Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

C:N:P stoichiometry of plants, soils, and microorganisms: Response to altered precipitation

Precipitation changes modify C, N, and P cycles, which regulate the functions and structure of terrestrial ecosystems. Although altered precipitation affects above- and belowground C:N:P stoichiometry, considerable uncertainties remain regarding plant-microbial nutrient allocation strategies under increased (IPPT) and decreased (DPPT) precipitation. We meta-analyzed 827 observations from 235 field studies to investigate the effects of IPPT and DPPT on the C:N:P stoichiometry of plants, soils, and microorganisms. DPPT reduced leaf C:N ratio, but increased the leaf and root N:P ratios reflecting stronger decrease of P compared with N mobility in soil under drought. IPPT increased microbial biomass C (+13%), N (+15%), P (26%), and the C:N ratio, whereas DPPT decreased microbial biomass N (-12%) and the N:P ratio. The C:N and N:P ratios of plant leaves were more sensitive to medium DPPT than to IPPT because drought increased plant N content, particularly in humid areas. The responses of plant and soil C:N:P stoichiometry to altered precipitation did not fit the double asymmetry model with a positive asymmetry under IPPT and a negative asymmetry under extreme DPPT. Soil microorganisms were more sensitive to IPPT than to DPPT, but they were more sensitive to extreme DPPT than extreme IPPT, consistent with the double asymmetry model. Soil microorganisms maintained stoichiometric homeostasis, whereas N:P ratios of plants follow that of the soils under altered precipitation. In conclusion, specific N allocation strategies of plants and microbial communities as well as N and P availability in soil critically mediate C:N:P stoichiometry by altered precipitation that need to be considered by prediction of ecosystem functions and C cycling under future climate change scenarios.

Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

Characteristics of soil N2O emission and N2O-producing microbial communities in paddy fields under elevated CO2 concentrations

The effects of elevated carbon dioxide (CO₂) concentration (e[CO₂]) on nitrous oxide (N₂O) emissions from paddy fields and the microbial processes involved in N₂O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N₂O in paddy soils. To better understand the dynamics of N₂O production under e[CO₂], a field experiment was conducted after five years of CO₂ fumigation based on three treatments: CK (ambient atmospheric CO₂), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N₂O fluxes, soil physicochemical properties, and N₂O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N₂O emissions decreased by 173% and 41% under the two e[CO₂] treatments during grain filling and milk ripening, respectively (P < 0.05). N₂O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N₂O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N₂O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N₂O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO₂], the abundance of nirK-type denitrifying bacteria significantly affected the N₂O flux (P < 0.05). Linear regression analysis showed that the N₂O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N₂O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO₂] suppressed N₂O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).

Partial substitution of manure reduces nitrous oxide emission with maintained yield in a winter wheat crop

Conventional fertilization of agricultural soils results in increased N₂O emissions. As an alternative, the partial substitution of organic fertilizer may help to regulate N₂O emissions. However, studies assessing the effects of partial substitution of organic fertilizer on both N₂O emissions and yield stability are currently limited. We conducted a field experiment from 2017 to 2021 with six fertilizer regimes to examine the effects of partial substitution of manure on N₂O emissions and yield stability. The tested fertilizer regimes, were CK (no fertilizer), CF (chemical fertilizer alone, N 300 kg ha^-1, P₂O₅ 150 kg ha^-1, K₂O 90 kg ha^-1), CF + M (chemical fertilizer + organic manure), CFR (chemical fertilizer reduction, N 225 kg ha^-1, P₂O₅ 135 kg ha^-1, K₂O 75 kg ha^-1), CFR + M (chemical fertilizer reduction + organic manure), and organic manure alone (M). Our results indicate that soil N₂O emissions are primarily regulated by soil mineral N content in arid and semi-arid regions. Compared with CF, N₂O emissions in the CF + M, CFR, CFR + M, and M treatments decreased by 16.8%, 23.9%, 42.0%, and 39.4%, respectively. The highest winter wheat yields were observed in CF, followed by CF + M, CFR, and CFR + M. However, the CFR + M treatment exhibited lower N₂O emissions while maintaining high yield, compared with CF. Four consecutive years of yield data from 2017 to 2021 illustrated that a single application of organic fertilizer resulted in poor yield stability and that partial substitution of organic fertilizer resulted in the greatest yield stability. Overall, partial substitution of manure reduced N₂O emissions while maintaining yield stability compared with the synthetic fertilizer treatment during the wheat growing season. Therefore, partial substitution of manure can be recommended as an optimal N fertilization regime for alleviating N₂O emissions and contributing to food security in arid and semi-arid regions.

