Nitrogen acquisition by plants and microorganisms in a temperate grassland

Influence of phenotypic variation of Paenibacillus polymyxa E681 on growth promotion in cucumbers

The goal of the current study is to better understand how bacteria may adapt to survive under adverse environmental conditions by altering and improving their phenotypes. In this study, we report the consequences of phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR), isolated from winter barley root that has a variety of advantageous effects on crop plants. In our previous study, two different types of bacterial cells in E681 were distinguished. We used the term F-type for the variant that doesn't produce endospores and B-type for the endospore-producing wild type. Under the circumstances of our experiment, the cucumber rhizosphere soil and the surface of the seeds produced phenotypic variance. On tryptic soy agar (TSA) plates, the B-type spontaneously converted into the F-type, but the reverse was not reversible. Intriguingly, the plant growth promotion test displayed that cucumber seedlings treated with F-type cells had characteristics resembling those of the untreated control. Whereas, growth promotion of cucumber seedlings treated with B-type depends on temperature conditions. In particular, an increased growth promotion was observed at a low temperature of 20°C. The phenotypic change from B-type to F-type did not occur at 20°C for 6 days in the growth curve analysis of E681, but it did occur on the fourth and second days at 30 and 37°C, respectively. Therefore, before using PGPR strains as a bacterial inoculant for sustainable agriculture, it is imperative to resolve phenotypic variance in these strains.

The effects of litter input and increased precipitation on soil microbial communities in a temperate grassland

Global warming has contributed to shifts in precipitation patterns and increased plant productivity, resulting in a significant increase in litter input into the soils. The enhanced litter input, combined with higher levels of precipitation, may potentially affect soil microbial communities. This study aims to investigate the effects of litter input and increased precipitation on soil microbial biomass, community structure, and diversity in a temperate meadow steppe in northeastern China. Different levels of litter input (0%, +30%, +60%) and increased precipitation (0%, +15%, +30%) were applied over a three-year period (2015-2017). The results showed that litter input significantly increased the biomass of bacteria and fungi without altering their diversity, as well as the ratio of bacterial to fungal biomass. Increased precipitation did not have a notable effect on the biomass and diversity of bacteria and fungi, but it did increase the fungal-to-bacterial biomass ratio. However, when litter input and increased precipitation interacted, bacterial diversity significantly increased while the fungal-to-bacterial biomass ratio remained unchanged. These findings indicate that the projected increases in litter and precipitation would have a substantial impact on soil microbial communities. In energy-and water-limited temperate grasslands, the additional litter inputs and increased precipitation contribute to enhanced nutrient and water availability, which in turn promotes microbial growth and leads to shifts in community structure and diversity.

Uneven distributions of unique species promoting N niche complementarity explain the stability of degraded alpine meadow

Alpine meadow degradation, usually involving decreased soil nitrogen (N) and patchy landscapes, is a challenge for natural restoration. However, the mechanism underlying plant species coexistence under degradation is unclear. In this study, we evaluated plant N niche complementarity in degraded alpine meadows on the Qinghai-Tibet Plateau using a 15N-labeling (15NO3-, 15NH4+, and 15N-glycine) experiment. At the community level, the concentration of 15NO3- in the degraded alpine meadow was 1.5 times higher than that in the undegraded alpine meadow; both alpine meadows had a significant preference for NO3- (60.72 % and 66.84 % for the degraded and undegraded alpine meadows, respectively), and the degree of glycine preference was significantly higher in the degraded alpine meadow (30.77 %) relative to the undegraded alpine meadow (21.85 %). At the species level, dominant species in both alpine meadows consistently preferred NO3-; the generalist species that can be found in both meadows and unique species of the two alpine meadows generally showed NO3- preferences, while the other plant species that were unevenly distributed in the degraded alpine meadow tended to show increased utilization of glycine, which could reduce N competition. We observed that differentiation among N sources and the uneven distribution of unique species may explain the stability of degraded alpine meadows. Our results suggested that uneven distributions of plants could have strong impacts on community stability and highlighted the importance of considering fine-scale analysis in studies of niche theory. This study has important implications for the restoration of degraded alpine meadows.

Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective

Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.

