Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon

Nitrogen-cycling microbial communities respond differently to nitrogen addition under two contrasting grassland soil types

Introduction

The impact of nitrogen (N) deposition on the soil N-transforming process in grasslands necessitates further investigation into how N input influences the structural composition and diversity of soil N-cycling microbial communities across different grassland types.

Methods

In this study, we selected two types of grassland soils in northwest Liaoning, temperate steppe and warm-temperate shrub, and conducted short-term N addition experiments using organic N, ammonium N, and nitrate N as sources with three concentration gradients to simulate N deposition. Illumina MiSeq sequencing technology was employed to sequence genes associated with N-cycling microbes including N-fixing, ammonia-oxidizing and denitrifying bacteria, and ammonia-oxidizing archaea.

Results and discussion

The results revealed significant alterations in the structural composition and diversity of the N-cycling microbial community due to N addition, but the response of soil microorganisms varied inconsistent among different grassland types. Ammonium transformation rates had a greater impact on soils from temperate steppes while nitrification rates were more influential for soils from warm-temperate shrubs. Furthermore, the influence of the type of N source on soil N-cycling microorganisms outweighed that of its quantity applied. The ammonium type of nitrogen source is considered the most influential driving factor affecting changes in the structure of the microbial community involved in nitrogen transformation, while the amount of low nitrogen applied primarily determines the composition of soil bacterial communities engaged in nitrogen fixation and nitrification. Different groups of N-cycling microorganisms exhibited distinct responses to varying levels of nitrogen addition with a positive correlation observed between their composition, diversity, and environmental factors examined. Overall findings suggest that short-term nitrogen deposition may sustain dominant processes such as soil-N fixation within grasslands over an extended period without causing significant negative effects on northwestern Liaoning's grassland ecosystems within the next decade.

Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

The regulation effect of preventing soil nitrogen loss using microbial quorum sensing inhibitors

Preventing soil nitrogen (N) losses driven by microbial nitrification and denitrification contributes to improving global environmental concerns caused by NO3--N leaching and N2O emission. Quorum sensing (QS) signals regulate nitrification and denitrification of N-cycling bacteria in pure culture and water treatment systems, and mediate the composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in activated sludge. However, whether disrupting QS could prevent soil N losses remains unclear. This study explored the feasibility of applying quorum sensing inhibitors (QSIs) as an innovative strategy to reduce N losses from agricultural soils. The two QSIs, penicillic acid and 4-iodo-N-[(3S)-tetrahydro-2-oxo-3-furanyl]-benzeneacetamide (4-iodo PHL), were more effective in reducing N losses than traditional inhibitors, including N-(n-butyl) thiophosphoric triamide and 3,4-dimethylpyrazole phosphate. After 36 days of aerobic incubation, penicillic acid and 4-iodo PHL inhibited nitrification by 39% and 68%, respectively. The inhibitory effects are attributed to the fact that 4-iodo PHL decreased the abundance of archaeal and bacterial amoA genes, as well as the relative abundance of Candidatus Nitrocosmicus (AOA), Candidatus Nitrososphaera (AOA), and Nitrospira (nitrite-oxidizing bacteria/comammox), while penicillic acid reduced archaeal amoA abundance and the relative abundance of Nitrosospira (AOB) and the microbes listed above. Penicillic acid also strongly inhibited denitrification (33%) and N2O emissions (61%) at the peak of N2O production (day 4 of anaerobic incubation) via decreasing nitrate reductase gene (narG) abundance and increasing N2O reductase gene (nosZ) abundance, respectively. Furthermore, the environmental risks of QSIs to microbial community structure and network stability, CO2 emissions, and soil animals were acceptable. Overall, QSIs have application potential in agriculture to reduce soil N losses and the associated effect on climate change. This study established a new method to mitigate N losses from the perspective of QS, and can serve as important basis of decreasing the environmental risks of agricultural non-point source pollution.

Isolation of a Moderately Acidophilic Nitrobacter from a Nitrifying Community Supplied with Urea

Nitrite-oxidizing bacteria (NOB), which perform the second step of aerobic nitrification, play an important role in soil. In the present study, we report a novel isolate from agricultural soil affiliated with the genus Nitrobacter and its physiological characteristics. We sampled the surface soil of a vegetable field and obtained mixed culture A31 using the most probable number (MPN) method with inorganic medium containing 0.75‍ ‍mM urea (pH 5.5). The dilution-extinction procedure on culture A31 led to the isolation of a strain that was designated as Nitrobacter sp. A67. The nxrB1 gene sequence of Nitrobacter sp. A67 (302 bp) was classified into Cluster 5, and the highest sequence identity was 96.10% with Nitrobacter sp. BS5/19. The NO2- oxidation activity of Nitrobacter sp. A67 was investigated at various pH. The optimum pH for NO2- oxidation was 5.8-6.4. This result indicates that Nitrobacter sp. A67 is a moderately acidophilic nitrite-oxidizing bacterium.