Reference for different sensitivities of greenhouse gases effluxes to warming climate among types of desert biological soil crust

There is much uncertainty about how climate warming will impact greenhouse gases (GHG) budget in dry environments due to the lack of available data for desert biocrust soil. We implemented a 2.5-year field measurement of CO₂, CH₄ and N₂O effluxes in cyanobacteria-dominated, moss-dominated and mixed (cyanobacteria, moss and lichen) biocrust soils using open-top-chambers to simulate climate warming (1.2 °C on average). Desert biocrust soils generally acted as a weak sink of atmospheric CH₄ and N₂O. Although warming effects on daily CO₂, CH₄, and N₂O effluxes varied depending on sampling date and biocrust soil, there was no significant difference in daily, monthly and seasonal average CO₂, CH₄ and N₂O effluxes between warming and control in most cases for three biocrust soils. However, warming caused a marginal (p = 0.06) decrease (14.2%) in annual accumulative CO₂ efflux in moss-dominated biocrust soil due to the drought effects caused by warming indirectly and OTC sheltering of precipitation directly, while there was no significant difference between warming and control for cyanobacteria-dominated and mixed biocrust soils, implying a neutral response of GHG effluxes to climate warming. These results suggest that the GHG budget in arid desert biocrust soil would not be significantly changed in the warmer future when the direct negative effects of drought on CO₂ effluxes were excluded. Therefore, a marginal decrease of accumulative CO₂ effluxes in response to warming coupled with drought for moss-dominated biocrust soil might offer a weak negative feedback to warming and drier climate change pattern.

Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation

Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics-contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.

Predictive microbial-based modelling of wheat yields and grain baking quality across a 500km transect in Québec

Crops yield and quality are difficult to predict using soil physico-chemical parameters. Because of their key roles in nutrient cycles, we hypothesized that there is an untapped predictive potential in the soil microbial communities. To test our hypothesis, we sampled soils across 80 wheat fields of the province of Quebec at the beginning of the growing season in May-June. We used a wide array of methods to characterize the microbial communities, their functions, and activities, including: 1) amplicon sequencing, 2) real-time PCR quantification, and 3) community-level substrate utilization. We also measured grain yield and quality at the end of the growing season, and key soil parameters at sampling. The diversity of fungi, the abundance of nitrification genes, and the use of specific organic carbon sources were often the best predictors for wheat yield and grain quality. Using 11 or less parameters, we were able to explain 64 to 90% of the variation in wheat yield and grain and flour quality across the province of Quebec. Microbial-based regression models outperformed basic soil-based models for predicting wheat quality indicators. Our results suggest that the measurement of microbial parameters early in the season could help predict accurately grain quality and quantity.

Distinct patterns of abundant and rare subcommunities in paddy soil during wetting-drying cycles

