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Purpose: Nitrogen (N) and phosphorus (P) amendments considerably influence fungal diversity and community composition in various ecosystems. Nevertheless, how N and P additions would change arbuscular mycorrhizal (AM) fungal community and functional guilds in forest soil remains largely unclear. Materials and methods: A 5-year N and P addition experiment was conducted in a subtropical forest of southeastern China. Soil AM fungal communities were detected by the high throughput sequencing of 18S rRNA gene-fragments. We investigated the six-seasonal responses of AM fungal diversity, community assembly pattern and functional guild composition to N and/or P amendments. Results and discussion: The AM fungal Shannon index changed from a positive (3–4 years) to a nonsignificant (4–5 years) effect under P and NP additions as the duration of fertilization increased. P addition, but not N addition, changed the AM fungal community assembly pattern from stochastic- to deterministic-dominant processes. In contrast, P and NP additions significantly influenced AM fungal functional guild components, and the relative abundances of ancestral and edaphophilic guilds increased with increasing years of fertilization. Additionally, the AM fungal guild structure was significantly affected by soil P-related parameters. Conclusions: Our results emphasize the substantial impacts of P amendment on soil AM community assembly pattern and functional guild composition. This study contributes to a better understanding of the temporal dynamics and potential ecological functioning of AM fungi under global environmental changes. [ABSTRACT FROM AUTHOR]

Purpose: The compounds 1-octyne and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) are frequently used as nitrification inhibitors for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively, but their influence on comammox Nitrospira remains unclear. In this study, we examine how will 1-octyne and PTIO influence AOA, AOB, and comammox Nitrospira in an acidic Ultisol. The results will provide guidance for the nitrification inhibitor selections in the relevant research and field management practices. Materials and methods: We carried out a microcosm experiment using acetylene, 1-octyne, and PTIO as nitrification inhibitors to investigate their effects on ammonia oxidizers, especially comammox Nitrospira. The abundance of ammonia oxidizers was determined by real-time quantitative PCR while the community structure of comammox Nitrospira was examined by Illumina MiSeq sequencing. Results and discussion: Acetylene, 1-octyne, and PTIO significantly reduced the net nitrification rate, with a more pronounced effect observed for acetylene and 1-octyne amendments. The addition of 1-octyne suppressed the growth of comammox Nitrospira clade A, indicating that 1-octyne was not an exclusive inhibitor for AOB in the acidic Ultisols. Moreover, PTIO reduced the abundance of AOB and comammox Nitrospira clade A, rather than that of AOA, suggesting that AOB and comammox Nitrospira were more sensitive than AOA to the PTIO inhibition in the tested soils. Acetylene, 1-octyne, and PTIO did not show observed changes to comammox Nitrospira community structure. Conclusions: We provide novel evidence that 1-octyne and PTIO can significantly inhibit the growth of comammox Nitrospira, but have no significant effects on their community structure in the acidic Ultisols. Our findings have implications for proper selection of nitrification inhibitors 1-octyne and PTIO in both laboratory experiments and field practices. [ABSTRACT FROM AUTHOR]

Purpose: Temperature is a key factor influencing the growth and activities of microorganisms and their associated biogeochemical processes including nitrification. However, limited studies have been performed to evaluate the response of the newly discovered comammox Nitrospira to temperature change and nitrogen (N) addition in agroecosystems, which has hindered our understanding of the ecophysiology and environmental adaption of comammox Nitrospira in agroecosystems. Materials and methods: We set up a microcosm experiment with 3 temperature treatments (15 °C, 25 °C, and 35 °C) × 3 levels of N addition (0 mg kg−1, 25 mg kg−1, and 50 mg kg−1) in an acidic Ultisol. We explored the impact of temperature and N addition on the abundance and community structure of comammox Nitrospira. Results and discussion: The addition of N and increasing temperature generally increased the net nitrification rate. The comammox Nitrospira clade A abundance decreased with the increase of temperature, indicating that clade A might favor environments with relatively lower temperature. However, the addition of N did not significantly influence the abundance of comammox Nitrospira clade A. Moreover, temperature had a stronger effect than N addition on the community structure of comammox Nitrospira. Clade A.2.1 were the exclusively dominant comammox Nitrospira phylotype in the tested soils, and were not affected by temperature and N addition, suggesting that temperature influenced comammox Nitrospira mainly through regulating the internal subclades of clade A.2.1. Conclusions: Our findings provide novel evidence that temperature had a stronger effect than N addition on the abundance and community structure of comammox Nitrospira and suggest that comammox Nitrospira are temperature sensitive and favor relatively lower temperature in the acidic Ultisols. [ABSTRACT FROM AUTHOR]

Purpose: Protists play important roles in soils by regulating organic matter decomposition, catalysing biogeochemical nutrient cycling processes and maintaining soil fertility and plant productivity, but they remain poorly characterized in the plant-soil system under long-term intensive agricultural management. Methods: We investigated the impacts of multiple inorganic fertilization regimes on the diversity, composition and potential functions of protists and their interactions with bacteria and fungi in the rhizosphere and bulk soils of sorghum plants in a long-term field experiment. Results: Protists were dominated by the supergroups Rhizaria, Stramenopiles, Alveolata, Amoebozoa and Archaeplastida in both rhizosphere and bulk soils. The diversity of protists was significantly lower in rhizosphere than bulk soils, and the community compositions of total protists were remarkably different in the two compartments. Inorganic fertilization had no significant impacts on the total protistan diversity or compositions but significantly changed the relative abundances of specific taxa of consumers and parasites. Protists were significantly correlated with bacteria and fungi as revealed by the co-occurrence network analysis, indicating their intensive trophic interactions with bacteria and fungi in soil food webs. Soil properties and the community compositions of bacteria and fungi were important factors shaping the variation in the protistan communities, as revealed by variation partitioning modelling analysis. Conclusion: Altogether, we provide new information for the impacts of fertilization on the protist communities in rhizosphere and bulk soils and identified specific functional groups of protists that are most responsive to long-term agricultural management. [ABSTRACT FROM AUTHOR]

