates with biological nitrification inhibition (BNI) effects is a strategy adopted by ammonium-N (NH4+-N) tolerant plant species that occur in N-limited environments. Most knowledge on BNI comes from plant species that occur in acidic soils.

Methods

Here, combining field sampling and laboratory culture, we assessed the BNI-capacity of Leymus chinensis, a dominant grass species in alkaline grasslands in eastern Asia, and explored why L. chinensis has BNI ability.

Results and discussion

The results showed that L. chinensis has strong BNI-capacity. At a concentration of 1 mg mL^-1, L. chinensis' root exudates inhibited nitrification in soils influenced by Puccinellia tenuiflora by 72.44%, while DCD only inhibited it by 68.29%. The nitrification potential of the soil of L. chinensis community was only 53% of the P. tenuiflora or 41% of the Suaeda salsa community. We also showed that the supply of NH4+-N driven by L. chinensis' BNI can meet its requirements . In addition, NH4+-N can enhance plant adaptation to alkaline stress by regulating pH, and in turn, the uptake of nitrate-N (NO3--N). We further demonstrated that the regulatory function of NH4+-N is greater than its nutritional function in alkaline environment. The results offer novel insights into how L. chinensis adapts to high pH and nutrient deficiency stress by secreting BNIs, and reveal, for the first time, differences in the functional roles of NH4+-N and NO3--N in growth and adaptation under alkaline conditions in a grass species.

A microplate spectrophotometric method for analysis of indole-3-carbinol in dietary supplements using p-dimethylaminocinnamaldehyde (DMACA) as a chromogenic reagent

This work presents the development of a microplate spectrophotometric method for determination of indole-3-carbinol in dietary supplements. The colorimetric procedure is based on the reaction of indole-3-carbinol with the p-dimethylaminocinnamaldehyde (DMACA) reagent under acidic conditions. The absorbance of the colored product measured at 675 nm was used to determine the target analyte. To achieve optimal spectrophotometric performance, the DMACA reagent concentration, the hydrochloric acid concentration, and the reaction time were optimized. The developed technique performed well under the optimal conditions, with a linear calibration range of 30 to 300 mg L^-1 and a high correlation coefficient (r² = 0.9954). The limit of detection and limit of quantification were 7.8 mg L^-1 and 26.2 mg L^-1, respectively. This approach demonstrated good repeatability (intra- and inter-day precision) with a % RSD lower than 9.4%, good accuracy with acceptable relative recoveries in the range of 98 to 106%, and high sample throughput (24 detection per min). This simple, rapid, and multi-sample analysis approach for routine analysis of indole-3-carbinol has the potential to be used for the quality control of dietary supplements.

Microbial diversity and composition in acidic sediments of freshwater finfish culture ponds fed with two types of feed - A metagenomic approach

Microbial community profile associated with acidic pond sediments (APS) (pH=3.0-4.5) of freshwater finfish aquaculture ponds (n=8) was investigated. Sediment DNA extracted from the eight APS were subjected to high-throughput sequencing of V3 and V4 regions which yielded 7236 operational taxonomic units (OTUs) at a similarity of 97%. Overall results showed higher proportion of bacterial OTUs than archaeal OTUs in all the APS. Euryarchaeota (23%), Proteobacteria (19%), Chloroflexi (17%) Crenarchaeota (5.3%), Bacteroidetes (4.8%), Nitrospirae (3.2%), Nanoarchaeaeota (3%) which together constituted 75% of the microbial diversity. At the genus level, there was high preponderance of methanogens namely Methanolinea (5.4%), Methanosaeta (4.5%) and methanotrops, Bathyarchaeota (5%) in APS. Moreover, the abundant phyla in the APS were not drastically affected by the administration of chicken slaughter waste (R-group ponds) and commercial fish feed (C-group ponds), since 67% of the OTUs generated remained common in the APS of both the groups of ponds. There was a minimal difference of 24-26% of OTUs between C-group and R-group ponds suggesting the existence of a core microbial community in these ponds driven by acidic pH over the years. This study concludes that microbial diversity in pond sediment was influenced to a lesser extent by the addition of chicken slaughter waste but was majorly driven by acidic nature of the pond.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite - can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

