Ammonia-oxidizing bacteria: a model for molecular microbial ecology

In-situ study of migration and transformation of nitrogen in groundwater based on continuous observations at a contaminated desert site

The objective of this study was to explore the controlling factors on the migration and transformation of nitrogenous wastes in groundwater using long-term observations from a contaminated site on the southwestern edge of the Tengger Desert in northwestern China. Contamination was caused by wastewater discharge rich in ammonia. Two long-term groundwater monitoring wells (Wells 1# and 2#) were constructed, and 24 water samples were collected. Five key indicators were tested: ammonia, nitrate, nitrite, dissolved oxygen, and manganese. A numerical method was used to simulate the migration process and to determine the migration stage of the main pollutant plume in groundwater. The results showed that at Well 1# the nitrogenous waste migration process had essentially been completed, while at Well 2# ammonia levels were still rising and gradually transitioning to a stable stage. The differences for Well 1# and Well 2# were primarily caused by differences in groundwater flow. The change in ammonia concentration was mainly controlled by the migration of the pollution plume under nitrification in groundwater. The nitrification rate was likely affected by changes in dissolved oxygen and potentially manganese.

Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans

The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria- to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soil-borne Fusarium wilt disease.

Microbial community structure and function in aerobic granular sludge

Aerobic granular sludge (AGS), a self-immobilized microbial consortium containing different functional microorganisms, is receiving growing attention, since it has shown great technological and economical potentials in the field of wastewater treatment. Microbial community is crucial for the formation, stability, and pollutant removal efficiency of aerobic granules. This mini-review systematically summarizes the recent findings of the microbial community structure and function of AGS and discusses the new research progress in the microbial community dynamics during the granulation process and spatial distribution patterns of the microbiota in AGS. The presented information may be helpful for the in-depth theoretical study and practical application of AGS technology in the future.

Responses and recovery assessment of continuously cultured Nitrosomonas europaea under chronic ZnO nanoparticle stress: Effects of dissolved oxygen

Although the antibacterial performances of emerging nanoparticles (NPs) have been extensively explored in the nitrifying systems, the impacts of dissolved oxygen (DO) levels on their bio-toxicities to the nitrifiers and the impaired cells' recovery potentials have seldom been addressed yet. In this study, the physiological and transcriptional responses of the typical ammonia oxidizers - Nitrosomonas europaea in a chemostat to the chronic ZnO NP exposure under different DO conditions were investigated. The results indicated that the cells in steady-growth state in the chemostat were more persevering than batch cultured ones to resist ZnO NP stress despite the dose-dependent NP inhibitory effects were observed. In addition, the occurred striking over-expressions of amoA and hao genes at the initial NP exposure stage suggested the cells' self-regulation potentials at the transcriptional level. The low DO (0.5 mg/L) cultured cells displayed higher sensitivity to NP stress than the high DO (2.0 mg/L) cultured ones, probably owning to the inefficient oxygen-dependent electron transfer from ammonia oxidation for energy conversion/production. The following 12-h NP-free batch recovery assays revealed that both high and low DO cultured cells possessed the physiological and metabolic activity recovery potentials, which were in negative correlation with the NP exposure time. The duration of NP stress and the resulting NP dissolution were critical for the cells' damage levels and their performance recoverability. The membrane preservation processes and the associated metabolism regulations were expected to actively participate in the cells' self-adaption to NP stress and thus be responsible for their metabolic activities recovery.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats

Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

Nitrification in agricultural soils: impact, actors and mitigation

Nitrogen is one of the most important nutrients for plant growth and hence heavily applied in agricultural systems via fertilization. Nitrification, that is, the conversion of ammonium via nitrite to nitrate by soil microorganisms, however, leads to nitrate leaching and gaseous nitrous oxide production and as such to an up to 50% loss of nitrogen availability for the plant. Nitrate leaching also results in eutrophication of groundwater, drinking water and recreational waters, toxic algal blooms and biodiversity loss, while nitrous oxide is a greenhouse gas with a global warming potential 300× greater than carbon dioxide. Logically, inhibition of nitrification is an important strategy used in agriculture to reduce nitrogen losses, and contributes to a more environmental-friendly practice. However, recently identified and crucial players in nitrification, that is, ammonia-oxidizing archaea and comammox bacteria, seem to be under-investigated in this respect. In this review, we give an update on the different pathways in ammonia oxidation, the relevance for agriculture and the interaction with nitrification inhibitors. As such, we hope to pinpoint possible strategies to optimize the efficiency of nitrification inhibition.

Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary

Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs’ abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs’ abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs’ distribution patterns in estuarine ecosystems.

A comparative study of composting the solid fraction of dairy manure with or without bulking material: Performance and microbial community dynamics

The present study compared the development of various physicochemical properties and the composition of microbial communities involved in the composting process in the solid fraction of dairy manure (SFDM) with a sawdust-regulated SFDM (RDM). The changes in several primary physicochemical properties were similar in the two composting processes, and both resulted in mature end-products within 48days. The bacterial communities in both composting processes primarily comprised Proteobacteria and Bacteroidetes. Firmicutes were predominant in the thermophilic phase, whereas Chloroflexi, Planctomycetes, and Nitrospirae were more abundant in the final mature phase. Furthermore, the succession of bacteria in both groups proceeded in a similar pattern, suggesting that the effects of the bulking material on bacterial dynamics were minor. These results demonstrate the feasibility of composting using only the SFDM, reflected by the evolution of physicochemical properties and the microbial communities involved in the composting process.

Disentangling the influence of climate, soil and belowground microbes on local species richness in a dryland ecosystem of Northwest China

Xinjiang Uygur Autonomous Region (XUAR) covers one of the largest drylands in the world, while the relative effects of different environmental factors on plant diversity are poorly understood. We sampled 66 sites in a typical dryland of XUAR, which covers more than 450,000 km², to evaluate the relative influences of different factors on the patterns of local plant species richness (LPSR). We found that overall and herbaceous LPSR were positively correlated with water availability, soil nutrients but negatively correlated with energy availability, while the shrub LPSR showed the opposite response. Climate, soil attributes together explained 53.2% and 59.2% of the variance in overall and herbaceous LPSR, respectively; revealing that LPSR patterns were shaped by abiotic and underground biotic factors together. Only 31.5% of the variance in the shrub LPSR was explained by soil attributes, indicating that shrub LPSR was mainly limited by non-climatic factors. There findings provide robust evidence that relative contribution of climate and soil attributes differ markedly depending on the plant functional group. Furthermore, we found the different relationship between microbes and plant diversity, indicating that the linkages between soil microbial diversity and plant diversity may vary across functional groups of microbes and plant. These findings provide robust evidence that the relative roles of climate, soil and microbes differ markedly depending on the plant functional group. Microbial richness showed a significantly pure influence on the LPSR of all groups, suggesting that microbes play a non-negligible role in regulating plant diversity in dryland ecosystems.

Nitrospira are more sensitive than Nitrobacter to land management in acid, fertilized soils of a rapeseed-rice rotation field trial

Nitrite oxidation is recognized as an essential process of biogeochemical nitrogen cycling in agricultural ecosystems. How nitrite-oxidizing bacteria (NOB) respond to land managements (the effect from the long-term straw incorporation and environmental variability caused by the shift from the upland stage to the paddy stage) in a rapeseed-rice rotation field remains unclear. We found the nitrite oxidation (NO) in soils increased from the upland stage to the paddy stage. An inhibitory effect of the long-term straw incorporation on NO was detectable in the upland stage. The abundance of Nitrospira was always greater than Nitrobacter, and it was affected by the rice-growing and straw incorporation while Nitrobacter was not. NO correlated positively with the abundance of Nitrospira and with soluble sulfate (SO₄^2-), soil moisture, pH and NH₄⁺. The high-throughput sequencing analysis of the nitrite oxidoreductase nxrA and nxrB genes for Nitrobacter- and Nitrospira-like NOB was performed respectively. The dominating (relative abundance>1%) operational taxonomic units (OTUs) from Nitrobacter were closely related to Nitrobacter hamburgensis, whereas those from Nitrospira were affiliated with or related to lineage II, lineage V and several unknown groups. Heatmap analysis showed that a few dominant Nitrobacter OTUs were affected by the straw treatment or the rice-growing, and half of the dominant Nitrospira ones were explained by at least one of the variables. Multi-response permutation procedure (MRPP) and redundancy analyses showed that the Nitrospira-like NOB community changes were significantly shaped by the land managements and the soil chemical properties, including pH, moisture and NH₄⁺, whereas that of the Nitrobacter-like NOB community was not. These results suggested that Nitrospira are more sensitive than Nitrobacter to land management in acid and fertilized soils of a rapeseed-rice rotation field trial.

Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols

Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro

Cyanobacterial blooms drastically influence carbon and nutrient cycling in eutrophic freshwater lakes. To understand the mineralization process of cyanobacteria-derived particulate organic matter (CyanPOM), the aerobic degradation of cyanobacterial blooms dominated by Microcystis sp. was investigated over a 95-day microcosm experiment. Approximately 91%, 95% and 83% of the initial particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP) were decomposed, respectively. The POC:PON ratio gradually increased from 5.9 to 13.5, whereas the POC:POP ratio gradually decreased from 230.3 to 120. These results indicated that the coupling of POC, PON, and POP changed during the decomposition of CyanPOM. Moreover, approximately 29%, 51% and 46% of POC, PON, and POP were mineralized to dissolved organic carbon, NO₃^-, and PO₄^3-, respectively. Rhodospirillales (10.9%), Burkholderiales (16.5%), and Verrucomicrobiales (14.3%) dominated during the rapid phase (days 0-21), whereas Sphingomonadales (12.8%), Rhizobiales (11.8%), and Xanthomonadales (36.5%) dominated during the slow phase (days 21-50) of CyanPOM decomposition. Nitrospira (16.6%-32.9%) dominated and NO₃^- increased during the refractory phase (days 50-95), thus suggesting the occurrence of nitrification. Redundancy analysis revealed that bacterial communities during rapid decomposition were distinct from those during the slow and refractory periods. POC:POP, NH₄⁺, and NO₃^- were the major driving factors for the patterns of bacterial communities. Furthermore, increase in nitrogen metabolism, methane metabolism, amino acid related enzymes and pyruvate metabolism characterized the functional variation of bacterial communities during degradation. Therefore, CyanPOM is an important nutrient source, and its decomposition level shapes bacterial communities.

Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil

Soil amended with single biochar or nitrogen (N) fertilizer has frequently been reported to alter soil nitrification process due to its impact on soil properties. However, little is known about the dynamic response of nitrification and ammonia-oxidizers to the combined application of biochar and N fertilizer in intensive vegetable soil. In this study, an incubation experiment was designed to evaluate the effects of biochar and N fertilizer application on soil nitrification, abundance and community shifts of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Hangzhou greenhouse vegetable soil. Results showed that single application of biochar had no significant effect on soil net nitrification rates and ammonia-oxidizers. Conversely, the application of only N fertilizer and N fertilizer + biochar significantly increased net nitrification rate and the abundance of AOB rather than AOA, and only AOB abundance was significantly correlated with soil net nitrification rate. Moreover, the combined application of N fertilizer and biochar had greater effect on AOB communities than that of the only N fertilizers, and the relative abundance of 156 bp T-RF (Nitrosospira cluster 3c) decreased but 60 bp T-RF (Nitrosospira cluster 3a and cluster 0) increased to become a single predominant group. Phylogenetic analysis indicated that all the AOB sequences were grouped into Nitrosospira cluster, and most of AOA sequences were clustered within group 1.1b. We concluded that soil nitrification was stimulated by the combined application of N fertilizer and biochar via enhancing the abundance and shifting the community composition of AOB rather than AOA in intensive vegetable soil.

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 10⁴ – 4.9 × 10⁷ archaeal amoA copies ∗ μg DNA^-1, 1.5 × 10³ – 5.3 × 10⁵ AOB 16S rRNA copies ∗ μg DNA^-1, and 1.3 × 10⁶ – 7.7 × 10⁷Nitrospira nxrB copies ∗ μg DNA^-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.