Purpose: Intensified livestock system produced large amount of bio-waste, and improper disposal of livestock manure has led to severe environmental consequences. However, knowledge about the time-dependent changes of manure-derived nitrate and soil bacterial diversity along the soil profiles is limited. Materials and methods: Vertical variation of soil bacterial diversity and composition in a manure-amended maize field and adjacent non-manured woodland was investigated using high-throughput sequencing technique in spring and autumn along a 1-m profile depth. The soil is classified as aquic inceptisol with a bulk density of 1.31 g cm−3, and a sandy loam texture. Results: The results showed that significant higher amount of nitrate (up to 172.13 mg kg−1) was detected along the soil profile loaded with cattle manure compared with the adjacent non-manured woodland. Soil δ15N-NO3− composition from maize field fall between + 5 and 25‰, while those from woodland fall between − 5 and 15‰. No significant difference in bacterial richness between the two land uses was found, while clear separation of bacterial structure was detected even to the deep soil layers. Canonical correspondence analysis showed that soil organic matter, C/N ratio, nitrate content, pH, and moisture were the major factors influencing the variance of bacterial community composition. Bacterial networks in the maize field harbor more modules than those in the adjacent woodland. Negative standardized effect size measure of mean nearest taxon distance in the soils tended to be more phylogenetically clustered than expected by chance, and was more likely to be clustered along the depth. Conclusions: These findings suggested that soil bacterial β diversity was strongly affected by multi-nutrient properties in terms of high livestock manure load, and had important implications for assessing the environmental impacts on belowground biodiversity in sandy loam soils. [ABSTRACT FROM AUTHOR]

Purpose: Urease inhibitors (UIs) such as N-(n-butyl)thiophosphoric triamide (NBPT) and nitrification inhibitors (NIs) such as 3,4-dimethylpyrazole phosphate (DMPP) have been reported to improve the efficiency of nitrogen (N) fertilizers. However, their effects on the ureolytic and ammonia-oxidizing microbes in agricultural soils are uncertain. This study aimed to investigate the effects of DMPP and NBPT on the abundance and community composition of ureolytic and nitrifying microbes in selected agricultural soils in Australia. Materials and methods: Soil was collected from five agricultural farms and used to establish an incubation experiment. Urea, urea + NBPT, urea + DMPP, and urea + NBPT + DMPP were applied on the soils which were incubated under 25 °C and 60% water-filled pore space for 28 days. Sampling was done on different days for DNA extraction and measurement of ammonium (NH4+) and nitrate (NO3−) concentration. Results and discussion: NBPT inhibited NH4+ accumulation in all the soils but had no significant effect on nitrification in any soil. DMPP alone or DMPP + NBPT significantly inhibited nitrification. The abundances of ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox Nitrospira), but not ammonia-oxidizing archaea (AOA), were significantly influenced by the application of NBPT, DMPP, or DMPP + NBPT. AOA, AOB, and comammox Nitrospira clade B might be significant contributors to nitrification in the studied soils. Conclusions: These findings suggest that NBPT and DMPP can reduce N losses and improve N fertilizer efficiency by directly inhibiting the growth of AOB and comammox organisms in the soils, with implications for our mechanistic understanding of the molecular mechanisms of urease and nitrification inhibitors. [ABSTRACT FROM AUTHOR]

Purpose: The recently discovered complete ammonia oxidizers (comammox Nitrospira) challenged our concept of the whole nitrification process, i.e., ammonia oxidation catalyzed by autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB), followed by the oxidation of nitrite to nitrate. However, the relative contributions of different ammonia oxidizers to soil nitrification are poorly understood. Materials and methods: Soil samples were collected from five land use types (i.e., cropland, grassland, bushland, transition land, and forest land) from a subtropical soil in Yunnan Province, Southwest China. The quantitative distribution of comammox Nitrospira, AOA and AOB in soils was firstly investigated using the QPCR approach and three of which (cropland, transition land and forest land) with pH below 6 were further examined using DNA stable isotope probing approach with 13CO2. Clone library combined with sequencing was applied to detect the phylogenetic information of active microbial groups. Results and discussion: The results showed that the amoA gene abundance of ammonia oxidizers except AOB was significantly lower in croplands than other land uses. Based on the 13CO2 labeling method, AOA, rather than AOB or comammox Nitrospira, was found to incorporate 13CO2 into their genomes during the incubation in cropland and transition land but not in forest land, suggesting the dominant role of AOA in ammonia oxidation. Phylogenetic analysis of the active AOA group revealed that autotrophic AOA community was mainly affiliated with the cluster of Nitrososphaera in transition land, whereas Nitrososphaera, Nitrosopumilus, and Nitrosotalea in cropland. Conclusions: These findings suggested niche differentiation of AOB, AOA, and comammox Nitrospira in the subtropical acid soil with different land uses, and AOA played a more important role in nitrification process of this acid soil. [ABSTRACT FROM AUTHOR]

Purpose: The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems. Materials and methods: We evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils. Results and discussion: The amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils. Conclusions: We provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils. [ABSTRACT FROM AUTHOR]