Organic amendments improved soil quality and reduced ecological risks of heavy metals in a long-term tea plantation field trial on an Alfisol

Tea plantation can cause strong soil degradation, e.g. acidification, basic nutrient decrease and microbial diversity loss, naturally by its root activity and secondary by practically tremendous synthetic N input. Organic amendments application is considered a practical way to mitigate the above adverse consequence. However, the trade-off between agronomic and environmental effects on the application of the organic amendments is still under debate. Herein, we conducted a long-term field experiment with four treatments, including control (without and fertiliser) (CK), chemical fertiliser treatment (CF), chicken manure treatment (CM) and chicken manure combined with biochar treatment (CMB) to investigate the effects of organic amendments application on soil quality, heavy metal contamination and tea production in a tea plantation. Totally 16 plots were arranged randomly with a completely randomised design. The results showed that CM and CMB treatments improved soil nutrient, mitigated soil acidification and ameliorated soil porosity compared to CF treatment. CMB treatment displayed a relatively high tea yield and quality in three consecutive years of monitoring. However, CM and CMB treatments elevated the heavy metal (HM) potential ecological risk (RI) and Nemerow's composite index (Ps). CM treatment significantly increased available As, Pb, Cu and Zn concentrations compared to CF treatment, while CMB treatment significantly decreased available Cr and Cu concentrations and slightly decreased available Cd, Pb and Ni concentrations compared to CM treatment. But the increase of available As and Zn in CMB treatment compared to CM treatment also indicated adverse effects of biochar addition. The PLS-PM model showed HM risk had direct negative effects on tea quality. Moreover, soil fungal community revealed positive effects on tea yield and negative effects on tea quality. Overall, our study proved that CMB treatment could improve soil quality, reduce available Cr and Ni concentrations, maintain tea yield and increase tea quality.

Deepened snow loosens temporal coupling between plant and microbial N utilization and induces ecosystem N losses

Seasonal differences in plant and microbial nitrogen (N) acquisition are believed to be a major mechanism that maximizes ecosystem N retention. There is also a concern that climate change may interrupt the delicate balance in N allocation between plants and microbes. Yet, convincing experimental evidence is still lacking. Using a ¹⁵ N tracer, we assessed how deepened snow affects the temporal coupling between plant and microbial N utilization in a temperate Mongolian grassland. We found that microbial ¹⁵ N recovery peaked in winter, accounting for 22% of the total ecosystem ¹⁵ N recovery, and then rapidly declined during the spring thaw. By stimulating N loss via N₂ O emission and leaching, deepened snow reduced the total ecosystem ¹⁵ N recovery by 42% during the spring thaw. As the growing season progresses, the ¹⁵ N released from microbial biomass was taken up by plants, and the competitive advantage for N shifted from microbes to plants. Plant ¹⁵ N recovery reached its peak in August, accounting for 17% of the total ecosystem ¹⁵ N recovery. The Granger causality test showed that the temporal dynamics of plant ¹⁵ N recovery can be predicted by microbial ¹⁵ N recovery under ambient snow but not under deepened snow. In addition, plant ¹⁵ N recovery in August was positively correlated with and best explained by microbial ¹⁵ N recovery in March. The lower microbial ¹⁵ N recovery under deepened snow in March reduced plant ¹⁵ N recovery by 73% in August. Together, our results provide direct evidence of seasonal differences in plant and microbial N utilization that are conducive to ecosystem N retention; however, deepened snow disrupted the temporal coupling between plant-microbial N use and turnover. These findings suggest that changes in snowfall patterns may significantly alter ecosystem N cycling and N-based greenhouse gas emissions under future climate change. We highlight the importance of better representing winter processes and their response to winter climate change in biogeochemical models when assessing N cycling under global change.

Acquisition pattern of nitrogen by microorganisms and plants affected by gravel mulch in a semiarid Tibetan grassland

As an important coarse inorganic fraction of soil, gravel may regulate the effects of the interaction between above- and belowground communities and affect the relationship between microorganisms and plants in alpine ecosystems. However, comparatively little is known about the effects of gravel on the acquisition pattern of nitrogen (N) by microorganisms and plants in alpine ecosystems. In this study, a ¹⁵N-labelling experiment was conducted to investigate the acquisition pattern of organic (¹⁵N-glycine) and inorganic N (¹⁵N-NO₃^- and ¹⁵N-NH₄⁺) by microorganisms and plants under three particle sizes of gravel mulch (fine: 2-10 mm, medium: 10-20 mm, coarse: 20-40 mm) on a semiarid Tibetan grassland. Gravel mulch significantly improved the ¹⁵N recovery of Stipa purpurea, but had no significant impacts on A. nanschanica. Therefore, gravel mulch decreased the ratio of microbial biomass ¹⁵N recovery to plant biomass ¹⁵N recovery for S. purpurea, but caused little effect on the state of N competition between plants and soil microbes for A. nanschanica. The N absorption preference of plants from both species shifted from an individual preference for ¹⁵N-NO₃^- in the natural (i.e., control) microplots to a common preference for ¹⁵N-NO₃^-and ¹⁵N-NH₄⁺ in the fine- and medium-sized gravel mulch microplots, while there were no significant differences in microbial N recovery between ¹⁵N-NO₃^- and ¹⁵N-NH₄⁺ across all treatments. The results helped to improve the understanding of the acquisition pattern of N by microorganisms and plants under the influence of gravel mulch in alpine ecosystems, and provide theoretical support for revegetation in alpine ecosystems in the future.

