Candidatus Nitrosocosmicus Research Articles

Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.

Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.

Soil physicochemical and microbial properties affect nitrogen cycling in technogenically transformed coal dump soils

Mining industrial sectors deteriorate local and regional environmental quality, contributing to global ecosystem contamination. The activities of microorganisms and enzymes involved in nitrogen cycling processes were investigated in coal dump soils that had undergone technogenic transformations and reclamation. Compared to the background uncontaminated soil, the heavy metal concentrations increased to high contamination levels (the contents of mobile forms of Zn, Ni, and Cu were 66.9; 35.6; 12.9 mg/kg, respectively), salinity increased to 0.1–2.41 %. The activities of nitrification and denitrification as well as the abundance of ammonifiers reduced due to high concentrations of mobile forms, the presence of coal particles, and the salinity of soil samples. The urease activity decreased due to reduced content of soluble organic matter in disturbed soils (2.3 times lower than the background soils). Mechanical reclamation leads to a 4-fold decrease in soil toxicity levels; however, it does not enhance nitrogen cycling activity. The activity of nitrification and urease decreased by >4 times as compared to the soil of the protected area. Microbial community composition of coal mine soils was similar to that of undisturbed soil. Nitrifiers in coal mine soil were represented by the genera Nitrososphaera, Candidatus Nitrosocosmicus, Nitrosospira, Nitrosomonas, Nitrosococcus, Nitrospira, Nitrobacter. The results indicated that the disruption of nitrification process led to low nitrate content in technogenically transformed coal dump soils.

Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media

Abstract. Saukoly SA, Meitiniarti VI, Nugroho RA, Krave AS. 2024. Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media. Biodiversitas 25: 916-923. Nitrification is the process of ammonium oxidation to form nitrites and nitrates. Ammonium availability in the soil is one of the factors influencing the activity, abundance, and diversity of ammonia-oxidizing microorganisms (AOM). This study aimed to determine the effect of enriching a soil media with different ammonium concentrations on the abundance and diversity of AOM as well as the potential for nitrification. Soil as the media was prepared from an agricultural land receiving cow dung sewage. The media was then placed in the microcosms, and was added to a nitrification medium containing ammonium at three levels; 0 (control soil), 200 (low ammonium-enriched soil), and 500 mg L-1 (high ammonium-enriched soil). The microcosms were further incubated for 42 days at room temperature. The nitrification potential determination was based on the formation of nitrite from ammonium oxidation. The abundance of AOM and the potential nitrification were measured every 14-day interval, including day 0 as the initial condition. The AOM composition was analyzed based on the similarity level of the amoA gene sequence to the NCBI BLAST GenBank database. However, this analysis was only conducted for the control and high ammonium-enriched soil. This study indicated that ammonium enrichment increased the nitrification activity and the abundance of AOM, but it decreased the diversity of AOM communities. There were positive correlations between nitrification and nitrate potential, as well as between ammonium content and AOM abundance. Negative correlations appeared between pH and nitrification potential, nitrate concentrations, ammonium concentrations, and MPN. The diversity of ammonium-oxidizing archaea (AOA) in the control soil was higher than in the high ammonium-enriched soil. The enrichment with ammonium also changed the AOA composition. The Candidatus Nitrosocosmicus oleophilus strain of the MY3 chromosome was the most dominant archaea in the control and high ammonium-enriched soil. This implies that the high diversity of AOA in this soil may be beneficial for further use of the soil as a source for inocula in the development of nitrifiers-based biofertilizers.

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains.

Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.

Effect of co-application of straw and various nitrogen fertilizers on N2O emission in acid soil

In order to explore the alteration of N transformation and N2O emissions in acid soil with the co-application of straw and different types of nitrogen (N) fertilizers, an incubation experiment was carried out for 40 days. There are totally five treatments in the study: (a) without straw and N fertilizer (N0), (b) straw alone application (SN0), (c) straw with NH4Cl (SN1), (d) straw with NaNO3 (SN2), and (e) straw with NH4NO3 (SN3). N2O emissions, soil physicochemical properties, and abundance/activity of ammonia-oxidizing archaea (AOA) were measured. The results showed that the combined application of straw and N enhanced N2O emissions, particularly, SN2 and SN3 treatments. Moreover, the soil pH was lower in co-application treatments and the average decreasing rate was 9.69%. Specially, the pH was lowest in the SN1 treatment. The results of correlation analysis indicated a markedly negative relationship between pH and N2O, as well as a negative relationship between pH and net mineralization rate. These findings suggest that pH alteration can affect the N transformation process in soil and thus influence N2O emissions. In addition, the dominant AOA at the genus level in the SN2 treatment was Nitrosopumilus, and Candidatus nitrosocosmicus in the SN3 treatment. The reshaped AOA structure can serve as additional evidence of the changes in the N transformation process. In conclusion, as the return of straw, the cumulation of N2O from arable acid soil depends on the form of N fertilizer. It is also important to consider how N fertilizer is applied to reduce the possibility of N being lost in the soil as gas.

Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit.

Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.

The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'.

The ammonia monooxygenase (AMO) is a key enzyme in ammonia-oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia-oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one-carbon (C1) compounds in ammonia-oxidizing archaea.

Alcohols as inhibitors of ammonia oxidizing archaea and bacteria.

Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.

Rice Straw Composting Improves the Microbial Diversity of Paddy Soils to Stimulate the Growth, Yield, and Grain Quality of Rice

This study aimed to explore the effects of straw compost with different proportions as replacement to chemical fertilizer on soil microorganisms as well as rice growth yield and quality. The rice variety Quan9you 063 in Fengyang, Anhui province was employed as the research subject. Four experimental treatments were set: local conventional fertilization as a control (CK) and compost substituting chemical fertilizer at 10% (T1), 20% (T2), and 30% (T3) to investigate the effects of straw composting. Our findings revealed that T1 treatment had the best rice yield-increasing effect (p < 0.05). Compared with CK, the rice yield, grain number per panicle, and rice polishing rate increased by 6.43%, 21.60%, and 0.47%, respectively; the chalkiness and chalky grain rate decreased by 25.77% and 55.76%, respectively. The T1 treatment achieved significantly higher relative abundance of β-Proteobacteria, Sideroxydans, Methanoregula, and Candidatus Nitrosocosmicus, indicating that the compost replacing 10% chemical fertilizer notably increased the microbial diversity. Hence, the replacement of 10% of chemical fertilizers with compost can enhance the rice yield.

Cultivation of ammonia-oxidising archaea on solid medium

Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: ‘Candidatus Nitrosocosmicus franklandus C13’, Nitrososphaera viennensis EN76 and ‘Candidatus Nitrosotalea sinensis Nd2’. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both ‘Ca. N. franklandus C13’ and N. viennensis EN76 tolerated Phytagel™ while the acidophilic ‘Ca. N. sinensis Nd2’ was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from ‘Ca. N. franklandus C13’ and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.

Salinity and N input drive prokaryotic diversity in soils irrigated with treated effluents from fish-processing industry

Wastewater reuse for irrigation has become an important practice in many countries in the context of global water scarcity. However, knowledge about the potential soil impact of reusing treated fish-processing (TFP) effluents for irrigation is still limited. The aim of this study was to investigate the response of the soil prokaryotic community in general, and the nitrifying taxa in particular, to TFP-effluent irrigation. We analyzed the impacts of irrigation with two effluent dilutions (EF1 and EF2, with electrical conductivities of 2.7 and 6 mS cm−1, respectively) or water (W) as a control on soil chemical properties, dehydrogenase and nitrifying activities, amoA gene abundances of ammonia-oxidizing bacteria (AOB) and archaea (AOA), and soil prokaryotic community structure and diversity. At the end of the irrigation experiment, soil ammonium, nitrate plus nitrite, dehydrogenase and nitrifying activities, soil electrical conductivity (EC), and sodium adsorption ratio (SAR) were significantly higher in TFP-irrigated treatments than in water irrigated controls. Prokaryotic richness and diversity indices followed the pattern W > EF1 > EF2, and negatively correlated with soil EC, SAR, ammonium, nitrate plus nitrite, and total N concentrations. In particular, EF2-irrigation stimulated soil copiotrophic bacteria (e.g. Proteobacteria and Bacteroidetes) to the detriment of oligotrophic members such as Acidobacteria. TFP-effluent irrigation also influenced the relative abundance of the amoA gene of AOB but not that of AOA; and the composition of nitrifying taxa, by inducing a significant increase in OTUs whose closest cultured matches were ‘Candidatus Nitrosocosmicus franklandus’ and Nitrosospira briensis Nsp10. Overall, irrigation with the more diluted effluent (classified as slight to moderate degree of restriction by local regulations) induced a reduction of soil prokaryotic diversity, whereas the less diluted effluent (severe irrigation restriction) promoted the greatest changes in the prokaryotic community due to the increase in soil salinity and N content.