Purpose: Viruses are the most abundant biological entities and play significant biological roles in marine system. However, little is known about their biodiversity in mud volcanic soil, which is salty and covered with emitting sludge. In this study, we report metagenomic analysis results of viral community composition and function from the Dushanzi mud volcanic soil (named NHS) in Xinjiang, China, and provide a comparative analysis with other environmental types.Materials and methods: We utilized metagenomes to obtain the virus data and carried out viral automatic phylogenetic and functional analyses by the metagenomics analysis server. After assembling by metaSPAdes, scaffolds were rapidly identified and annotated with the PHAge Search Tool in order to identify new phage genomes.Results and discussion: For the ssDNA viral group, Microviridae were the most abundant viral family, which were above 95%. Other plant viruses (Geminiviridae, Nanoviridae) and animal viruses (Circoviridae, Parvoviridae) were also detected. The majority of viral significant hits belonged to Siphoviridae (80.36%). Phages, which infect bacteria, were widely distributed in the soil sample. There were eight novel viral genomes identified in the NHS virome. The two longest scaffolds were annotated to Pseudomonas aeruginosa phage YMC11 and Acinetobacter baumannii phage LZ35, respectively. Other six new viral genomes were identified as Microviridae. Comparisons of NHS virome with other published viromes revealed that the type of ecosystem mainly drove the viral community structure.Conclusions: This work provided detailed viral community composition and function information, which supplemented microbial community research on mud volcanoes. Importantly, we also identified eight complete viral genomes in the NHS virome which were obviously different from known viruses. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.Materials and methods: Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson's correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.Results and discussion: Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.Conclusions: In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils. [ABSTRACT FROM AUTHOR]

Purpose: Changes of nitrogen (N) cycle caused by N fertilization and precipitation regimes have affected the key ecosystem structure and functions in temperate steppe, which may modify the structure of soil microbial communities involved in N transformation. This paper was designated to examine the response of soil ammonia oxidizers and denitrifiers to the N fertilization and precipitation regimes in a semi-arid steppe where N and water contents are major limiting factors of the grassland productivity.Materials and methods: This study was based on a long-term N fertilization and precipitation regimes experiment in Inner Mongolia (116° 17′ 20″ E, 42° 2′ 29″ N). The treatments including CK (control), R (reduced precipitation), W (30% increase in precipitation), N (10 g N m−2 y−1), RN (reduced precipitation and 10 g N m−2 y−1), and WN (30% increase in precipitation and 10 g N m−2 y−1). Soil basic chemical properties and microbial activities were analyzed. Molecular methods were applied to determine the abundance, structure and diversity of ammonia oxidizers and denitrifiers. Statistical analysis detected the main and interactive effect of treatments on soil microbial communities and revealed the relationship between soil microbial community structures and environmental factors.Results and discussion: N fertilization significantly increased ammonia-oxidizing bacteria (AOB) abundance. Ammonia-oxidizing archaea (AOA) community structure was markedly changed in N fertilizer treatment and strongly affected by soil pH, while soil nitrate and water content correlated with AOB community structure. Soil nitrate was the key factor influencing nirK gene community structure, while soil pH and water content explained much of the variations of nosZ gene community. AOB-amoA and nosZ gene community diversities were influenced by precipitation regimes and interaction of N fertilization and precipitation regimes, respectively.Conclusions: N fertilization and precipitation regimes had significant influences on the changes of soil properties and microbial functional communities. Soil nitrification was mainly driven by AOB in the semi-arid grassland. Changes of substrate content and soil pH were the key factors in shifting functional microbial communities. The non-synergistic effects of N fertilization and precipitation regimes on the microbial functional groups indicated that the negative effect of lower pH induced by N fertilization would be alleviated by precipitation regimes, which should be well considered in grassland restoration. [ABSTRACT FROM AUTHOR]

Purpose: Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems. Materials and methods: This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH. Results and discussion: Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons. Conclusions: The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability. [ABSTRACT FROM AUTHOR]

Purpose: Nitrous oxide (NO) is a trace gas and is mainly produced through the microbial-mediated nitrification and denitrification processes in agricultural soils. Dicyandiamide (DCD) is a powerful nitrification inhibitor (NI) which can mitigate NO production from soil. However, it remains poorly understood how NO emission and associated microbes are affected by DCD application across different agricultural soils. Materials and methods: Here, we carried out a 21-day laboratory microcosm incubation experiment to examine the impact of ammonium sulfate and DCD applications on NO production and the abundance of nitrifiers and denitrifiers in two contrasting agricultural soils. The abundance of the functional genes was quantified by quantitative PCR to investigate the population changes in response to ammonium sulfate and DCD addition. Results and discussion: Higher NO production emitted followed the application of ammonium sulfate (287.9 ng NO-N g soil) in the alluvial soil was obtained compared to that (84.9 ng NO-N g soil) in the red soil. The average NO emission rate in the NH treatment from the alluvial soil was significantly higher than that from the red soil, and DCD addition remarkably reduced NO emission rates in both soils during the 21-day incubation. We also observed that the abundance of ammonia-oxidizing bacteria (AOB) amoA gene and the nirK gene was positively correlated with total NO emissions in the alluvial soil, but only AOB amoA gene abundance was significantly related to the total NO emissions in the red soil. Conclusions: These results suggested that DCD was more effective in inhibiting NO production in the alluvial soil than in the red soil. DCD could effectively reduce NO emission by suppressing the growth of microorganisms containing AOB amoA gene and the nirK gene in the alluvial soil. [ABSTRACT FROM AUTHOR]