Wetting-drying cycles typically result in a wide range of soil moistures and redox potentials (Eh) that significantly affect the soil microbial community. Although numerous studies have addressed the effects of soil moisture on soil microbial community structure and composition, the response of active microbes to the fluctuation in soil Eh is still largely unknown; this is especially true for the ecological roles of abundant and rare taxa. To explore the dynamics of active and total microbial communities in response to wetting-drying cycles, we conducted a microcosm experiment based on three wetting-drying cycles and 16S rRNA transcript (active) and 16S rRNA gene (total) amplicon sequencing. We found that both active and total microbial communities during three wetting-drying cycles were clustered according to the number of wetting-drying cycles (temporal factor) rather than soil moisture or Eh. Dynamics of the active microbial community, however, were redox dependent during the first wetting-drying cycle. In addition, rare taxa in the active microbial community exhibited more obvious differences than abundant ones during three wetting-drying cycles. Species turnover of abundant and rare taxa of total and active microbes, rather than species richness, explained the highest percentage of community variation. Rare taxa exhibited the most marked temporal turnover during three wetting-drying cycles. Members of Rhodospirillaceae were the major contributor to the resilience of abundant taxa of active microbes during the first wetting-drying cycle. Overall, these findings expand our current understanding of underlying assembly mechanisms of soil microbial communities responding to wetting-drying cycles.

Effects of cadmium on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings under elevated atmospheric CO2 scenarios

The individual impacts of elevated CO₂ and heavy metals on soil nitrification have been widely reported. However, studies on the combined effects of elevated CO₂ and heavy metals on soil nitrification are still limited. Here, a 135-day growth chamber experiment was conducted to investigate the impacts of elevated CO₂ and cadmium (Cd) levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. Elevated CO₂ combined with Cd pollution generally stimulated ammonia monooxygenase (AMO), hydroxylamine oxidase (HAO), and nitrite oxidoreductase (NXR) activities. Compared to the control, the abundance of ammonia-oxidizing bacteria (AOB) at day 135 and ammonia-oxidizing archaea (AOA) increased significantly (p < 0.05) and the abundance of AOB at days 45 and 90 and that of the nitrite-oxidizing bacteria (NOB) decreased under elevated CO₂ + Cd. Elevated CO₂ mostly led to a significant (p < 0.05) decrease in soil nitrification intensity in the rhizosphere of R. pseudoacacia exposed to Cd. The effects of Cd, CO₂, and their interaction on HAO and NXR activities were significant (p < 0.01). Soil pH, the C/N ratio, water-soluble organic carbon, water-soluble organic nitrogen (WSON), and total carbon were the dominant factors (p < 0.05) affecting nitrifying enzyme activities and nitrification intensity in rhizosphere soils. Elevated CO₂ clearly affected AOA, AOB, and NOB community structures and dominant genera by shaping C/N ratio, pH, and Cd and WSON contents in rhizosphere soils under Cd exposure. Overall, the responses of pH, C/N ratio, WSON, and Cd to elevated CO₂ led to changes in rhizosphere soil nitrification under the combination of elevated CO₂ and Cd pollution.

Paddy-upland rotation with Chinese milk vetch incorporation reduced the global warming potential and greenhouse gas emissions intensity of double rice cropping system

It is a common practice to maintain soil fertility based on the paddy-upland rotation with green manure in the subtropical region of China. However, rare studies are known about greenhouse gas (GHG) emissions from the paddy-upland rotation with green manure incorporation. Therefore, we conducted a field experiment of two years to compared with the effect of two kinds of green manure (CV: Chinese milk vetch and OR: Oilseed rape), and two kinds of cropping system (DR: double rice system and PR: paddy-upland rotation) on greenhouse gases emissions. We have found that the annual accumulation of CH₄ of Chinese milk vetch-rice-sweet potato || soybean was significantly reduced by 32.95%∼63.22% compared with other treatments, mainly because Chinese milk vetch reduced the abundance of methanogens by reducing soil C/N ratio. Meanwhile increasing soil permeability resulting from paddy-upland rotation also reduced soil CH₄ emission. However, The annual accumulation of N₂O of Chinese milk vetch-rice-sweet potato || soybean was increased by 17.39%∼870.11% compared with other treatments, mainly attributed to paddy-upland rotation decreased soil pH and nosZ abundance and increased nirK and nirS, thus enhancing N₂O emission, meanwhile the Chinese milk vetch incorporation and its interaction with the paddy-upland rotation has greatly enhanced the contents of NO₃^--N and abundance of ammonia-oxidizing archaea (AOA). The area-scaled global warming potential (GWP) and the biomass-scaled greenhouse gas emissions intensity (GHGI) of Chinese milk vetch-rice-sweet potato || soybean was reduced by 19.01%∼50.69% and 5.38%∼35.77% respectively. Thereby, the Chinese milk vetch-rice-sweet potato || soybean cropping system was suitable for agricultural sustainable development.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