Greenhouse gas emissions from a Cu-contaminated soil remediated by in situ stabilization and phytomanaged by a mixed stand of poplar, willows, and false indigo-bush

Phytomanagement of trace element-contaminated soils can reduce soil toxicity and restore soil ecological functions, including the soil gas exchange with the atmosphere. We studied the emission rate of the greenhouse gases (GHGs) CO₂, CH₄, and N₂O; the potential CH₄ oxidation; denitrification enzyme activity (DEA), and glucose mineralization of a Cu-contaminated soil amended with dolomitic limestone and compost, alone or in combination, after a 2-year phytomanagement with a mixed stand of Populus nigra, Salix viminalis, S. caprea, and Amorpha fruticosa. Soil microbial biomass and microbial community composition after analysis of the phospholipid fatty acids (PLFA) profile were determined. Phytomanagement significantly reduced Cu availability and soil toxicity, increased soil microbial biomass and glucose mineralization capacity, changed the composition of soil microbial communities, and increased the CO₂ and N₂O emission rates and DEA. Despite such increases, microbial communities were evolving toward less GHG emission per unit of microbial biomass than in untreated soils. Overall, the aided phytostabilization option would allow methanotrophic populations to establish in the remediated soils due to decreased soil toxicity and increased nutrient availability.

Phenol biodegradation and microbial community dynamics in extractive membrane bioreactor (EMBR) for phenol-laden saline wastewater

An extractive membrane bioreactor (EMBR) for phenol-laden saline wastewater was set up in this study to investigate the variations of phenol removal, extracellular polymeric substance (EPS) release and microbial community dynamics. The gradual release of phenol and the total separation of salt were achieved by silicon rubber tube membrane. Only phenol (55.6-273.9mg/L) was extracted into microorganism unit from wastewaters containing 1.0-5.0g/L phenol and 35.0g/L NaCl. After 82d of EMBR operation, maximal 273.9mg/L of phenol was removed in EMBR. Low concentration of phenol in wastewater (2.5g/L) played a favorable effect on the microbial community structure, community and dynamics. The enumeration of Proteobacteria (30,499 sequences) significantly increased with more released EPS (82.82mg/gSS) to absorb and degrade phenol, compared to the virgin data without phenol addition. However, high concentration of phenol showed adverse effects on EPS release, microbial abundance and biodiversity.

[Nitrous oxide emission, nitrification, denitrification and nitrogen mineralization during rice growing season in 2 soils from Uruguay]

Microbial processes such as mineralization, nitrification and denitrification regulate nitrogen dynamics in the soil. The last two processes may produce nitrous oxide (N₂O). In this work N₂O fluxes were quantified at four moments of the rice cycle, sowing, tillering, panicle initiation and maturity, in two sites that differed mainly in their soil organic matter (OM) content, Salto (higher OM) and Treinta y Tres. Potential net N mineralization, ammonium oxidation and denitrification as well as the most probable numbers (MPN) of ammonia oxidizers and denitrifiers were determined. Potential N mineralization did not vary with the soil type and increased at rice maturity. Neither ammonia oxidation potential nor MPN were different among the soils. However, the soil with higher OM exhibited higher activity and MPN of denitrifiers, irrespective of the rice stage. In turn, at the latest phases of the crop, the MPN of denitrifiers increased coinciding with the highest mineralization potential and mineral N content of the soil. Significant differences in N₂O flux were observed in Salto, where the highest emissions were detected at rice maturity, after the soil was drained (44.2 vs 20.8g N-N₂O/ha d in Treinta y Tres). This work shows the importance of considering the soil type and end-of-season drainage of the rice field to elaborate GHGs (greenhouse gases) inventories.