Purpose: The nitrification inhibitor 3,4-dimethylpyrazol-phosphate (DMPP) and the urease inhibitor N-( n-butyl) thiophosphoric triamide (nBTPT) can mitigate N losses through reducing nitrification and ammonia volatilization, respectively. However, the impact of repeated applications of these inhibitors on nitrogen cycling microorganisms is not well documented. This study aimed to investigate the changes in the abundance and community structure of the functional microorganisms involved in nitrification and denitrification in Australian pasture soils after repeated applications of DMPP and nBTPT. Materials and methods: Soil was collected in autumn and spring, 2014 from two pasture sites where control, urea, urea ammonium nitrate, and urea-coated inhibitors had been repeatedly applied over 2 year. Soil samples were analyzed to determine the potential nitrification rates (PNRs), the abundances of amoA, narG, nirK and bacterial 16S rRNA genes, and the community structure of ammonia oxidizers. Results and discussion: Two years of urea application resulted in a significantly lower soil pH at Terang and a significant decrease in total bacterial 16S rRNA gene abundance at Glenormiston and led to significantly higher PNRs and abundances of ammonia oxidizers compared to the control. Amendment with either DMPP or nBTPT significantly decreased PNRs and the abundance of amoA and narG genes. However, there was no fertilizer- or inhibitor-induced change in the community structure of ammonia oxidizers. Conclusions: These results suggest that there were inhibitory effects of DMPP and nBTPT on the functional groups mediating nitrification and denitrification, while no significant impact on the community structure of ammonia oxidizers was observed. The application of nitrification or urease inhibitor appears to be an effective approach targeting specific microbial groups with minimal effects on soil pH and the total bacterial abundance. [ABSTRACT FROM AUTHOR]

Purpose: Glaciers of the Tianshan Mountains have been geographically isolated for a long time with little human interference. This study aimed to understand the viral community structures and their ecological functions in a unique glacier soil. Materials and methods: The abundances of purified virus particles and bacteria in the glacier soil were examined using epifluorescence microscopy and quantitative PCR of the 16S rRNA gene, respectively. Metagenomic analysis was employed to investigate the taxonomic and functional compositions as well as the phylogenetic relationship of the functional genes of the viruses in the glacier soil. Results and discussion: A total of eight double-stranded DNA (dsDNA) virus families were identified in the glacier soil, with Siphoviridae, Podoviridae, and Myoviridae being the more abundant families. The diverse dsDNA viruses and few ssDNA and other types of viruses formed the unique community structure of viruses in the Tianshan Mountains glacier soil. The functional genes identified from the virome mainly belonged to phage-related proteins. The phage terminase of Caudovirales presented high diversity, and its amino acid sequences were different from those in other environments. Conclusions: The results showed a unique viral diversity and taxonomic composition in the glacier soil, which suggests the significant ecological role of Caudovirales in this environment. [ABSTRACT FROM AUTHOR]

Purpose: Many biotic and abiotic factors influence the structural and functional diversity of microbial communities in the rhizosphere. This study aimed to understand the dynamics of fungal community in the soybean rhizosphere during soybean growth and directly compare the influence of abiotic and biotic factors in shaping the fungal communities across different growth periods. Materials and methods: High-throughput sequencing based on internal transcribed spacer (ITS) region, quantitative PCR, and statistical analysis approaches were used to measure the fungal community structure, abundance, and dynamic changes of 63 rhizosphere soil samples which were taken from different fertilization regimes and rhizobium inoculation treatments during three soybean growth stages. Results and discussion: Among the taxa examined, more than 16 fungal classes were detected from the 21 soil samples. Sordariomycetes was the most abundant class, followed by Dothideomycetes, Agaricomycetes, and Eurotiomycetes. Soybean growth stage was the most important factor determining the diversity patterns of the fungal communities. Fungal community diversity was closely related to the base-fertilizer application, and fungal community richness was associated with rhizobium inoculation. Beta diversity of the fungal community based on the Bray-Curtis distance was significantly related to plant growth stage. Network analysis showed that mutual cooperation among fungal taxa became more intimate during the plant growth. Conclusions: Compared with edaphic properties, plant growth stage was the dominant factor in determining soil fungal community dynamics. Base-fertilizer and rhizobium inoculation affected the alpha diversity of the soil fungi. [ABSTRACT FROM AUTHOR]

Purpose: Nitrification and denitrification processes dominate nitrous oxide (NO) emission in grassland ecosystems, but their relative contribution as well as the abiotic factors are still not well understood. Materials and methods: Two grassland soils from Duolun in Inner Mongolia, China, and Canterbury in New Zealand were used to quantitatively compare NO production and the abundance of bacterial and archaeal amoA, denitrifying nirK and nirS genes in response to N additions (0 and 100 μg NH -N g dry soil) and two soil moisture levels (40 and 80 % water holding capacity) using microcosms. Results and discussion: Soil moisture rather than N availability significantly increased the nitrification rate in the Duolun soil but not in the Canterbury soil. Moreover, N addition promoted denitrification enzyme activities in the Canterbury soil but not in the Duolun soil. The abundance of bacterial and archaeal amoA genes significantly increased as soil moisture increased in the Duolun soil, whereas in the Canterbury soil, only the abundance of bacterial amoA gene increased. The increase in NO flux induced by N addition was significantly greater in the Duolun soil than in the Canterbury soil, suggesting that nitrification may have a dominant role in NO emission for the Duolun soil, while denitrification for the Canterbury soil. Conclusions: Microbial processes controlling NO emission differed in grassland soils, thus providing important baseline data in terms of global change. [ABSTRACT FROM AUTHOR]