Tuber melanosporum shapes nirS-type denitrifying and ammonia-oxidizing bacterial communities in Carya illinoinensis ectomycorrhizosphere soils

Background

NirS-type denitrifying bacteria and ammonia-oxidizing bacteria (AOB) play a key role in the soil nitrogen cycle, which may affect the growth and development of underground truffles. We aimed to investigate nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of Carya illinoinensis seedlings inoculated with the black truffle (Tuber melanosporum) during the early symbiotic stage.

Methods

The C. illinoinensis seedlings inoculated with or without T. melanosporum were cultivated in a greenhouse for six months. Next-generation sequencing (NGS) technology was used to analyze nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of these seedlings. Additionally, the soil properties were determined.

Results

The results indicated that the abundance and diversity of AOB were significantly reduced due to the inoculation of T. melanosporum, while these of nirS-type denitrifying bacteria increased significantly. Proteobacteria were the dominant bacterial groups, and Rhodanobacter, Pseudomonas, Nitrosospira and Nitrosomonas were the dominant classified bacterial genera in all the soil samples. Pseudomonas was the most abundant classified nirS-type denitrifying bacterial genus in ectomycorrhizosphere soils whose relative abundance could significantly increase after T. melanosporum inoculation. A large number of unclassified nirS-type denitrifying bacteria and AOB were observed. Moreover, T. melanosporum inoculation had little effect on the pH, total nitrogen (TN), nitrate-nitrogen (NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3−-N) and ammonium-nitrogen (NH\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{4}^{+}$\end{document}4+-N) contents in ectomycorrhizosphere soils. Overall, our results showed that nirS-type denitrifying bacterial and AOB communities in C. illinoinensis rhizosphere soils were significantly affected by T. melanosporum on the initial stage of ectomycorrhizal symbiosis, without obvious variation of soil N contents.

Rice straw biochar mitigated more N2O emissions from fertilized paddy soil with higher water content than that derived from ex situ biowaste

Biochar could mitigate greenhouse gas emissions, especially nitrous oxide (N₂O). Effects of interactions between different biochar and water content on N₂O emissions from rice (Oryza sativa L.) paddy soils have not been thoroughly understood. We evaluated effects of different biochar (derived from Camellia oleifera fruit shell, FS; spent mushroom substrate made of Camellia oleifera fruit shell, MS; rice straw, RS; at the rate of 40 g kg^-1) and water contents (70% and 120% water holding capacity, WHC) on N₂O emissions from rice paddy soil fertilized with nitrogen (N, 0.2 g kg^-1), and examined microbial functional genes associated with N₂O emissions to understand the underlining mechanisms. The results showed that RS biochar was higher in pH, available N, dissolved organic N, and decreased more N₂O emissions from soils with N and 120% WHC treatment relative to MS and FS biochar (by 363% and 200%, respectively). Although RS biochar potentially increased the abundance of ammonia-oxidizing archaea amoA gene (AOA), changes in functional gene abundance did not concur with decreases in N₂O emissions. Instead of changes in microbial communities, the relatively higher pH as well as lower available N and dissolved organic C and N of RS biochar could have contributed to the decrease in N₂O emissions compared with MS and FS biochar. Thereby, the in situ application of rice straw via biochar could be considered in the mitigation of N₂O emissions from fertilized rice paddy soil instead of biochar derived from ex situ feedstock.