Seasonal and soil-type dependent emissions of nitrous oxide from irrigated desert soils amended with digested poultry manures

Expansion of dryland agriculture requires intensive supplement of organic fertilizers to improve the fertility of nutrient-poor desert soils. The environmental impact of organic supplements in hot desert climates is not well understood. We report on seasonal emissions of nitrous oxide (N₂O) from sand and loess soils, amended with limed and non-limed anaerobic digestate of poultry manure in the Israeli Negev desert. All amended soils had substantially higher N₂O emissions, particularly during winter applications, compared to unammended soils. Winter emissions from amended loess (10-175mgN₂Om^-2day^-1) were markedly higher than winter emissions from amended sand (2-7mgN₂Om^-2day^-1). Enumeration of marker genes for nitrification and denitrification suggested that both have contributed to N₂O emissions according to prevailing environmental conditions. Lime treatment of digested manure inhibited N₂O emissions regardless of season or soil type, thus reducing the environmental impact of amending desert soils with manure digestate.

Research trends and hotspots related to ammonia oxidation based on bibliometric analysis

Ammonia oxidation is the rate-limiting and central step in global biogeochemistry cycle of nitrogen. A bibliometric analysis based on 4314 articles extracted from Science Citation Index Expanded database was carried out to provide insights into publication performances and research trends of ammonia oxidation in the period 1991-2014. These articles were originated from a wide range of 602 journals and 95 Web of Science Categories, among which Applied and Environmental Microbiology and Environmental Sciences took the leading position, respectively. Furthermore, co-citation analysis conducted with help of CiteSpace software clearly illustrated that ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia oxidation (anammox) were three dominant research themes. A total of 15 landmark works identified with the highest co-citation frequencies at every 8 years were extracted, which demonstrated that the establishments of culture-independent molecular biotechnologies as well as the discoveries of anammox and AOA played the most significant roles in promoting the evolution and development of ammonia oxidation research. Finally, word cluster analysis further suggested that microbial abundance and community of AOA and AOB was the most prominent hotspot, with soil and high-throughput sequencing as the most promising ecosystem and molecular biotechnology. In addition, application of anammox in nitrogen removal from wastewater has become another attractive research hotspot. This study provides a basis for better understanding the situations and prospective directions of the research field of ammonia oxidation.

Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application

Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.

Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas

The moist savanna zone covers 0.5 × 10⁶ km² in West Africa and is characterized by very low soil N levels limiting primary production, but the ecology of nitrifiers in these (agro)ecosystems is largely unknown. We compared the effects of six agricultural practices on nitrifier activity, abundance and diversity at nine sites in central Ivory Coast. Treatments, including repeated fertilization with ammonium and urea, had no effect on nitrification and crop N status after 3 to 5 crop cycles. Nitrification was actually higher at low than medium ammonium level. The nitrifying community was always dominated by ammonia oxidizing archaea and Nitrospira. However, the abundances of ammonia oxidizing bacteria, AOB, and Nitrobacter increased with fertilization after 5 crop cycles. Several AOB populations, some affiliated to Nitrosospira strains with urease activity or adapted to fluctuating ammonium levels, emerged in fertilized plots, which was correlated to nitrifying community ability to benefit from fertilization. In these soils, dominant nitrifiers adapted to very low ammonium levels have to be replaced by high-N nitrifiers before fertilization can stimulate nitrification. Our results show that the delay required for this replacement is much longer than ever observed for other terrestrial ecosystems, i.e. > 5 crop cycles, and demonstrate for the first time that nitrifier characteristics jeopardize the efficiency of fertilization in moist savanna soils.

Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau

Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand

The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities at the two sites will result in different responses to environmental change.

Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition

The nitrogen (N)-use efficiency of agricultural plants is notoriously poor. Globally, about 50% of the N fertilizer applied to cropping systems is not absorbed by plants, but lost to the environment as ammonia (NH₃), nitrate (NO₃^-), and nitrous oxide (N₂O, a greenhouse gas with 300 times the heat-trapping capacity of carbon dioxide), raising agricultural production costs and contributing to pollution and climate change. These losses are driven by volatilization of NH₃ and by a matrix of nitrification and denitrification reactions catalysed by soil microorganisms (chiefly bacteria and archaea). Here, we discuss mitigation of the harmful and wasteful process of agricultural N loss via biological nitrification inhibitors (BNIs) exuded by plant roots. We examine key recent discoveries in the emerging field of BNI research, focusing on BNI compounds and their specificity and transport, and discuss prospects for their role in improving agriculture while reducing its environmental impact.