Purpose: Anammox bacteria have been widely investigated in both natural aquatic habitats and wastewater treatment reactors. However, their distribution in agricultural ecosystems which receive high reactive nitrogen input is hardly known. This study aims to examine the distribution and diversity of anammox bacteria in different Chinese paddy soils and along soil profile horizons. Materials and methods: DNA was extracted from paddy soils which were collected from ten sites and along four soil depth horizons (0-20, 20-40, 40-60, 60-80 cm). Community structure and diversity of the anammox bacteria were analyzed using cloning and sequencing methods by targeting 16S ribosomal RNA (rRNA) genes. Quantitative PCR was conducted to study the abundance of anammox hzsB genes. Results and discussion: Anammox bacterial 16S rRNA genes were not detected in most of the surface soil profile layers but present in all subsurface and deep horizons. Two genera, Candidatus Brocadia and Candidatus Kuenenia, were the only groups detected, and the former was predominant in tested soils. A site-specific distribution pattern of anammox bacteria and significant relationship between anammox bacteria community composition and soil pH and ammonium concentration were observed. The abundance of anammox bacteria hzsB gene ranged from 3.78 × 10 to 1.64 × 10 per gram of dry soil in all soils and significantly varied along the soil profile horizons. Conclusions: Anammox bacteria were widely distributed in paddy soils, especially in subsurface and profile depth horizons. Candidatus Brocadia and Candidatus Kuenenia were the dominating anammox groups in the tested soils, and the two genera showed a site-specific distribution pattern across large Chinese paddy soil areas and along soil depth profiles. [ABSTRACT FROM AUTHOR]

Purpose: Despite their symbiotic relationship with trees and the vital role as decomposer in forest, soil fungi received limited attention regarding their changes with altitude in forest ecosystems. This study aimed to determine the diversity patterns of soil fungi along an altitudinal gradient on Mt. Shegyla, a typical forest ecosystem on the Tibetan Plateau. Materials and methods: High-throughput barcoded pyrosequencing and quantitative PCR approaches were employed to measure the community composition, diversity, and abundance patterns of soil fungal 18S ribosomal RNA (rRNA) gene in 20 samples collected along the altitudinal gradient of Mt. Shegyla. Results and discussion: Abundant taxa in the fungal community were Agaricomycetes and Leotiomyceta on Mt. Shegyla. Fungal abundance decreased significantly with increasing altitude. Beta diversity of the fungal community, as measured using weighted UniFrac distance, was significantly related to altitude. Significant correlation was observed between altitude and alpha diversity including richness and phylodiversity, but not with evenness. Network analysis revealed that Ceramothyrium and Clavulina were two important hubs in the community, and an uncultured fungal taxon that previously detected in glacier forefront dominated this network. Distance-based linear model identified soil pH as the dominant driver which significantly related with fungal alpha diversity including richness, phylodiversity, and evenness. However, fungal abundance and the first component of PCoA on weighted UniFrac matrix (beta diversity) did not change significantly with pH. Conclusions: These results provided strong evidence that soil pH was the dominant driver for structuring altitudinal alpha diversity pattern but not beta diversity pattern or community abundance of soil fungi in this typical forest on the Tibetan Plateau. [ABSTRACT FROM AUTHOR]

Purpose: Human disturbance is a major culprit driving imbalances in the biological transformation of nitrogen from the nonreactive to the reactive pool and is therefore one of the greatest concerns for nitrogen (N) cycling. The objective of this study was to compare potential nitrification rates and the abundance of ammonia oxidizers responsible for nitrification, with the amendment of external N in different agricultural soils. Materials and methods: Three typical Chinese agricultural soils, QiYang (QY) acid soil, ShenYang (SY) neutral soil, and FengQiu (FQ) alkaline soil, were amended with 0, 20, 150, and 300 μg NH-N g soil and incubated for 40 days. The abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) at the end of incubation in the soil microcosms was determined using the real-time PCR. Results and discussion: There was a significant decrease in ammonium concentration in the QY soil from the highest to the lowest N-loading treatments, while no significant difference in ammonium concentrations was detected among the different N-loading treatments for the SY and FQ soils. A significantly higher potential nitrification rate (PNR) was observed in the FQ soil while lowest PNR was found in the QY soil. Quantitative PCR analysis of AOB amoA genes demonstrated that AOB abundance was significantly higher in the high N-loading treatments than in the control for the QY soil only, while no significant difference among treatments in the SY and FQ soils. A significant positive correlation between PNR and AOB amoA abundance, however, was found for the SY and FQ soils, but not for the QY soil. Little difference in AOA amoA abundance between different N-loading treatments was observed for all the soils. Conclusions: This study suggested that ammonia oxidation capacity in the FQ and SY soils was higher than those in the QY soil with the addition of ammonium fertilizer for a short-term. These findings indicated that understanding the differential responses of biological nitrification to varying input levels of ammonium fertilizer is important for maximizing N use efficiency and thereby improving agricultural fertilization management. [ABSTRACT FROM AUTHOR]