Preferential temperature and ammonia concentration for in-situ growth of Candidatus Nіtrоѕосоѕmісuѕ ammonia oxidising archaea

Among cultivated and characterised ammonia oxidising archaea (AOA), representatives of Candidatus Nitrosocosmicus are unique in their ability to grow at high ammonia concentration (up to 100 mM), at concentrations that are tolerated by many ammonia oxidising bacteria (AOB). These strains also grow at a wide range of incubation temperatures (4–45 °C), with highest ammonia oxidation rates at relatively high temperature (28–40 °C). In addition, ammonia oxidiser growth is often promoted by reduced competition for ammonia, such as in the presence of a specific inhibitor against ammonia oxidiser competitors. Therefore, this study aimed at assessing the optimal conditions (temperature and ammonia concentration) of Ca. Nitrosocosmicus in soil by determining the nitrification rate and the growth of Ca. Nitrosocosmicus AOA and AOB in pH 7.5 soil microcosms amended with inorganic ammonia and octyne and incubated at a range of temperatures (15–35 °C). It demonstrated that growth of Ca. Nitrosocosmicus AOA increases with incubation temperature in soil, with an optimum of 25 °C. In addition, growth of Ca. Nitrosocosmicus is greater when AOB are inhibited, especially under high NH4+ concentration. This study indicates that Ca. Nitrosocosmicus is tolerant to high NH4+ concentration in soils, which contradicts the accepted belief that AOA growth is inhibited in soil with high NH4+ concentration, and it also confirms the role of a near-neutrophilic AOA in nitrification activity in soil with higher nitrogen content. This study also shows the relevance and limitations of cultivated strains in predicting microbial growth in natural environments.

Comparison of Novel and Established Nitrification Inhibitors Relevant to Agriculture on Soil Ammonia- and Nitrite-Oxidizing Isolates.

Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; “Candidatus Nitrosocosmicus franklandus,” “Candidatus Nitrosotalea sinensis”), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3–0.7 μM) compared to EQ (EC50 = 1–1.4 μM) and EQNL (EC50 = 26.6–129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9–248.7 μM vs EC50 = 0.6–2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8–2.1 and 1.0–6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.

Applying constructed wetland-microbial electrochemical system to enhance NH4+ removal at low temperature

NH4+ removal at low temperature (<10 °C) has baffled researchers and engineers for decades. Bioelectrochemical process has been increasingly valued as a promising approach to enhance NH4+ removal by both electrochemical and stimulated microbial processes. The feasibility and the mechanism of enhanced NH4+ removal were investigated in Constructed Wetland-Microbial Electrochemical System (CW-MES) with different electrode spacings including Constructed Wetland-Microbial Fuel Cell (CW-MFC) and Constructed Wetland-Microbial Electrolysis Cell (CW-MEC) at low temperature. Solar cell panel was firstly implemented in CW-MEC to enhance NH4+ removal. The low-temperature operation lasted for about four months, CW-MEC successfully enhanced NH4+ removal while CW-MFC did not exhibit positive effect. The NH4+-N removal efficiency of CW-MEC achieved 88.2 ± 7.0%, which was 11.7 ± 6.5% higher than conventional constructed wetland (CCW). The maximum NH4+-N removal efficiency of CW-MEC achieved 100%. The average NH4+-N mass removal rate was 436.02 mg m−2 d−1. It was found that NH4+ was mainly removed by the nitrification-autotrophic denitrification process in CW-MES while it was mainly converted to NO3− in CCW. Ammoxidation and denitrification were both enhanced by electricity while NH4+ was used as the main substrate for electricity generation. AOA (Candidatus Nitrosocosmicus) and NOB (Nitrospira) were the main contributors to nitrification. This study provided a cost-effective and sustainable method for electrochemically enhanced microbial NH4+ removal at low-temperature and revealed the relevant mechanism.

The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study

Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L−1) and increased at high salinities (10, 15, 20 and 30 g L−1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while 13C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L−1 salinity, respectively.

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures.

Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (−13–4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20–45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4–8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.)

A plant’s microbiota has various implications for the plant’s health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the ‘Soil Crenarchaeotic Group’ and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.