Impact of irrigation with fish-processing effluents on nitrification and ammonia-oxidizer abundances in Patagonian arid soils

This study aimed to evaluate the short-term effects of irrigation with diluted fish-processing effluents on soil pH, electrical conductivity, nitrification rate and abundance of ammonia oxidizers. To accomplish that, we constructed microcosms of soil from an undisturbed arid ecosystem of Patagonia, and irrigated them for 2 months with diluted effluents from a fish-processing factory or with water as control. In the initial soil sample, and along the experiment, we determined soil pH, electrical conductivity, and the concentration of inorganic nitrogen forms, which we used to calculate the net nitrification rate. We further estimated the abundances of ammonia-oxidizing archaea and bacteria in the initial soil sample and at the end of the experiment, by qPCR of amoA genes. Soil pH decreased and electrical conductivity increased in both irrigation treatments, although the effect was higher in effluent-irrigated microcosms. Soil nitrate + nitrite concentration, and thus the nitrification rate, was higher in effluent than in water-irrigated microcosms. The abundance of archaeal amoA genes was higher under effluent than water-irrigation, but that of bacterial amoA genes did not vary significantly between treatments. Neither ammonia-oxidizing archaea nor bacteria were influenced by the changes in soil pH and electrical conductivity induced by effluent irrigation.

Gross Ammonification and Nitrification Rates in Soil Amended with Natural and NH4-Enriched Chabazite Zeolite and Nitrification Inhibitor DMPP

Using zeolite-rich tuffs for improving soil properties and crop N-use efficiency is becoming popular. However, the mechanistic understanding of their influence on soil N-processes is still poor. This paper aims to shed new light on how natural and NH4+-enriched chabazite zeolites alter short-term N-ammonification and nitrification rates with and without the use of nitrification inhibitor (DMPP). We employed the 15N pool dilution technique to determine short-term gross rates of ammonification and nitrification in a silty-clay soil amended with two typologies of chabazite-rich tuff: (1) at natural state and (2) enriched with NH4+-N from an animal slurry. Archaeal and bacterial amoA, nirS and nosZ genes, N2O-N and CO2-C emissions were also evaluated. The results showed modest short-term effects of chabazite at natural state only on nitrate production rates, which was slightly delayed compared to the unamended soil. On the other hand, the addition of NH4+-enriched chabazite stimulated NH4+-N production, N2O-N emissions, but reduced NO3−-N production and abundance of nirS-nosZ genes. DMPP efficiency in reducing nitrification rates was dependent on N addition but not affected by the two typologies of zeolites tested. The outcomes of this study indicated the good compatibility of both natural and NH4+-enriched chabazite zeolite with DMPP. In particular, the application of NH4+-enriched zeolites with DMPP is recommended to mitigate short-term N losses.

Mitigating nitrogen pollution with under-sown legume-grass cover crop mixtures in winter cereals

Nitrogen (N) pollution from N inputs to agricultural soils contributes to widespread eutrophication and global climate change. One period susceptible to N losses is between winter grain harvest in summer and corn planting in spring in a corn (Zea mays L.)-soybean [Glycine max (L.) Merr.]-winter grain rotation. Cover crops used to immobilize N during this period often depend on tillage, which can exacerbate N losses. Therefore, we evaluated whether reduced-till cover crops could decrease nitrate (NO₃ ^- ) leaching and nitrous oxide (N₂ O) emissions during this period. We tested this strategy in a cropping systems experiment on a 4-ha plot in central Pennsylvania over 2 yr. This experiment compared a clover (Trifolium pratense L.)-timothy (Phleum pratense L.) cover crop no-till underseeded into a standing spelt crop with a vetch (Vicia villosa Roth)-triticale (× Triticosecale Wittm. ex A. Camus) cover crop established with tillage after spelt harvest. These systems were compared based on fortnightly N₂ O emissions using static chambers (n = 4 per six sample dates) and potential NO₃ ^- leaching using anion resin bags (n = 4 per system per year). Reduced-till cover crops minimized peak N₂ O emissions during the fall compared with tilled cover crops. However, reduced-till cover crops did not decrease potentially leachable NO₃ ^- relative to tilled cover crops despite decreases in soil inorganic N. Cover crop N isotopes revealed that clover N may have mineralized and leached over the winter. Our results suggest that reduced-till cover crops can decrease N₂ O emissions to mitigate the climate impact of agriculture but that winter-hardy cover crops should be chosen to mitigate leaching.