Purpose: Two recent discoveries in nitrogen (N) cycling processes, i.e., archaeal ammonia oxidizers and anaerobic ammonia (ammonium) oxidation (anammox), have triggered great interest in studying microbial ammonia oxidation processes. The purpose of this review is to highlight recent progress in ammonia oxidation processes in soils and sediments and to propose future research activities in this topic. Results and discussion: Aerobic ammonia oxidation and anammox processes are linked through the production and consumption of nitrite, respectively, thereby removing the reactive N (NH, NO, NO) from soil and sediment ecosystems. Ammonia-oxidizing microorganisms are widely distributed in soils and sediments, and increasing evidence suggests that ammonia-oxidizing archaea and bacteria are functionally dominant in the ammonia oxidation of acid soils and other soils, respectively. The widespread occurrence and great variation in the abundance of anammox bacteria indicate their heterogeneous distribution and niche differentiation. Therefore, the worldwide distribution of both microbial groups in nature has stimulated researchers to investigate the physiology and metabolism of related groups, as well as appraising their contribution to N cycling. Conclusions: We summarized the current progress and provided future perspectives in the microbiology of aerobic and anaerobic ammonia oxidation in soils and sediments. With increasing concern and interest in soil and sediment ammonia oxidation processes, studies in the microbial mechanisms underlying nitrification and anammox, as well as their interactions, are essential for understanding their contribution to the loss of N either through nitrate leaching or N-related gas emissions. [ABSTRACT FROM AUTHOR]

Purpose: The rationale of this paper is to review the state of the art regarding the biotic and abiotic reactions that can influence Fe availability in soils. In soil, the management-induced change from oxic to anoxic environment results in temporal and spatial variations of redox reactions, which, in turn, affect the Fe dynamics and Fe mineral constituents. Measuring the Fe forms in organic complexes and the interaction between bacteria and Fe is a major challenge in getting a better quantitative understanding of the dynamics of Fe in complex soil ecosystems. Materials and methods: We review the existing literature on chemical and biochemical processes in soils related with the availability of Fe that influences plant nutrition. We describe Fe acquisition by plant and bacteria, and the different Fe-organic complexes in order to understand their relationships and the role of Fe in the soil carbon cycle. Results and discussion: Although total Fe is generally high in soil, the magnitude of its available fraction is generally very low and is governed by very low solubility of Fe oxides. Plants and microorganisms can have different strategies in order to improve Fe uptake including the release of organic molecules and metabolites able to form complexes with Fe. Microorganisms appear to be highly competitive for Fe compared with plant roots. Crystalline Fe and poorly crystalline (hydro)oxides are also able to influence the carbon storage in soil. Conclusion: The solubility of crystalline Fe minerals in soil is usually very low; however, the interaction with plant, microbes, and organic substance can improve the formation of soluble Fe complexes and increase the availability of Fe for plant growth. Microbes release siderophores and plant exudates (e.g., phytosiderophores, organic acids, and flavonoids), which can bind and solubilize the Fe present in minerals. The improved understanding of this topic can enable the identification of effective solutions for remedying Fe deficiency or, alternatively, restricting the onset of its symptoms and yield's limitations in crops. Therefore, development and testing of new analytical techniques and an integrated approach between soil biology and soil chemistry are important prerequisites. [ABSTRACT FROM AUTHOR]

Purpose: Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are ubiquitous and important for nitrogen transformations in terrestrial ecosystems. However, the distribution patterns of these microorganisms as affected by the terrestrial environments across a large geographical scale are not well understood. This study was designed to gain insights into the ecological characteristics of AOA and AOB in 65 soils, collected from a wide range of soil and ecosystem types. Materials and methods: Barcoded pyrosequencing in combination with quantitative PCR was employed to characterize the relative abundance, diversity, and community composition of archaeal 16S rRNA gene, and AOA and AOB amoA genes in 65 soil samples. Results and discussion: The operational taxonomic unit richness and Shannon diversity of Thaumarchaeota, AOA, and AOB were highly variable among different soils, but their variations were best explained by soil pH. Soil pH was strongly correlated with the overall community composition of ammonia oxidizers, as measured by the pairwise Bray-Curtis dissimilarity across all sites. These findings were further corroborated by the evident pH-dependent distribution patterns of four thaumarchaeal groups (I.1a-associated, I.1b, I.1c, and I.1c-associated) and four AOB clusters (2, 3a.1, 10, and 12). The ratios of AOA to AOB amoA gene copy numbers significantly decreased with increasing pH, suggesting a competitive advantage of AOA over AOB in acidic soils. Conclusions: These results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils. [ABSTRACT FROM AUTHOR]

Purpose: Disturbances such as cultivation, logging, and plantation occurred widely in acid red soil area of China, yet little is known about their effects on soil microbial community which is closely related to soil function. In this study, microbial community compositions were investigated in a red soil with different long-term land utilization patterns to understand the potential effects of cultivation and vegetation successions on relevant soil functions. Materials and methods: Land utilization patterns include restoration, degradation (logging), cropland, and pine plantation. Both DNA- and phospholipid fatty acid (PLFA)-based methods were used to measure the abundance and community structure of microorganisms. Results and discussion: In general, DNA- and PLFA-based methods showed similar results of microbial composition, but for some parameters, only one approach showed significant differences between different land utilization patterns. Land utilization patterns showed significant effects on abundance of total microbial community, bacteria, fungi, and actinomycetes which were all lowest in the cropland plot either by PLFA or DNA analyses. 17:0 cyclo/16:1 ω7c and 19:0 cyclo/18:1 ω7c which are possibly associated with environmental stresses also varied among different land utilization patterns. Both PLFA and T-RFLP analyses showed that each land utilization pattern possessed a specific microbial community structure. Conclusions: These results revealed significant effects of different land utilization patterns especially cultivation and logging on soil microbial communities and suggested that we should be cautious in utilizing red soils to sustain soil properties and functions. Combination of DNA- and PLFA-based methods is effective to provide precise results of microbial composition. [ABSTRACT FROM AUTHOR]