Soil bacterial taxonomic diversity is critical to maintaining the plant productivity

Soil microbial communities play a central role in driving multiple ecosystem functions and ecological processes that are key to maintaining the plant productivity. However, we lack sound evidence for the linkage between soil microbial diversity and plant productivity, which hinders our ability to predict the consequences of microbial diversity loss for food security under the context of global environmental change. Here, we used the dilution-to-extinction approach to test the consequences of soil microbial diversity loss for the aboveground plant biomass in a glasshouse experiment. Compared with original soils, the bacterial alpha-diversity (Observed operational taxonomic units and Shannon index) significantly decreased in treatments with serially diluted inoculum. Principal coordinates analysis showed that the overall bacterial community compositions (beta-diversity) in original soils were clearly separated from the treatments with serially diluted inoculum. The aboveground biomass of lettuce harvested from the original soils was significantly higher than that from the sterilized soils regardless of the inoculation. The ordinary least squares regression model showed a significant linear relationship between the plant biomass and bacterial alpha-diversity, indicating that reduction in soil microbial diversity could result in a significant decline in the biomass of lettuce. No significant correlation was observed between plant biomass and soil processes including soil basal respiration and denitrification rates. Structural equation models suggested that the effects of soil microbial diversity on the plant biomass were maintained even when simultaneously accounting for other drivers (soil properties and biological processes). Our study provides experimental evidence that soil microbial diversity is important to the maintenance of the plant productivity and suggests that the functional redundancy in soil microbial communities may be overestimated especially in the agroecological system.

Divergent gross nitrogen transformation paths in the topsoil and subsoil between abandoned and agricultural cultivation land in irrigated areas

The nitrate concentration in groundwater has increased in many irrigated areas worldwide due to the excessive use of both water and fertilizers. Abandoned farmlands in such irrigated areas may alter the nitrogen (N) cycle because of drastically changed water and N inputs. However, the mechanisms of the N cycle in response to such changes remain unclear. We studied biogeochemical N cycling and microbiological responses from abandoned arable lands (AF), for the topsoil (20 cm depth) and subsoil (100 cm depth) layers, in comparison with irrigation-fertilization (control = CK) land, by using ¹⁵N tracing techniques, the 16S rRNA gene, and real-time PCR (qPCR) to reveal the mechanisms underpinning the N cycle. We found that the biogeochemical environment of abandoned soils shifted their N-cycling pathways. Except for reduced soil moisture, soil properties of total C and N, as well pH, showed improvement in the two layers of AF. But the microbial abundances of ammonia-oxidizing bacteria (AOB-amoA), archaea (AOA-amoA), bacteria and fungi were all significantly lower in the AF; and they presented a consistent trend in the subsoil of the two lands. Significant differences in gross N transformation rates were found for mineralization rates (M_N) and autotrophic nitrification rate (O_NH4) between lands or depths. Compared with AF, M_N was increased by 1.45- and 11.75-times, and O_NH4 by 1.69- and 2.89-times in the topsoil and subsoil of CK, respectively. Our results suggest that the SM × C/N interaction provides insight into the mechanisms underlying the soil microbe-driven changes to transformation rates in nitrogen dynamics after abandoning water-limited lands. The high moisture and N inputs reported here highlight the dynamics and prevalence of M_N and O_NH4, and an increasing the nitrate leaching rate in the unsaturated zone, which poses a major threat to groundwater quality.

Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes

Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.

IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

Spatial patterns in soil physicochemical and microbiological properties in a grassland adjacent to a newly built lake

Soil water content (SWC) is an important determinant for nutrient cycling and microorganism activity in the grassland ecosystem. Lakes have a positive effect on the water supply of the neighboring ecosystem. However, information evaluating whether newly built lakes improve the physiochemical properties and microorganism activity of adjacent grassland soil is rare. A 15‐hectare artificial lake with a 2 m depth was built on grazed grassland to determine whether the change of soil physiochemical properties and microorganism activity of the adjacent grassland depended on the distance from the lake. SWC and total nitrogen (TN) were greater within 150 m of the lake than at distances over 150 m from the lake. The total organic carbon (TOC) increased first at 100–150 m from the lake and then decreased. The soil microbial biomass and the bacterial and fungal contents increased with increasing years after the construction of the lake. Gram‐negative bacteria and methanotrophic bacteria were greater within a 30 m distance of the lake. Over 60 m away from the lake, Actinobacteria, gram‐positive bacteria, and anaerobic bacteria showed higher abundances. In the area near the lake (<250 m distance), microorganisms were strongly correlated with SWC, EC, TN, and TOC and greatly correlated with the changes of total phosphorous (TP) and pH when the distance from the lake was over 250 m. The results indicated that the newly built lake could be a driving factor for improving the physiochemical properties and microorganism activity of adjacent grassland soil within a certain range.