Community pattern of potential phenanthrene (PHE) degrading bacteria in PHE contaminated soil revealed by 13C-DNA stable isotope probing

Quantification of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and identification of potential PAH degraders are essential for comprehending their environmental fate and conducting bioremediation. However, the microbial population responsible for the breakdown of phenanthrene (PHE) in polluted soil environments is frequently disregarded. In this study, via DNA-stable-isotope probing (DNA-SIP), we found that soil microbiota likely plays a crucial part in the PHE degradation. The PHE removal rates were 98% and 99%, in 13C-PHE and 12C-PHE microcosmic incubations, respectively. 13CO2 was produced along with the degradation of 13C-PHE. According to the analysis of 16S rRNA gene, there was a relatively higher presence of unidentified bacteria in the 'heavy' DNA fractions treated with 13C-PHE. Genus of Enterobacteriales, Acidobacteria, Alphaproteobacteria, Paenibacillaceae, Flavobacteriia, Chloroflexi, Cyanobacteria, Caldilineae, Latescibacteria, Armatimonadetes and Blastocatellia were succseesfully labeled during the degradation of 13C-PHE, indicating their capacity of utilizing PHE. Co-occurrence network of 13C-heavy fractions exhibited greater complexity compared with that of 12C-heavy fractions, revealling an enhancement of bacterial interspecies interactions. Collectivley, this study eluidated the soil microbes involed in the PHE degradation and offered fresh perspectives on the community pattern of potential PHE degrading bacteria.

Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites

The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.

Co-immobilization of AOA strains with anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions

Hydrogel encapsulation of ammonium oxidizing archaea (AOA) along with anammox bacteria holds potential to enable mainstream partial nitritation (PN)-anammox process attributing to AOA's high affinity to ammonia and oxygen. This study explored the growth of AOA and anammox in hydrogel-based synthetic biogranules by testing two AOA strains, three types of hydrogel beads and two substrate levels, to identify the optimal combination favoring the concomitant growth of AOA and anammox. The AOA Nitrososphaera viennensis (AOA-NV) exhibited higher abundance (10-2.3±0.6 AOA/16S) than the AOA-DW (10-4.7±0.8 AOA/16S) during the entire experimental period. Amongst the three types of hydrogel beads, the PVA-SA-BaCl2 (140 days) and PVA-SA-H3BO3 beads (>180 days) exhibited better long-term structural stability than the PEGDMA-SA-CaCl2 beads. The PVA-SA-H3BO3 beads exhibited the best long-term stability and both the PVA/SA BaCl2 and PVA-SA-H3BO3 beads had comparable ability to retain AOA, anammox and the overall microbial community. Substrate conditions rather than the bead type primarily controlled the microbial community structure. Modest substrate concentrations (1 mM NH4+-N in the feed and 0.8 mg/L dissolved oxygen (DO) in the reactor during aeration phase) followed by low substrate conditions (0.1 mM NH4+-N and 0.2 mg DO/L) both supported the growth of AOA and anammox, while the low substrate condition also suppressed the growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), with AOA /AOB and anammox/NOB ratio of 0.7 and 0.4 at moderate substrate condition and 16.5 and 2.6 at low substrate condition.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0-6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3--N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3--N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3--N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions

Background

Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification.

Materials and Methods

A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively.

Results and discussions

Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH₃ concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH₄ ⁺ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA.

Conclusions

PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH₄ ⁺, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.

Distinct Patterns of Rhizosphere Microbiota Associated With Rice Genotypes Differing in Aluminum Tolerance in an Acid Sulfate Soil

Rhizosphere microbes are important for plant tolerance to various soil stresses. Rice is the most aluminum (Al)-tolerant small grain cereal crop species, but the link between rice Al tolerance and rhizosphere microbiota remains unclear. This study aimed to investigate the microbial community structure of aluminum-sensitive and Al-tolerant rice varieties in acid sulfate soil under liming and non-liming conditions. We analyzed the rice biomass and mineral element contents of rice plants as well as the chemical properties and microbial (archaea, bacteria, and fungi) communities of rhizosphere and bulk soil samples. The results showed that the Al-tolerant rice genotype grew better and was able to take up more phosphorus from the acid sulfate soil than the Al-sensitive genotype. Liming was the main factor altering the microbial diversity and community structure, followed by rhizosphere effects. In the absence of liming effects, the rice genotypes shifted the community structure of bacteria and fungi, which accounted for the observed variation in the rice biomass. The Al-tolerant rice genotype recruited specific bacterial and fungal taxa (Bacillus, Pseudomonas, Aspergillus, and Rhizopus) associated with phosphorus solubilization and plant growth promotion. The soil microbial co-occurrence network of the Al-tolerant rice genotype was more complex than that of the Al-sensitive rice genotype. In conclusion, the bacterial and fungal community in the rhizosphere has genotype-dependent effects on rice Al tolerance. Aluminum-tolerant rice genotypes recruit specific microbial taxa, especially phosphorus-solubilizing microorganisms, and are associated with complex microbial co-occurrence networks, which may enhance rice growth in acid sulfate soil.