Purpose: New water retention materials, super absorbent polymers (SAPs), have shown the potential to improve some soil physicochemical properties and promote growth of some crop species in arid and semi-arid areas. However, the impacts of SAPs on soil microbial properties are unclear. This study was conducted to clarify the effects of two SAPs on soil microbial properties and Chinese cabbage ( Brassica chinensis) growth under different water conditions in the greenhouse. Materials and methods: Experimental conditions included different irrigation conditions and different quantities of SAPs. Chinese cabbage was harvested after 1-month growth in the greenhouse. Meanwhile, soil samples were collected and sieved (<2-mm mesh). Some of the soils were kept at −4 °C for analysis of soil physicochemical properties, and some at −20 °C for analysis of soil microbial properties. Chinese cabbage samples were thoroughly washed with deionized water for the measurement of fresh weight, shoot length, and root length. Results and discussion: The effects from SAPs were not obvious under water sufficient (WC1, watered every 2 days, and WC2, watered every 4 days) since plant properties were smaller in some SAP treatments than those in control. However, under water deficit (WC3, watered every 8 days), there were significant differences in plant shoot length and fresh weight between SAP treatments. There were also significant differences in relative soil water content between water condition (WC) or SAP treatments. The SAPs were beneficial for the formation of large aggregates. Under WC3, the soil organic matter (SOM) increased by 16.9 and 11.5 %, soil microbial biomass C (SMBC) by 32.5 and 19.3 %, and soil microbial respiration (SMR) by 52.1 and 37.2 % with Jaguar C (JC) and Jaguar S (JS), respectively. Under WC1 and WC2, significantly higher copy numbers of AOA in bulk treatment of JC were found compared with control treatment in this study. Under water deficit, the abundance of bacteria was significantly increased by application of SAPs. For almost every property of soil and plant, JC was showing better effects than JS. Conclusions: Our results showed that cabbage growth was restricted under water-deficit conditions and the application of SAPs could conserve soil water and be useful for increasing cabbage growth under water deficit, improving SOM, SMBC, and SMR under different WC, and stimulating amoA gene AOA copy numbers and bacterial gene copy numbers. Thus, there should be no adverse effects of SAP application on soil microbial environment and Chinese cabbage growth. [ABSTRACT FROM AUTHOR]

Purpose: There have been a number of studies on the succession of vegetation; however, the succession of soil microbes and the collaborative relationships between microbes and vegetation during land restoration remain poorly understood. The objectives of this study were to characterize soil microbial succession and to explore the collaborative mechanisms between microbes and vegetation during the restoration of abandoned land through quantitative ecology methods. Materials and methods: The present research was carried out in the succession of a 5-year abandoned land and its conversion to Hippophae rhamnoides shrubs, Larix principis-rupprechtii plantation, and a naturally regenerated forest (mixed forest). Soil bacterial, archaeal and fungal characteristics were tested by real-time quantitative PCR assays and terminal restriction fragment length polymorphism. The richness, diversity, and evenness indices were employed to analyze plant and microbial communities' structure. The stability of plant and microbial communities was tested using Spearman's rank correlation. The relationships between the regeneration scenarios and environmental factors were determined through canonical correspondence analysis. Results and discussion: The aboveground biomass was significantly different among the sites. Soil bacterial, archaeal, and fungal rRNA gene abundances did not increase significantly with increasing soil organic carbon content. There were higher correlation coefficients between plant and total microbial communities on the richness, diversity, and evenness indices and ratios of positive to negative association compared to ones between plant and individual bacteria, archaea, and fungi. Soil bulk density, clay, pH, and litter were the primary significant environmental factors affecting the structure of plant and microbial communities. The positive relationships between plant and soil bacteria, fungi, and total microbe communities, as well as the negative relationships between plant and archaea, were demonstrated. Conclusions: The results suggested that plants promote the growth of soil bacteria and fungi during the process of community succession on a small scale; however, plants inhibit the growth of soil archaea. [ABSTRACT FROM AUTHOR]

Purpose: The nitrification inhibitor dicyandiamide (DCD) has been shown to be highly effective in reducing nitrate (NO) leaching and nitrous oxide (NO) emissions when used to treat grazed pasture soils. However, there have been few studies on the possible effects of long-term DCD use on other soil enzyme activities or the abundance of the general soil microbial communities. The objective of this study was to determine possible effects of long-term DCD use on key soil enzyme activities involved in the nitrogen (N) cycle and the abundance of bacteria and archaea in grazed pasture soils. Materials and methods: Three field sites used for this study had been treated with DCD for 7 years in field plot experiments. The three pasture soils from three different regions across New Zealand were Pukemutu silt loam in Southland in the southern South Island, Horotiu silt loam in the Waikato in the central North Island and Templeton silt loam in Canterbury in the central South Island. Control and DCD-treated plots were sampled to analyse soil pH, microbial biomass C and N, protease and deaminase activity, and the abundance of bacteria and archaea. Results and discussion: The three soils varied significantly in the microbial biomass C (858 to 542 μg C g soil) and biomass N (63 to 28 μg N g), protease (361 to 694 μg tyrosine g soil h) and deaminase (4.3 to 5.6 μg NH g soil h) activity, and bacteria (bacterial 16S rRNA gene copy number: 1.64 × 10 to 2.77 × 10 g soil) and archaea (archaeal 16S rRNA gene copy number: 2.67 × 10 to 3.01 × 10 g soil) abundance. However, 7 years of DCD use did not significantly affect these microbial population abundance and enzymatic activities. Soil pH values were also not significantly affected by the long-term DCD use. Conclusions: These results support the hypothesis that DCD is a specific enzyme inhibitor for ammonia oxidation and does not affect other non-target microbial and enzyme activities. The DCD nitrification inhibitor technology, therefore, appears to be an effective mitigation technology for nitrate leaching and nitrous oxide emissions in grazed pasture soils with no adverse impacts on the abundance of bacteria and archaea and key enzyme activities. [ABSTRACT FROM AUTHOR]