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop

Rising global air temperature and atmospheric CO₂ are expected to have considerable effects on soil nutrient cycling and plant productivity. Soil nitrification controlled by ammonia-oxidizing bacteria and archaea (AOB and AOA) communities plays a key role in contributing to plant nitrogen (N) availability; however, response of soil nitrification and functional microbial communities to climate change and subsequent consequences for crop yields remain largely unknown. Cotton productivity is a function of temperature and N availability under well-watered conditions. In general, cotton growth responds positively to elevated CO₂, but simultaneous warming may offset benefits of rising CO₂. In this study, cotton was used as a model system to elucidate the short-term response of soil nitrification and ammonia-oxidizing communities to elevated temperature and elevated CO₂ using field-based environmentally-controlled chambers. Elevated temperature (ambient + 1.1 °C) altered the AOA community, while elevated temperature and elevated CO₂ (ambient + 132 ppm) significantly increased soil nitrification rate and shifted AOB and AOA communities, but these effects depended on cotton developmental stages. Ammonia-oxidizing community abundance and structure were statistically correlated with nitrifying activity. Our findings suggest that climate change will positively affect soil nitrifying communities, leading to an increase in process rates and subsequent N availability, which is directly linked to crop productivity.

Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest

Acid rain can cause severe effects on soil biota and nutrient biogeochemical cycles in the forest ecosystem, but how plant-symbiotic ectomycorrhizal fungi will modulate the effects remains unknown. Here, we conducted a full factorial field experiment in a Masson pine forest by simultaneously controlling the acidity of the simulated rain (pH 5.6 vs. pH 3.5) and the ectomycorrhizal fungi Pisolithus tinctorius inoculation (non-inoculation vs. inoculation), to investigate the effects on ammonia oxidizers and denitrifiers. After 10 months, compared with the control (rain pH 5.6, and non-inoculation), simulated acid rain (pH 3.5) reduced soil nutrient content, decreased archaeal amoA gene abundance and inhibited denitrification enzyme activity. Also, simulated acid rain altered the community compositions of all the examined functional genes (archaeal amoA, bacterial amoA, nirK, nirS and nosZ). However, inoculation with ectomycorrhizal fungi under acid rain stress recovered soil nutrient content, archaeal amoA gene abundance and denitrification enzyme activity to levels comparable to the control, suggesting that ectomycorrhizal fungi inoculation ameliorates simulated acid rain effects. Taken together, ectomycorrhizal fungi inoculation - potentially through improving soil substrate availability - could alleviate the deleterious effects of acid rain on nitrogen cycling microbes in forest soils.

Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.

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

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

Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau

Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime

Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6 years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change.

Legacy effects of simulated short-term climate change on ammonia oxidisers, denitrifiers, and nitrous oxide emissions in an acid soil