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.

Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils

Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using ¹³CO₂-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The ¹³C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary

The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO₃^–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO₃^–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO₃^–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing

Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.

Impact of Cover Crops on the Soil Microbiome of Tree Crops

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems.

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: Ecology, physiology, biochemistry and why they must all come together

Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.

Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing

Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO₃) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm

This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.

Insight into the short-term effect of titanium dioxide nanoparticles on active ammonia oxidizing microorganisms in a full-scale wastewater treatment plant: a DNA-stable isotope probing study

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two distinct ammonia-oxidizing microorganisms (AOMs) responsible for nitrification in wastewater treatment plants (WWTPs).

Effects of atmospheric deposition nitrogen flux and its composition on soil solution chemistry from a red soil farmland, southeast China

A detailed study on the solution chemistry of red soil in South China is presented. Data are collected from two simulated column-leaching experiments with an improved setup to evaluate the effects of atmospheric N deposition (ADN) composition and ADN flux on agricultural soil acidification using a (15)N tracer technique and an in situ soil solution sampler. The results show that solution pH values decline regardless of the increase of the NH4(+)/NO3(-) ratio in the ADN composition or ADN flux, while exchangeable Al(3+), Ca(2+), Mg(2+), and K(+) concentrations increase at different soil depths (20, 40, and 60 cm). Compared with the control, ADN (60 kg per ha per year N, NH4(+)/NO3(-) ratio of 2 : 1) decreases solution pH values, increases solution concentrations of NO3(-)-N, Al(3+), Ca(2+) and Mg(2+) at the middle and lower soil depths, and promotes their removal. NH4(+)-N was not detected in red soil solutions of all the three soil layers, which might be attributed to effects of nitrification, absorption and fixation in farmland red soil. Some of the NO3(-)-N concentrations at 40-60 cm soil depth exceed the safe drinking level of 10 mg L(-1), especially when the ADN flux is beyond 60 kg ha(-1) N. These features are critical for understanding the ADN agro-ecological effects, and for future assessment of ecological critical loads of ADN in red soil farmlands.

Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients

Stable isotope probing (SIP) of rRNA directly identifies microorganisms assimilating an isotopically labelled substrate. High-throughput DNA sequencing is available for label screening at high resolution and high sensitivity, yet its effectiveness and validity remain to be clarified. Here, we investigated whether the detection sensitivity of rRNA-SIP could be improved by using Illumina sequencing in place of terminal restriction fragment length polymorphism (T-RFLP) analysis. A dilution series of (13) C-labelled RNA from Escherichia coli (1-0.0001%) and unlabelled RNA from Bacillus subtilis was density separated and fractionated. Illumina sequencing of isopycnic centrifugation gradients was able to detect (13) C-labelled RNA in the heaviest fraction with a buoyant density of 1.798 g ml(-1) even at the mixing ratio of 0.001%, whereas the detection ability of T-RFLP was not lower than 0.5%. Quantitative reverse transcription polymerase chain reaction of the density-separated RNAs showed that (13) C-labelled RNAs at mixing ratios of 0.05-0.001% had definitely accumulated in the heaviest fraction. Consequently, high-throughput sequencing provided up to 500-fold higher sensitivity for screening of (13) C-labelled RNA than T-RFLP. Ultra-high-sensitivity rRNA-SIP represents a clear advance towards a more complete understanding of microbial ecosystem function, including the ecophysiology of rare microorganisms in various natural environments.

Variability of the transporter gene complement in ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are a widespread and abundant component of microbial communities in many different ecosystems. The extent of physiological differences between individual AOA is, however, unknown. Here, we compare the transporter gene complements of six AOA, from four different environments and two major clades, to assess their potential for substrate uptake and efflux. Each of the corresponding AOA genomes encode a unique set of transporters and although the composition of AOA transporter complements follows a phylogenetic pattern, few transporter families are conserved in all investigated genomes. A comparison of ammonia transporters encoded by archaeal and bacterial ammonia oxidizers highlights the variance among AOA lineages as well as their distinction from the ammonia-oxidizing bacteria, and suggests differential ecological adaptations.