Purpose: Methane-oxidizing bacteria (methanotrophs) biologically consume and consequently affect the concentration of atmospheric methane (CH), the second most prominent greenhouse gas, and therefore play critical roles in the mitigation of global warming effect. Long-term fertilization often affects the methanotrophic community and CH oxidation in various soils. Here, the immediate effects of nitrogen (N), phosphorus (P), and potassium (K) amendments on the CH oxidation activity and methanotrophic community structure were evaluated. Materials and methods: Paddy soil samples were collected from the Taoyuan Experimental Station of the Chinese Academy of Sciences in central Hunan Province of China. A laboratory-based incubation experiment was conducted to investigate the immediate effects of N, P, and K amendments on the methanotrophs in soil. The CH oxidation rates and methanotrophic activities were determined by measuring the dynamic changes of CH concentration in the incubation system. The methanotrophic abundance and community changes in all of the seven treatments with and without nutrients addition were studied using real-time PCR and denaturing gradient gel electrophoresis, respectively. Results and discussion: All of the N, P, and K treatments significantly decreased the CH oxidation activities. Compared with the control, the P and K amendments significantly increased the methanotrophic population size, but the N treatments have no effect on the methanotrophic abundance. A negative correlation was found between methanotrophic activity and methanotrophic abundance. We suggested that methanotrophic activity may not be inferred through the pmoA gene copies, especially in the short-term simulation experiments. Investigation of the methanotrophic population size and diversity is not enough to evaluate the soil CH sink accurately. Conclusions: We concluded that the additions of N, P, and K reduce the activity but enhance the abundance of methanotrophs in a Chinese paddy soil through a short-term incubation experiment. Additionally, we found that the CH oxidation activity could be completely inhibited by Cl toxicity. Our results implied that caution should be exercised in the types and amounts of fertilizers, especially KCl in agricultural systems to control the instantaneous increase in CH emission from the field. [ABSTRACT FROM AUTHOR]

Background, aim, and scope As the second most important greenhouse gas, methane (CH[sub4]) is produced from many sources such as paddy fields. Methane-oxidizing bacteria (methanotrophs) consume CH[sub4] in paddy soil and, therefore, reduce CH[sub4] emission to the atmosphere. In order to estimate the contribution of paddy fields as a source of CH[sub4], it is important to monitor the effects of fertilizer applications on the shifts of soil methanotrophs, which are targets in strategies to combat global climate change. In this study, real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA and pmoA genes, respectively, were used to analyze the soil methanotrophic abundance and community diversity under four fertilization treatments: urea (N), urea and potassium chloride (NK), urea, superphosphate, and potassium chloride (NPK), and urea, superphosphate, potassium chloride, and crop residues (NPK+C), compared to an untreated control (CON). The objective of this study was to examine whether soil methanotrophs responded to the long-term, different fertilizer regimes by using a combination of quantitative and qualitative molecular approaches. Materials and methods Soil samples were collected from the Taoyuan Experimental Station of Agro-ecosystem Observation at Changde (28°55' N, 111°26' E), central Hunan Province of China, in July 2006. Soil DNAs were extracted from the samples, then the 16S rRNA genes were quantified by real-time PCR and the pmoA genes were amplified via general PCR followed by DGGE, cloning, sequencing, and phylogenetic analysis. The community diversity indices were assessed through the DGGE profile. Results Except for NPK, other treatments of N, NK, and NPK+C showed significantly higher copy numbers of type I methanotrophs (7.0-9.6x 10[sup7]) than CON (5.1 x 10[sup7]). The copy numbers of type II methanotrophs were significantly higher in NPK+C (2.8 x 10[sup8]) and NK (2.5 x 10[sup8]) treatments than in CON (1.4x 10[sup8]). Moreover, the ratio of type II to type I methanotrophic copy numbers ranged from 1.88 to 3.32, indicating that the type II methanotrophs dominated in all treatments. Cluster analyses based on the DGGE profile showed that the methanotrophic community in NPK+C might respond more sensitively to the environmental variation. Phylogenetic analysis showed that 81% of the obtained pmoA sequences were classified as type I methanotrophs. Furthermore, the type I-affiliated sequences were related to Methylobacter, Methylomicrobium, Methylomonas, and some uncultured methanotrophic clones, and those type II- like sequences were affiliated with Methylocystis and Methylosinus genera. Discussion There was an inhibitory effect on the methanotrophic abundance in the N and a stimulating effect in the NK and NPK+C treatments, respectively. During the rice- growing season, the type II methanotrophs might be more profited from such a coexistence of low O[sub2] and high CH[sub4] concentration environment than the type I methanotrophs. However, type I methanotrophs seemed to be more frequently detected. The relatively complex diversity pattern in the NPK+C treatment might result from the strong CH[sub4] production. Conclusions Long-term fertilization regimes can both affect the abundance and the composition of the type I and type II methanotrophs. The inhibited effects on methanotrophic abundance were found in the N treatment, compared to the stimulated effects from the NK and NPK+C treatments. The fertilizers of nitrogen, potassium, and the crop residues could be important factors controlling the abundance and community composition of the methanotrophs in the paddy soil.… [ABSTRACT FROM AUTHOR]

A correction to the article "Candidatus Brocadia and Candidatus Kuenenia predominated in anammox bacterial community in selected Chinese paddy soils," by Ren Bai and colleagues that was published in August 14, 2015 issue is presented.