Although the effect of simulated climate change on nitrous oxide (N₂O) emissions and on associated microbial communities has been reported, it is not well understood if these effects are short-lived or long-lasting. Here, we conducted a field study to determine the interactive effects of simulated warmer and drier conditions on nitrifier and denitrifier communities and N₂O emissions in an acidic soil and the longevity of the effects. A warmer (+2.3 °C) and drier climate (-7.4% soil moisture content) was created with greenhouses. The variation of microbial population abundance and community structure of ammonia-oxidizing archaea (AOA), bacteria (AOB), and denitrifiers (nirK/S, nosZ) were determined using real-time PCR and high-throughput sequencing. The results showed that the simulated warmer and drier conditions under the greenhouse following urea application significantly increased N₂O emissions. There was also a moderate legacy effect on the N₂O emissions when the greenhouses were removed in the urea treatment, although this effect only lasted a short period of time (about 60 days). The simulated climate change conditions changed the composition of AOA with the species affiliated to marine group 1.1a-associated lineage increasing significantly. The abundance of all the functional denitrifier genes decreased significantly under the simulated climate change conditions and the legacy effect, after the removal of greenhouses, significantly increased the abundance of AOB, AOA (mainly the species affiliated to marine group 1.1a-associated lineage), and nirK and nosZ genes in the urea-treated soil. In general, the effect of the simulated climate change was short-lived, with the denitrifier communities being able to return to ambient levels after a period of adaptation to ambient conditions. Therefore, the legacy effect of simulated short-time climate change conditions on the ammonia oxidizer and denitrifier communities and N₂O emissions were temporary and once the conditions were removed, the microbial communities were able to adapt to the ambient conditions.

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N₂O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C₂H₂) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N₂O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C₂H₂ were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N₂O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N₂O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C₂H₂ was more effective in reducing N₂O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N₂O emission and net nitrification rate, was more inhibited by C₂H₂ than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C₂H₂) could potentially alter N₂O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.

Nitrification Is a Primary Driver of Nitrous Oxide Production in Laboratory Microcosms from Different Land-Use Soils

Most studies on soil N2O emissions have focused either on the quantifying of agricultural N2O fluxes or on the effect of environmental factors on N2O emissions. However, very limited information is available on how land-use will affect N2O production, and nitrifiers involved in N2O emissions in agricultural soil ecosystems. Therefore, this study aimed at evaluating the relative importance of nitrification and denitrification to N2O emissions from different land-use soils and identifying the potential underlying microbial mechanisms. A (15)N-tracing experiment was conducted under controlled laboratory conditions on four agricultural soils collected from different land-use. We measured N2O fluxes, nitrate ([Formula: see text]), and ammonium ([Formula: see text]) concentration and (15)N2O, (15)[Formula: see text], and (15)[Formula: see text] enrichment during the incubation. Quantitative PCR was used to quantify ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results showed that nitrification was the main contributor to N2O production in soils from sugarcane, dairy pasture and cereal cropping systems, while denitrification played a major role in N2O production in the vegetable soil under the experimental conditions. Nitrification contributed to 96.7% of the N2O emissions in sugarcane soil followed by 71.3% in the cereal cropping soil and 70.9% in the dairy pasture soil, while only around 20.0% of N2O was produced from nitrification in vegetable soil. The proportion of nitrified nitrogen as N2O (PN2O-value) varied across different soils, with the highest PN2O-value (0.26‰) found in the cereal cropping soil, which was around 10 times higher than that in other three systems. AOA were the abundant ammonia oxidizers, and were significantly correlated to N2O emitted from nitrification in the sugarcane soil, while AOB were significantly correlated with N2O emitted from nitrification in the cereal cropping soil. Our findings suggested that soil type and land-use might have strongly affected the relative contribution of nitrification and denitrification to N2O production from agricultural soils.

Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N2O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a (15)N tracing and (13)CO2-DNA-stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N2O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The (15)N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The (13)CO2-DNA-SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of (13)CO2 into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter.

IMPORTANCE

The combination of the (15)N tracing model and (13)CO2-DNA-SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.

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

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

Copper pollution decreases the resistance of soil microbial community to subsequent dry-rewetting disturbance

Dry-rewetting (DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown. Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils (fluvo-aquic soil and red soil) under three copper concentrations (zero, medium and high). Results showed that the fluctuations of substrate induced respiration (SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration (RS-SIR) were highest in non-copper-stressed (zero) soils. Structural equation model (SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in non-copper-stressed soil compared to the other two copper-stressed (medium and high) soils, which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance.

The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors

Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75–1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray–Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors.

Quantitative microbial ecology through stable isotope probing

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem

The Grain to Green Project (GGP) is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha) of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L.) or shrubs (Caragana korshinskii Kom.). In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.). A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.