Nutrient leaching potential along a time series of forest water reclamation facilities in northern Idaho.

Forest water reclamation is a decades-old practice of repurposing municipal reclaimed water using land application on forests to filter nutrients and increase wood production. However, long-term application may lead to nutrient saturation, leaching, and potential impairment of ground and surface water quality. We studied long-term effects of reclaimed water application on nutrient leaching potential in a four-decade time series of forest water reclamation facilities in northern Idaho. Our approach compared reclaimed water treated plots with untreated control plots at each of the forest water reclamation facilities. We measured soil nitrifier abundance and net nitrification rates and used tension lysimeters to sample soil matrix water and drain gauges to sample from a combination of matrix and preferential flow paths. We determined nutrient leaching as the product of soil water nutrient concentrations and model-estimated drainage flux. There was more than 450-fold increase in nitrifier abundance and a 1000-fold increase in net nitrification rates in treated plots compared with control plots at long-established facilities, indicating greater nitrate production with increased cumulative inputs. There were no differences in soil water ammonium, phosphate, and dissolved organic nitrogen concentrations between control and effluent treatments in tension lysimeter samples. However, concurrent with increased nitrifier abundance and net nitrification, nitrate concentration below the rooting zone was 2 to 4-fold higher and nitrate leaching was 4 to 10-fold higher in effluent treated plots, particularly at facilities that have been in operation for over two decades. Thus, net nitrification and nitrifier abundance assays are likely indicators of nitrate leaching potential. Inorganic nutrient concentrations in drain gauge samples were 2 to 11-fold higher than lysimeter samples, suggesting nutrient losses occurred predominantly through preferential flow paths. Nitrate was vulnerable to leaching during the wet season under saturated flow conditions. Although nitrogen saturation is a concern that should be mitigated at long-established facilities, these forest water reclamation facilities were able to maintain average soil water nitrate concentrations to less than 2 mg L-1, so that nitrogen and phosphorous are effectively filtered to below safe water standards.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil.

AIMS: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. METHODS AND RESULTS: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. CONCLUSIONS: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.

DLTN-LOSP: A Novel Deep-Linear-Transition-Network-Based Resource Allocation Model with the Logic Overhead Security Protocol for Cloud Systems.

Cloud organizations now face a challenge in managing the enormous volume of data and various resources in the cloud due to the rapid growth of the virtualized environment with many service users, ranging from small business owners to large corporations. The performance of cloud computing may suffer from ineffective resource management. As a result, resources must be distributed fairly among various stakeholders without sacrificing the organization's profitability or the satisfaction of its customers. A customer's request cannot be put on hold indefinitely just because the necessary resources are not available on the board. Therefore, a novel cloud resource allocation model incorporating security management is developed in this paper. Here, the Deep Linear Transition Network (DLTN) mechanism is developed for effectively allocating resources to cloud systems. Then, an Adaptive Mongoose Optimization Algorithm (AMOA) is deployed to compute the beamforming solution for reward prediction, which supports the process of resource allocation. Moreover, the Logic Overhead Security Protocol (LOSP) is implemented to ensure secured resource management in the cloud system, where Burrows-Abadi-Needham (BAN) logic is used to predict the agreement logic. During the results analysis, the performance of the proposed DLTN-LOSP model is validated and compared using different metrics such as makespan, processing time, and utilization rate. For system validation and testing, 100 to 500 resources are used in this study, and the results achieved a make-up of 2.3% and a utilization rate of 13 percent. Moreover, the obtained results confirm the superiority of the proposed framework, with better performance outcomes.

Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories.

Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.

Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan.

A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25T and N. ureiphilus PS0T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25T (=NBRC 111181T=ATCC TSD-147T).

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.

Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.

Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring.

Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2-10 and 0.2-2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW). The gene copy numbers of AOA-amoA were higher than those of AOB-amoA in ECS. The relative abundance of amoA to the total 16S rRNA gene level reached approximately 15% in KBW and CKBW for the free-living fraction of AOA, whereas the level was less than 0.01% throughout ECS for the AOB. A cluster analysis of the AOA-amoA-DGGE band pattern showed distinct genotype compositions in CSW in both the size fractions and in the surface of the TCSKB and KBW. Sequences of the DGGE bands were assigned to two clades. One of the clades exclusively consisted of sequences derived from the 2-10-µm fraction. This study revealed that AOA-amoA abundance dominated over AOB-amoA throughout the ECS, whereas the genotype composition of AOA-amoA were distributed heterogeneously across the water masses. Additionally, this is the first report showing the distribution of AOA-amoA genotypes characteristic to particle-associated AOA in the offshore of the East China Sea.

Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes.

Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Although a large part of the soil samples were found to be amoA-negative, bacterial amoA genes were detectable with new as well as old primer sets. The same results were obtained for the archaeal amoA genes. The relative distribution of archaeal and bacterial amoA genes varied between Andosol classes. Archaeal amoA genes were significantly more abundant in Brown than in Histic Andosols, while the opposite was observed for bacterial amoA genes. The numbers of archaeal and bacterial amoA genes in Gleyic Andosols were not significantly different from those in Histic and Brown Andosols. The numbers of bacterial amoA genes, but not the numbers of archaeal amoA genes, correlated significantly and positively with potential ammonia oxidation activities. The presence of the bacterial nitrification inhibitor allylthiourea inhibited the potential ammonia oxidation activities during the first 12 h of incubation. Hence, it was concluded that ammonia-oxidizing bacteria profited most from the conditions during the measurements of potential ammonia oxidation activities.

Diversity and community structure of ammonia oxidizers in a marsh wetland of the northeast China.

As an interface of terrestrial and aquatic ecosystems, wetland is a hotspot of the global nitrogen cycle. Ammonia oxidation is an essential part of the nitrogen cycle and is conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Based on the amoA gene, the distribution and genetic diversity of AOA and AOB in the marsh wetland soil with different soil layers and vegetation had been investigated. The result showed that both soil layer and vegetation significantly influenced the diversity and abundance of AOA and AOB. AOB dominated numerically in all soil samples. The average bacterial amoA gene copies (2.62 × 109 copies/g dry soil) was 100-fold higher than the average archaeal amoA gene copies. In the soil sample under the Phragmites australis, the highest archaeal amoA gene was in depth 20-40 cm, whereas the bacterial amoA gene was more abundant in depth 0-20 cm. For the soil under Calamagrostis angustifolia, the highest archaeal and bacterial amoA gene were both detected in depth 0-20 cm. The dominated AOA was cluster AII, which was most related to the amoA gene found in aquatic habitat. Cluster BI accounted for 59.1% of bacterial amoA gene and it was related to the amoA gene found in the terrestrial habitat. CCA analysis revealed that NO3- was the main factor for AOA and AOB community structure in the P. australis soil. However, NO2- and NH4+ were important factors for AOA and AOB in the soil under C. angustifolia.

Temporal and spatial distribution of ammonia-oxidizing organisms of two types of wetlands in Northeast China.

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contribute significantly to the nitrogen cycle. The community structure of AOA and AOB is diverse in the different wetlands. Few studies have comparatively investigated the community structure and dynamics of ammonia-oxidizing organisms in the marsh wetland (Sanjiang wetland) and inland saline-alkaline wetland (Zhalong wetland) in Northeast China. In this study, soil samples were collected from two wetlands with different soil properties in July and October. The community structure of AOA and AOB based on the amoA gene was investigated by high throughput sequencing. The result showed that AOA affiliated to the Nitrososphaera lineage (1.1b group) were the dominant AOA in both Sanjiang and Zhalong wetlands, while AOB belonging to the Nitrosospira lineage was the dominant AOB in the Sanjiang wetland. AOB belonging to the Nitrosospira lineage and Nitrosomonas lineage were the dominant AOB in the Zhalong wetland in July and October, respectively. The dominant AOA and AOB in the Sanjiang wetland had no obvious variation from July to October, but the AOA and AOB communities in the Zhalong wetland changed a lot from July to October. Shannon and Simpson indexes showed the diversity of AOA in the Zhalong wetland was higher than that in the Sanjiang wetland, but the diversity of AOB in the Zhalong wetland was lower than that in the Sanjiang wetland. Nitrate (NO3-) and ammonium (NH4+) concentration and pH were the most significant factors influencing the community structure of AOA and AOB.

Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils.

Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 108 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 108 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.

Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence.

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.

Effects of the herbicide mesotrione on soil enzyme activity and microbial communities.

Mesotrione (2-[4-(methylsulfonyl)-2-nithobenzoyl]-1, 3-cyclohexanedione) is a selective triketone herbicide that has been widely used in corn production for the past 15 years. However, its potential for risk to soil ecosystems is poorly documented. The present study investigated the soil enzyme activity and soil microbial community responses to a 20 days' mesotrione exposure at doses of 0.1, 1.0 and 5.0 mg/kg. On days 2, 5, 10 and 20, activities of soil ß-glucosidase, urease and acid phosphatase, soil microbe abundances, soil microbial community structure and abundance of the AOA-amoA and AOB-amoA genes were measured. Results showed that activities of urease and acid phosphatase were relatively stable, with no difference found between the mesotrione-treated group and control at the end of exposure. But ß-glucosidase activity was reduced in the 5.0 mg/kg mesotrione treatment. In the 1.0 and 5.0 mg/kg mesotrione-treated soil, abundance of bacteria, fungi and actinomycetes all were reduced. In the 0.1 mg/kg mesotrione-treated soil, only fungi abundance was reduced by the end of the exposure. The analysis of terminal restriction fragment length polymorphism (T-RFLP) revealed soil microbial community structure could be affected by mesotrione at all experimental doses, and microbial diversity declined slightly after mesotrione exposure. Abundance of AOA-amoA and AOB-amoA genes were reduced markedly in 1.0 and 5.0 mg/kg mesotrione-treated soil. The present study suggests that mesotrione at higher doses might induce negative impacts on soil microbes, a finding which merits additional research and which should be accounted for when application of this herbicide is considered.

