Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands

The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.

Long-term enclosure at heavy grazing grassland affects soil nitrification via ammonia-oxidizing bacteria in Inner Mongolia

Enclosure and grazing can significantly change the turnover of nitrogen in grassland soil. Changes of soil nitrogen mineralization and ammonium-oxidizing microorganisms caused by enclosure in different grazing intensities (about 30 years of grazing history) grassland, however, has rarely been reported. We selected the grassland sites with high and medium grazing intensity (HG and MG, 4 and 2 sheep ha^-1, respectively) and had them enclosed (45 × 55 m) in 2005 while outside the enclosure was continuously grazed year-round. A two factorial study was designed: grazing intensity (MG and HG sites) and enclosure (fence and non-fence). Nitrogen mineralization was detected through a laboratory incubation experiment. The abundance and community structure of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed using quantitative PCR (q-PCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning, and sequencing. Results showed that compared with MG site, at HG site the AOB abundance and community structure of AOB changed significantly while the AOA abundance and community structure did not change obviously. Enclosure significantly decreased the cumulative mineralized N, N mineralization rate, the abundance of AOB and the AOB community structure at the HG site, while at MG site, enclosure did not change these parameters. Potential nitrification rate (PNR) was positively correlated with the abundance of AOA and AOB at the MG and HG sites, respectively. The abundance of AOA was significantly correlated with soil pH; however, AOB abundance was significantly correlated with soil available N, total N, C/N ratio, pH, etc. The phylogenetic analysis showed that Nitrososphaeraceae and Nitrosomonadaceae were the dominant AOA and AOB, respectively. Totally, the responses of AOB and AOA mainly were associated to changes in soil physicochemical properties caused by different intensity grazing; AOB and AOA may be the dominant functional players in ammonia oxidation processes at HG and MG site, respectively.

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation

Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.

Effects of land use and climate on carbon and nitrogen pool partitioning in European mountain grasslands

European mountain grasslands are increasingly affected by land-use changes and climate, which have been suggested to exert important controls on grassland carbon (C) and nitrogen (N) pools. However, so far there has been no synthetic study on whether and how land-use changes and climate interactively affect the partitioning of these pools amongst the different grassland compartments. We analyzed the partitioning of C and N pools of 36 European mountain grasslands differing in land-use and climate with respect to above- and belowground phytomass, litter and topsoil (top 23 cm). We found that a reduction of management intensity and the abandonment of hay meadows and pastures increased above-ground phytomass, root mass and litter as well as their respective C and N pools, concurrently decreasing the fractional contribution of the topsoil to the total organic carbon pool. These changes were strongly driven by the cessation of cutting and grazing, a shift in plant functional groups and a related reduction in litter quality. Across all grasslands studied, variation in the impact of land management on the topsoil N pool and C/N-ratio were mainly explained by soil clay content combined with pH. Across the grasslands, below-ground phytomass as well as phytomass- and litter C concentrations were inversely related to the mean annual temperature; furthermore, C/N-ratios of phytomass and litter increased with decreasing mean annual precipitation. Within the topsoil compartment, C concentrations decreased from colder to warmer sites, and increased with increasing precipitation. Climate generally influenced effects of land use on C and N pools mainly through mean annual temperature and less through mean annual precipitation. We conclude that site-specific conditions need to be considered for understanding the effects of land use and of current and future climate changes on grassland C and N pools.

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns

A European transect was established, ranging from Sweden to the Azores, to determine the relative influence of geographic factors and agricultural small-scale management on the grassland soil microbiome. Within each of five countries (factor ‘Country’), which maximized a range of geographic factors, two differing growth condition regions (factor ‘GCR’) were selected: a favorable region with conditions allowing for high plant biomass production and a contrasting less favorable region with a markedly lower potential. Within each region, grasslands of contrasting management intensities (factor ‘MI’) were defined: intensive and extensive, from which soil samples were collected. Across the transect, ‘MI’ was a strong differentiator of fungal community structure, having a comparable effect to continental scale geographic factors (‘Country’). ‘MI’ was also a highly significant driver of bacterial community structure, but ‘Country’ was clearly the stronger driver. For both, ‘GCR’ was the weakest driver. Also at the regional level, strong effects of MI occurred on various measures of the soil microbiome (i.e. OTU richness, management-associated indicator OTUs), though the effects were largely regional-specific. Our results illustrate the decisive influence of grassland MI on soil microbial community structure, over both regional and continental scales, and, thus, highlight the importance of preserving rare extensive grasslands.