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic (N2-fixing) microbiota. Targeting these diazotrophs, we selected nearly 600 microbes of a collection obtained from mucilage and confirmed their ability to incorporate heavy nitrogen (15N2) metabolites in vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence of nif genes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed the canonical nif gene operons, as well as many other operon configurations with concomitant fixation and release of >700 different 15N labeled metabolites. We further demonstrated that many diazotrophs possessed alternative nif gene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiple nif gene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes.

Fish-processing effluent discharges influenced physicochemical properties and prokaryotic community structure in arid soils from Patagonia

Along the Patagonian coast, there are processing factories of marine products in land that produce fish-processing effluents. The aim of the present study was to assess the physicochemical properties and the prokaryotic community composition of soils receiving fish-processing effluent discharges (effluent site-ES), and to compare them with those of unaltered soils (control site-CS) in the arid Patagonian steppe. We analyzed soil prokaryotic communities (using amplicon-based sequencing of 16S rRNA genes), soil physicochemical properties and fish-processing effluent characteristics. Soil moisture, electrical conductivity (EC), total and inorganic C were significantly higher in ES than in CS (p < .05). Effluent discharges induced a decrease in the total number of operational taxonomic units (OTUs) and in the Shannon diversity index (p = .0009 and .01, respectively) of soil prokaryotic community. Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla in CS, while ES soil showed a more heterogeneous composition of phyla. Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that fish-processing effluent discharges promoted an enrichment of Firmicutes and Bacteroidetes, which are active contributors to organic matter mineralization, along with a decrease of oligotrophic phyla such as Acidobacteria, Chloroflexi, Armatimonadetes and Nitrospirae, commonly found in nutrient-poor arid soils. The concentrations of inorganic C and ammonium, the EC and the soil moisture explained 73% of the total variation within the community composition. Due to its salinity and nutrients, fish-processing effluents have potential mainly for native salt-tolerant plant irrigation, however the impacts of soil prokaryotic community shifts over plant growth remain to be determined.

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the N2O reductase-gene nosZ and N2O:N2 partitioning from agricultural soils

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (N₂O) from agricultural soils. However, their N₂O reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N₂ and N₂O emissions with ¹⁵N tracing analysis and the quantification of the N₂O-reductase gene (nosZ) in a soil microcosm study. Nitrogen fertilization suppressed nosZ abundance in both soils, showing that high nitrate availability and the preferential reduction of nitrate over N₂O is responsible for large pulses of N₂O after the fertilization of agricultural soils. DMPP attenuated this effect only in the horticultural soil, reducing nitrification while increasing nosZ abundance. DMPP reduced N₂O emissions from the horticultural soil by >50% but did not affect overall N₂ + N₂O losses, demonstrating the shift in the N₂O:N₂ ratio towards N₂ as a key mechanism of N₂O mitigation by NIs. Under non-limiting NO₃⁻ availability, the efficacy of NIs to mitigate N₂O emissions therefore depends on their ability to reduce the suppression of the N₂O reductase by high NO₃⁻ concentrations in the soil, enabling complete denitrification to N₂.

Designing Aquaponic Production Systems towards Integration into Greenhouse Farming