Niche partitioning in nitrogen uptake among subtropical tree species enhances biomass production

Nitrogen (N) is a main nutrient limiting plant growth in most terrestrial ecosystems, but so far it remains unknown which role plant N uptake plays for the positive relationship between species richness and productivity. An in situ¹⁵N labeling experiment was carried out by planting four subtropical tree species (i.e., Koelreuteria bipinnata, Lithocarpus glaber, Cyclobalanopsis myrsinaefolia and Castanopsis eyrei) in pots, at richness levels 1, 2 and 4 species per pot. Plant N uptake preference for inorganic N form of NO₃^- to NH₄⁺ and organic N form of glycine, as well as biomass and plant functional traits was evaluated under different tree species richness level. Overall, pot biomass productivity increased with tree species richness. Biomass of the most productive species, K. bipinnata increased, but not at the expense of a decreased growth of the other species. In mixtures, the species shifted their preference for the inorganic N form, from NO₃^- to NH₄⁺ or vice versa. The uptake preference for glycine remained stable along the species richness gradient. Plant N uptake was well correlated with numerous functional traits, both aboveground, such as height and shoot diameter, and belowground, such as root diameter and root length. We conclude that increased ecosystem biomass production with tree species richness could be largely explained by niche partitioning in N uptake among tree species. Our findings highlight that niche partitioning for N uptake should be a possible important mechanism maintaining species diversity and ecosystem production in subtropical forests.

Evaluating the environmental profiles of winter wheat rotation systems under different management strategies

Climate change poses a remarkable challenge to global food security, for which wheat is one of the main staple agricultural commodities. The cultivation of different varieties of winter wheat in Galicia (commercial and native) under rotation systems with potato, maize and oilseed rape was evaluated from an environmental point of view. The general approach of this study included the gathering of the inventory data of the different crops, the quantification of their environmental impacts and economic benefits, to identify the best land management system. Life Cycle Assessment (LCA) was used as environmental tool. The environmental profiles of each rotation system were reported in terms of nine impact categories. Crop rotations were analysed both per hectare and per € of gross margin, so that the information can be relevant to land-management decisions. Preference ranks were established based on an environmental normalized score for both units. The results suggest that arable operations contribute decisively to the environmental profile of the rotations. The avoided mineral fertilization processes, the carbon storage in the soil when returning straw to the field, as well as the electricity production clearly influence the environmental impact of the rotations. Scenarios that include native wheat under organic management are always the environmentally preferred ones while the preferred alternate crop depends on the reference unit. Concerning the margin gross, scenarios including the native variety report the highest profits, being the potato the preferred alternate crop. Further assessment needs to be undertaken to identify differences in the results of different ways of conducting LCA, i.e. attributional vs consequential approaches.

Advances in monitoring soil microbial community dynamic and function

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.

Agricultural practices to improve nitrogen use efficiency through the use of arbuscular mycorrhizae: Basic and agronomic aspects

Nitrogen cycling in agroecosystems is heavily dependent upon arbuscular mycorrhizal fungi (AMF) present in the soil microbiome. These fungi develop obligate symbioses with various host plant species, thus increasing their ability to acquire nutrients. However, AMF are particularly sensitive to physical, chemical and biological disturbances caused by human actions that limit their establishment. For a more sustainable agriculture, it will be necessary to further investigate which agricultural practices could be favorable to maximize the benefits of AMF to improve crop nitrogen use efficiency (NUE), thus reducing nitrogen (N) fertilizer usage. Direct seeding, mulch-based cropping systems prevent soil mycelium disruption and increase AMF propagule abundance. Such cropping systems lead to more efficient root colonization by AMF and thus a better establishment of the plant/fungal symbiosis. In addition, the use of continuous cover cropping systems can also enhance the formation of more efficient interconnected hyphal networks between mycorrhizae colonized plants. Taking into account both fundamental and agronomic aspects of mineral nutrition by plant/AMF symbioses, we have critically described, how improving fungal colonization through the reduction of soil perturbation and maintenance of an ecological balance could be helpful for increasing crop NUE.