Seasonal changes in the abundance and activity of bacterial and fungal denitrifying communities associated with different compost amendments

Composts can be efficient organic amendments in potato culture as they can supply carbon and nutrients to the soil. However, more information is required to the effects of composts on denitrification and nitrous oxide emissions (N2O) and the emission-producing denitrifying communities. The effect of three compost amendments (municipal source separated organic waste compost (SSOC), forestry waste mixed with poultry manure compost (FPMC), and forestry residues compost (FRC)) on fungal and bacterial denitrifying communities and activity was examined in an agricultural field cropped to potatoes in during the fall, spring and summer seasons. The denitrification enzyme activity (DEA), N2O emissions and respiration were measured in parallel. N2O emission rates were greater in FRC-amended soils in the fall and summer, while soil respiration was highest in SSOC-amended soil in the fall. A large number of nirK denitrifying fungal transcripts was detected in the fall, coinciding with compost application while the greatest nirK bacterial transcripts were measured in the summer when plants were actively growing. Denitrifying community and transcript levels were poor predictors of DEA, N2O emissions or respiration rates in compost-amended soil. Overall, the sampling date was driving the population and activity levels of the three denitrifying communities under study.

Short term effects of climate change and intensification of management on the abundance of microbes driving nitrogen turnover in montane grassland soils

Montane grasslands in Europe are exposed to increasing temperatures twice as fast as the global average. Changes in climatic conditions are possibly accompanied by an increase in land use intensity, caused by a prolongation of the vegetation period and the need to improve productivity. Therefore, the investigation of combined effects of climate change and land use intensity is needed to further implement agricultural management strategies. Here we present results from a study performed in the pre-alpine region of southern Germany, where intact plant-soil mesocosms from grasslands, were translocated along an altitudinal gradient, resulting in an increase in soil temperature (moderate treatment: +0.5 K; strong treatment: +1.9 K warming) during the experimental period. Additionally, we applied an extensive or intensive agricultural management (two vs. five times of mowing and slurry application) on the transplanted mesocosms. After an exposure of one year, we measured plant growth and soil properties and quantified abundances of soil microorganisms catalyzing key steps in the nitrogen (N) cycle. Our data indicate, significant interactions between climate change and management. For example, microbial biomass was significantly reduced (-47.7% and -49.8% for C_mic and N_mic respectively), which was further accompanied by lower abundances of N₂-fixing bacteria (up to -89,3%), as well as ammonia oxidizing bacteria (-81.4%) under intensive management, whereas N-mineralizing bacteria increased in abundance (up to +139.8%) under extensive management. Surprisingly, the abundances of denitrifying bacteria as well as mean N₂O emissions were not affected by the treatments. Overall, our data suggest pronounced shifts in the abundance of microbes driving the N cycle in soil as a result of combined climate change and land use intensification already after a short simulation period of one year.

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil

Nitrate (NO₃^-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO₃^- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g^-1 h^-1and 2.4125-58.682 nmol N g^-1 h^-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO₃^- reduction, hence dominated NO₃^- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO₃^- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.

The effect of shrubland and grassland vegetation types on soil fauna and flora activities in a mountainous semi-arid landscape of Iran

The effect of vegetation types at mountainous sites on the relationships between soil biota and environmental variables applicable for the evaluation of soil quality and functions are barely studied and remain almost unknown. With the aim of studying the effect of shrubland and grassland plant coverings on soil fauna and flora activities, a mountainous semi-arid site in northern Iran (Diakooh) was selected for this research. Six vegetation types were selected with dominance in shrub and grassland coverage, i.e., (1) Crataegus microphylla CK. Koch., (2) Berberis integerrima Bunge, (3) Ribes uva-crispa L., (4) Prunus spinosa L., and with dominance in rangeland cover, i.e., (5) dominant Lecokia cretica (Lam.) DC., Orchis mascula L., Cardamine bulbifera (L.) Crantz, and (6) Fragaria vesca L. A total of 15 soil samples (30 × 30 × 10 cm) from each vegetation type were transferred to the laboratory. In addition, seasonal measurements (i.e. summer and autumn) were considered to achieve the temporal patterns of soil fauna and flora activities. Higher populations of soil earthworms (especially epigeic groups), acarina, collembola, nematode, and protozoa were found in the Crataegus site compared to other vegetation types with higher activities in the autumn season. Shrublands, especially with Crataegus cover, had increased activities of soil bacteria and fungi with higher abundances in the summer. Soils with higher fertility indicators and increased biota activities were attributed to the Crataegus and Berberis vegetation types by PCA. Overall, the findings of this study showed that shrubs can improve soil quality at high altitudes of mountainous, semi-arid sites that are often considered as especially fragile and sensitive ecosystems.

Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils

Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC_1:5) and NH₄-N compared to irrigation with freshwater, while NO₃-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO₃⁻N, and pH, while AOB communities were only significantly associated with NO₃⁻N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.