Aquaponics is a sustainable method of food production, whereby aquaculture and hydroponics are combined in one circular system. A few aquaponics startup companies are emerging in Europe with a limited production area of a few hundred or a few thousand square meters, whereas hydroponics is a common practice in a commercially viable manner most often with production units of several hectares. In Iceland, greenhouse farmers operate on relatively small production units, often between 2000 and 5000 m2. The aim of the present study was, therefore, to develop and design aquaponic production systems towards integration into small greenhouse farming strengthening economic viability and sustainability. Since the local market in Iceland is small and import is relatively expensive due to the distance from other markets, the suitability of commercially available fish feed and the selection of plant species were assessed in relation to production efficiency and available market and resources. The effects of water flow on plant growth and on nutrient utilization in culture water were measured and evaluated. Four aquaponics test systems were designed, built and operated, and results were used to develop a pilot commercial aquaponics system implemented for greenhouse farming in Iceland. One of the test systems was a media filled flood and drain system and the other three were deep water culture systems. Tilapia (Oreochromis niloticus), one of the most popular fish in aquaculture, was reared in all systems, while different leafy greens and fruiting vegetables were grown in the hydroponics. The fish was fed with commercial aquaculture feed made for cod and charr. The feed conversion ratio (FCR) was used to assess the effectiveness of feed on fish growth. The FCR observed in this research was between 0.9 and 1.2, within the typical values for tilapia growth in aquaculture. The production of the leafy green plants (e.g., pak-choi) was approximately four times, by weight, that of the production of fish, a similar yield as shown in other researches in the field. The continuous rise of nitrate and phosphate concentrations in the aquaponic system indicated the potential to support even higher crop yield. Long daylength in the summer in Iceland is clearly beneficial for crop production in aquaponics. Based on the results, it is concluded that aquaponics can be a feasible opportunity for greenhouse farming at least to diversify the current business model. Not only can the fish provide an extra income but also the effluent from the aquaculture is easily used as fertilizer for the plants, thus the circular production system offers new innovative ideas for diversifying and value-adding the business further, for example into crayfish production and/or into educational and experience tourism.

Microliter Operation for Determination of Nitrate-Nitrogen via Simple Zinc Reduction and Color Formation in a Well Plate with a Smartphone

We propose a simple greener colorimetric method for the determination of nitrate-nitrogen by operating on a 96-well microplate and using a smartphone camera as a simple detector. A slurry containing 0.3 mg zinc was used for reduction of nitrate to nitrite, the reduction solution was transferred to a 96-well microplate to react with Griess reagent to form a pink azo dye product. The color product image was captured and processed by a smartphone camera and ImageJ software, respectively. The limit of detection and limit of quantitation were 0.04 and 0.10 mg/L nitrate-nitrogen, respectively, for the smartphone camera. Application to real samples was demonstrated. The proposed method results showed no significant difference (at 95% confidence) with the hydrazine reduction method. The proposed method could be used as an alternative method for on-site analysis due to the advantages of portability and rapidity; duplicate run of 20 samples could be carried out simultaneously in 12 min.

Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment

Over three million tonnes of spent mushroom substrate (SMS) are produced in Europe every year as a by-product of the cultivation of Agaricus bisporus. The management of SMS has become an increasing challenge for the mushroom production industry, and finding environmentally and economically sustainable solutions for this organic residue is, therefore, highly desirable. Due to its physical properties and nutrient content, SMS has great potential to be employed in agricultural and horticultural sectors, and further contribute to reduce the use of non-renewable resources, such as peat. However, SMS is often regarded as not being stable and/or mature, which hampers its wide use for crop production. Here, we demonstrate the stabilisation of SMS and its subsequent use as organic fertiliser and partial peat replacement in horticulture. The stabilisation was performed in a laboratory-scale composting system, with controlled temperature and aeration. Physical and chemical parameters were monitored during composting and provided information on the progress of the process. Water soluble carbohydrates (WSC) content was found to be the most reliable parameter to predict SMS stability. In situ oxygen consumption indicated the main composting phases, reflecting major changes in microbial activity. The structure of the bacterial community was also found to be a potential predictor of stability, as the compositional changes followed the composting progress. By contrast, the fungal community did not present clear successional process along the experiment. Maturity and quality of the stabilised SMS were assessed in a horticultural growing trial. When used as the sole fertiliser source, SMS was able to support Lolium multiflorum (Italian ryegrass) growth and significantly improved grass yield with a concentration-dependent response, increasing grass biomass up to 300%, when compared to the untreated control. In summary, the results indicated that the method employed was efficient in generating a stable and mature product, which has a great potential to be applied in horticulture. This study represents a step forward in the management of SMS residue, and also provides an alternative to reduce the use of peat in horticulture, alleviating environmental impacts to peatland ecosystems.

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism.

IMPORTANCE

Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community.

Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation

In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies.