A multiomics approach to study the microbiome response to phytoplankton blooms

Phytoplankton blooms are predictable features of marine and freshwater habitats. Despite a good knowledge base of the environmental factors controlling blooms, complex interactions between the bacterial and archaeal communities and phytoplankton bloom taxa are only now emerging. Here, the current research on bacterial community's structural and functional response to phytoplankton blooms is reviewed and discussed and further research is proposed. More attention should be paid on structure and function of autotrophic bacteria and archaea during phytoplankton blooms. A multiomics integration approach is needed to investigate bacterial and archaeal communities' diversity, metabolic diversity, and biogeochemical functions of microbial interactions during phytoplankton blooms.

Frutexites-like structures formed by iron oxidizing biofilms in the continental subsurface (Äspö Hard Rock Laboratory, Sweden)

Stromatolitic iron-rich structures have been reported from many ancient environments and are often described as Frutexites, a cryptic microfossil. Although microbial formation of such structures is likely, a clear relation to a microbial precursor is lacking so far. Here we report recent iron oxidizing biofilms which resemble the ancient Frutexites structures. The living Frutexites-like biofilms were sampled at 160 m depth in the Äspö Hard Rock Laboratory in Sweden. Investigations using microscopy, 454 pyrosequencing, FISH, Raman spectroscopy, biomarker and trace element analysis allowed a detailed view of the structural components of the mineralized biofilm. The most abundant bacterial groups were involved in nitrogen and iron cycling. Furthermore, Archaea are widely distributed in the Frutexites-like biofilm, even though their functional role remains unclear. Biomarker analysis revealed abundant sterols in the biofilm most likely from algal and fungal origins. Our results indicate that the Frutexites-like biofilm was built up by a complex microbial community. The functional role of each community member in the formation of the dendritic structures, as well as their potential relation to fossil Frutexites remains under investigation.

Nitrifying Kinetics and the Persistence of Nitrite in the Seine River, France

Although a higher oxidation rate for nitrite than for ammonia generally prevents nitrite accumulation in oxic waters, nitrite concentrations in the Seine River (1-31 μM) exceed European norms. We investigated the kinetics of in situ ammonia- and nitrite-oxidizing communities in river water and wastewater treatment plant (WWTP) effluents to determine the role of pelagic nitrification in the origin and persistence of nitrite downstream of Paris. The main source of nitrite is the major Parisian WWTP, and its persistence, up to tens of kilometers downstream of the plant, is explained by low ammonia and nitrite oxidation rates and high river flow. Furthermore, similar nitrite and ammonia oxidation rates preclude a rapid consumption of both preexisting nitrite and nitrite produced by ammonia oxidation. Maximum ammonia oxidation rates are two to three times higher downstream than upstream of the WWTP, indicating the input of ammonia oxidizers and ammonia from the WWTP. In both river water and WWTP effluents, nitrite oxidizers were unable to oxidize all available nitrite. In the human-impacted Seine River, this phenomenon might be due to mixotrophy. This study highlights the low resilience of the river to nitrite contamination as well as the importance of managing nitrite, nitrifiers, and organic matter concentrations in WWTP effluents to avoid nitrite persistence in rivers.

N2O emission characteristics and its affecting factors in rain-fed potato fields in Wuchuan County, China

Representing an important greenhouse gas, nitrous oxide (N₂O) emission from cultivated land is a hot topic in current climate change research. This study examined the influences of nitrogen fertilisation, temperature and soil moisture on the ammonia monooxygenase subunit A (amoA) gene copy numbers and N₂O emission characteristics. The experimental observation of N₂O fluxes was based on the static chamber-gas chromatographic method. The ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) gene copy numbers in different periods were measured by real-time polymerase chain reaction (PCR). The results indicated that rain-fed potato field was a N₂O source, and the average annual N₂O emission was approximately 0.46 ± 0.06 kgN₂O-N/ha/year. N₂O emissions increased significantly with increase in fertilisation, temperatures below 19.6 °C and soil volumetric water content under 15%. Crop rotation appreciably decreases N₂O emissions by 34.4 to 52.4% compared to continuous cropping in rain-fed potato fields. The significant correlation between N₂O fluxes and AOB copy numbers implied that N₂O emissions were primarily controlled by AOB in rain-fed potato fields. The research has important theoretical and practical value for understanding N₂O emissions from rain-fed dry farmland fields.