Root-associated archaea: investigating the niche occupied by ammonia oxidising archaea within the wheat root microbiome

Root associated microbiomes (RAMs) are complex communities which provide benefits to host plants via disease suppression, abiotic stress relief and increased nutrient bioavailability. Most RAM studies have focussed on bacteria and fungi, archaea have largely been overlooked as many studies fail to utilize archaea-specific 16S primers. However, there are reports of archaea being detected and isolated from the rhizosphere and endosphere of crop species, and one report of a plant-growth promoting (PGP) ammonia oxidising archaeon (AOA). Here, we aimed to assess the role of AOA within the wheat (Triticum aestivum) RAM. We applied archaea-specific primers and 16S amplicon sequencing to profile the archaeal community associated with wheat roots grown in agricultural soil. To assess PGP capacity we treated wheat seeds with a concentrated inoculum of model AOA Candidatus Nitrosocosmicus franklandus C13. In contrast to prior reports this had no impact on plant biomass, indicating N. franklandus may be a passive member of the wheat RAM. Stable isotope probing (SIP) experiments have confirmed that bacterial species metabolise Arabidopsis thaliana root exudates. Fractions are being examined to assess whether archaeal species can do the same, and a similar SIP experiment will be performed in wheat. An enrichment culture experiment using root exudates will also be applied to identify and isolate archaea capable of metabolising wheat root exudates. Here we show that AOA are present within the wheat RAM; to understand the niche occupied by these microbes we must further probe how they interact with host metabolites, and whether they contribute to host fitness.

Abundance, contribution, and possible driver of ammonia-oxidizing archaea (AOA) in various types of aquatic ecosystems

In some habitats, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA), which are therefore important for studying biogeochemical nitrogen cycling. However, the behavior and distribution of AOA in aquatic ecosystems are not well characterized, especially on a global scale. We sampled 66 sites across all five continents to analyze the global abundance of AOA. Ammonium oxidation rates were measured using the dicyandiamide (DCD) and octyne inhibition method to separately evaluate the contributions of AOA to ammonium oxidation. High-throughput pyrosequencing and phylogenetic analysis were applied to study AOA community compositions, combined with DNA-stable isotope probing (DNA-SIP). The archaeal amoA gene was widespread and abundant across all aquatic ecosystem types. The average abundance was 3.59 × 108 copies g−1, with the highest values in lake samples and the lowest in river samples. The AOA abundance was influenced by pH. Archaeal ammonia oxidation rates were 0.81 ± 0.45 mg (NO3−-N) kg−1 day−1, corresponding to 63.75% of the total ammonia oxidation rate. Pyrosequencing analysis showed that the AOA community was dominated by the Group I.1b lineage (65.8%). Candidatus Nitrosocosmicus franklandus showed the highest positive correlation with archaeal ammonium oxidation rates and had the highest carbon use efficiency. Abundance, activity, and community composition of AOA were highly heterogeneous. pH negatively impacted the abundance of the archaeal amoA functional gene. AOA were the main ammonia oxidators in aquatic ecosystems. Ca. N. franklandus was found to dominate archaeal ammonium oxidation.

Temporal heterogeneity and temperature response of active ammonia-oxidizing microorganisms in winter in full-scale wastewater treatment plants

Ammonia-oxidizing microorganisms (AOMs) play important roles in nitrogen removal, but their metabolic activity in winter months in wastewater treatment plants (WWTPs) remains unclear. Here, two full-scale WWTPs were selected, and a total of 48 DNA-based stable isotope probing (DNA-SIP) microcosms of activated sludge samples at different winter months (November-January) and temperatures (13 °C, 25 °C and 37 °C) were constructed to evaluate the temporal heterogeneity and temperature response of active AOMs. The results provided direct evidence that the temporal heterogeneity of AOMs’ activity was not obvious in winter months. In general, ammonia-oxidizing archaea (AOA) and bacteria (AOB) co-participated in the active ammonia oxidation in three winter months at in situ temperature (13 °C) in two WWTPs, and AOA were the dominant active AOMs, even though AOB outnumbered AOA in seed sludge. In contrast, higher peaks of AOA in “heavy” fractions at 25 °C and 37 °C also provided compelling evidence for the dominant contribution of AOA to active ammonia oxidation under higher temperatures. The Illumina sequencing of 13C-DNA obtained from the DNA-SIP microcosms at 13 °C in three winter months further suggest that Candidatus Nitrososphaera evergladensis and Candidatus Nitrosocosmicus exaquare were the dominant active AOA in two WWTPs, while the active AOB were dominated by Nitrosomonas oligotropha. At higher temperatures, active AOA shifted to Ca. N. evergladensis and Candidatus Nitrososphaera gargensis, and Nitrosomonas marina, Nitrosomonas europaea and Nitrosomonas communis dominated in the active AOB. Overall, AOA rather than AOB dominated the active ammonia oxidation in winter months and at higher temperatures in the full-scale WWTPs tested.