Development of a cloud point extraction and spectrophotometry-based microplate method for the determination of nitrite in human urine and blood

A novel and simple method for the sensitive determination of trace amounts of nitrite in human urine and blood has been developed by combination of cloud point extraction (CPE) and microplate assay. The method is based on the Griess reaction and the reaction product is extracted into nonionic surfactant Triton-X114 using CPE technique. In this study, decolorization treatment of urine and blood was applied to overcome the interference of matrix and enhance the sensitivity of nitrite detection. Multi-sample can be simultaneously detected thanks to a 96-well microplate technique. The effects of different operating parameters such as type of decolorizing agent, concentration of surfactant (Triton X-114), addition of (NH4)2SO4, extraction temperature and time, interfering elements were studied and optimum conditions were obtained. Under the optimum conditions, a linear calibration graph was obtained in the range of 10-400 ng mL(-1) of nitrite with limit of detection (LOD) of 2.5 ng mL(-1). The relative standard deviation (RSD) for determination of 100 ng mL(-1) of nitrite was 2.80%. The proposed method was successfully applied for the determination of nitrite in the urine and blood samples with recoveries of 92.6-101.2%.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior

Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.

Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils

Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 10⁵ to 10⁶ copies archaeal amoA g⁻¹ soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.

Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater

Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

Determination of nitrate and nitrite in freshwaters using flow-injection with luminol chemiluminescence detection

A simple and sensitive flow-injection (FI) method for the determination of nitrate and nitrite in natural waters, based on luminol chemiluminescence (CL) detection, is reported. Nitrate was reduced online to nitrite via a copperized cadmium (Cu-Cd) column and then reacted with acidic hydrogen peroxide to form peroxynitrous acid. CL emission was observed from the oxidation of luminol in an alkaline medium in the presence of the peroxynitrite anion. The limits of detection (S:N = 3) were 0.02 and 0.01 µg N/L, with sample throughputs of 40 and 90 /h for nitrate and nitrite, respectively. Calibration graphs were linear over the range 0.02-50 and 0.01-50 µg N/L [R2  = 0.9984 (n = 8) and R2  = 0.9965 (n = 7)] for nitrate and nitrite, respectively, with relative standard deviations (RSDs; n = 3) in the range 1.8-4.6%. The key chemical and physical variables (reagent concentrations, buffer pH, flow rates, sample volume, Cu-Cd reductor column length) were optimized and potential interferences investigated. The effect of cations [Ca(II), Mg(II), Co(II), Fe(II) and Cu(II)] was masked online with EDTA. Common anions (PO4(3-) , SO4(2-) and HCO3-) did not interfere at their maximum admissible concentrations in freshwaters. The effect of salinity on the luminol CL reaction with and without nitrate and nitrite (2 and 0.5 µg N/L, respectively) was also investigated. The method was successfully applied to freshwaters and the results obtained were in good agreement with those obtained by an automated segmented flow analyser reference method.

Reversed-phase liquid chromatography/electrospray ionization/mass spectrometry with isotope dilution for the analysis of nitrate and nitrite in water

A new method was developed for the analysis of nitrate and nitrite in a variety of water matrices by using reversed-phase liquid chromatography/electrospray ionization/mass spectrometry in the negative ion mode. For this direct analysis method, nitrate and nitrite anions were well separated under the optimized LC conditions, detected by monitoring m/z 62 and m/z 46 ions, and quantitated by using an isotope dilution technique that utilized the isotopically labeled analogs. The method sensitivity, accuracy, and precision were investigated, along with matrix effects resulting from common inorganic matrix anions. The isotope dilution technique, along with sample pretreatment using barium, silver, and hydrogen cartridges, effectively compensated for the ionization suppression caused by the major water matrix anions, including chloride, sulfate, phosphate, and carbonate. The method detection limits, based on seven reagent water replicates fortified at 0.01 mg N/L nitrate and 0.1 mg N/L nitrite, were 0.001 mg N/L for nitrate and 0.012-0.014 mg N/L for nitrite. The mean recoveries from the replicate fortified reagent water and lab water samples containing the major water matrix anions, were 92-103% for nitrate with an imprecision (relative standard deviation, RSD) of 0.4-2.1% and 92-110% for nitrite with an RSD of 1.1-4.4%. For the analysis of nitrate and nitrite in drinking water, surface water, and groundwater samples, the obtained results were generally consistent with those obtained from the reference methods. The mean recoveries from the replicate matrix spikes were 92-123% for nitrate with an RSD of 0.6-7.7% and 105-113% for nitrite with an RSD of 0.3-1.8%.