Abundance of ammonia-oxidizing bacteria and archaea under different ventilation strategies during cattle manure composting.

Composting of cattle manure was conducted under four ventilation strategies, i.e., no-aeration (A-00), continuous aeration (B-44), non-aeration for 14 d and then aeration for 42 d (C-04), aeration for 14 d and then no-aeration for 42 d (D-40). Physicochemical parameters and potential ammonia oxidation (PAO) indicated that continuous and intermittent ventilation provide favourable conditions for ammonia-oxidizing bacteria (AOB) and archaea (AOA) to oxidize ammonia. Quantitative PCR (qPCR) analysis showed AOB amoA gene abundance of all treatments on every sampling day ranged from 2.25 × 105 to 2.76 × 109copies/g, was significantly lower than that of archaeal amoA gene from 2.71 × 108 to 9.05 × 1011copies/g. There was also a significantly positive relationship between PAO rates and AOB (r2 ≥ 0.066, p < 0.05) and AOA (r2 ≥ 0.300, p < 0.05) abundance. These data suggested that ammonia oxidation is driven by both AOA and AOB in cattle manure composting.

Impact of Heavy Metal Pollution on Ammonia Oxidizers in Soils in the Vicinity of a Tailings Dam, Baotou, China.

Soil heavy metal pollution has received increasing attention due to their toxicity to soil microorganisms. We have analyzed the effects of heavy metal pollution on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soils in the vicinity of a tailings dam of Baotou region, China. Results showed that AOB were dominated with Nitrosomonas-like clusters, while AOA was dominated by group1.1b (Nitrososphaera cluster). Single Cd and Cr contents, as well as compound heavy metal pollution levels, had a significant negative impact on soil potential nitrification rate and both diversities of AOA and AOB. No clear relationship was found between any single heavy metal and abundance of AOA or AOB. But compound pollution could significantly decrease AOA abundance. The results indicated that heavy metal pollution had an obviously deleterious effect on the abundance, diversity, activity and composition of ammonia oxidizers in natural soils.

Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil.

The increasing production and use of engineered silver nanoparticles (AgNP) in industry and private households are leading to increased concentrations of AgNP in the environment. An ecological risk assessment of AgNP is needed, but it requires understanding the long term effects of environmentally relevant concentrations of AgNP on the soil microbiome. Hence, the aim of this study was to reveal the long-term effects of AgNP on soil microorganisms. The study was conducted as a laboratory incubation experiment over a period of one year using a loamy soil and AgNP concentrations ranging from 0.01 to 1 mg AgNP/kg soil. The short term effects of AgNP were, in general, limited. However, after one year of exposure to 0.01 mg AgNP/kg, there were significant negative effects on soil microbial biomass (quantified by extractable DNA; p = 0.000) and bacterial ammonia oxidizers (quantified by amoA gene copy numbers; p = 0.009). Furthermore, the tested AgNP concentrations significantly decreased the soil microbial biomass, the leucine aminopeptidase activity (quantified by substrate turnover; p = 0.014), and the abundance of nitrogen fixing microorganisms (quantified by nifH gene copy numbers; p = 0.001). The results of the positive control with AgNO3 revealed predominantly stronger effects due to Ag+ ion release. Thus, the increasing toxicity of AgNP during the test period may reflect the long-term release of Ag+ ions. Nevertheless, even very low concentrations of AgNP caused disadvantages for the microbial soil community, especially for nitrogen cycling, and our results confirmed the risks of releasing AgNP into the environment.

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient.

Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of ammonia oxidizing archaea (AOA) and bacteria (AOB) in soil N cycling and availability by using a highly constrained natural mean annual temperature (MAT) elevation gradient in a tropical montane wet forest. We found that net nitrate (NO3- ) bioavailability is positively related to MAT (r2  = 0.79, P = 0.0033), and AOA DNA abundance is positively related to both NO3- availability (r2  = 0.34, P = 0.0071) and MAT (r2  = 0.34, P < 0.001). In contrast, AOB DNA was only detected in some soils across the gradient. We identified three distinct phylotypes within the AOA which differed from one another in abundance and relative gene expression. In addition, one AOA phylotype increased in abundance with MAT, while others did not. We conclude that MAT is the primary driver of ecosystem N availability across this gradient, and AOA population size and structure appear to mediate the relationship between the nitrification and N bioavailability. These findings hold important implications for nutrient limitation in forests and feedbacks to primary production under changing climate.