Effect of Environmental Variation on Estimating the Bacterial Species Richness

Estimating the species richness of microorganisms is of great importance in predicting, maintaining and managing microbial communities. Although the roles of environmental heterogeneity and geographical distance in structuring soil microbial communities have been studied intensively, the effects of environmental and spatial variation on the species richness estimation have not been examined. To this end, we have explored their effects on estimating the belowground soil bacterial species richness within a 50 ha forest dynamic plot (FDP) using a published massive sequencing dataset with intensive sampling scheme. Our resampling analyses showed that, for a given sequencing depth, increasing the sample size could significantly enhance the detection of rare species by capturing more of the environmental and spatial variation, thus obtaining higher observed and estimated species richness. Additionally, the estimates of bacterial species richness were significantly and positively correlated with environmental variation among samples, indicating that environmental filtering was the main mechanism driving the processes of community assembly for belowground soil bacterial communities in the plot. Moreover, this effect of environmental variation could be markedly alleviated when the sample size was higher than 450, and thus we predicted that there were at least 42,866 soil bacterial species based on 8,296,878 sequences from 550 samples in the whole 50 ha FDP. Furthermore, we built a power law environmental heterogeneity equation (EHE) as a decision-tool to determine an approximate sample size for comprehensively capturing the environmental gradient within a given habitat. Collectively, this work further links the inherent environmental and spatial variation to the estimation of soil bacterial species richness within a given region, and provides a useful tool of sampling design for a better understanding of microbial biogeographic patterns and estimation of microbial biodiversity.

Dynamic Response of Ammonia-Oxidizers to Four Fertilization Regimes across a Wheat-Rice Rotation System

Ammonia oxidation by microorganisms is a rate-limiting step of the nitrification process and determines the efficiency of fertilizer utilized by crops. Little is known about the dynamic response of ammonia-oxidizers to different fertilization regimes in a wheat-rice rotation system. Here, we examined ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities across eight representative stages of wheat and rice growth and under four fertilization regimes: no nitrogen fertilization (NNF), chemical fertilization (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilization (OF). The abundance and composition of ammonia oxidizers were analyzed using quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) of their amoA genes. Results showed that fertilization but not plant growth stages was the best predictor of soil AOB community abundance and composition. Soils fertilized with more urea-N had higher AOB abundance, while organic-N input showed little effect on AOB abundance. 109 bp T-RF (Nitrosospira Cluster 3b) and 280 bp T-RF (Nitrosospira Cluster 3c) dominated the AOB communities with opposing responses to fertilization regimes. Although the abundance and composition of the AOA community was significantly impacted by fertilization and plant growth stage, it differed from the AOB community in that there was no particular trend. In addition, across the whole wheat-rice rotation stages, results of multiple stepwise linear regression revealed that AOB played a more important role in ammonia oxidizing process than AOA. This study provided insight into the dynamic effects of fertilization strategies on the abundance and composition of ammonia-oxidizers communities, and also offered insights into the potential of managing nitrogen for sustainable agricultural productivity with respect to soil ammonia-oxidizers.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil

Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.

Microbial diversity in different compartments of an aquaponics system

Aquaponics is a solution for sustainable production of fish and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fish feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, biofilter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the first indications to functional groups of organisms in the different compartments of the aquaponic system. As other nitrifiers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitrospirae may perform the nitrification process in the biofilm.

The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand

An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg^-1), Zn (20 and 50 mg kg^-1), and Cd (2 and 10 mg kg^-1) were incubated for 14 days and then treated with 500 mg kg^-1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.