Long‐term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production

Organic management pattern improves microbial community diversity and alters microbial network structure in karst tea plantation

Soil microbiomes play a crucial role in enhancing plant growth, health, and overall agricultural productivity. Nevertheless, the influence of distinct agricultural management practices on the microbial diversity and community structure within tea (Camellia sinensis) plantations has remained enigmatic. This study postulates that organic agricultural management models can enhance microbial diversity and optimise the microbial community structure within tea plantations, indirectly augmenting soil fertility and tea quality. We employed metagenome technology and conducted molecular ecological network analysis to explore the impact of organic management, pollution-free management, and conventional management on the microbial network structure of tea plantation soil in Weng'an County in the southwestern karst region. Soils subjected to organic management exhibited a higher relative abundance of soil microbial and carbohydrate-active enzyme functional genes than those subjected to other management regimes. Additionally, the relative abundance and diversity of dominant bacteria and keystone species were notably higher under organic management than under the other management regimes. Correlation analysis showed that soil microorganisms were closely related to soil fertility and tea quality, respectively. One-way analysis of variance and the structural equation modelling results showed significant variability in soil fertility under the three agricultural management modes and that soil fertility and soil microbial diversity had a direct impact on tea quality (P > 0.05). In conclusion, this study underscores the profound impact of management modes on microbial diversity and community structure within tea plantations. These management practices alter the soil microbial network structure and potential function, ultimately regulating the microecological dynamics of the soil community in tea plantations.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Improvement and the relationship between chemical properties and microbial communities in secondary salinization of soils induced by rotating vegetables

Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.

Fungal community diversity and their contribution to nitrogen cycling in in-situ aerated landfills: Insights from field and laboratory studies

The application of in-situ aeration technology in landfills has been reported to promote fungal growth, but the community diversity and function of fungi in the aerated landfill system remain unknown. This study firstly investigated an in-situ aerated remediation landfill site to characterize the fungal community diversity in refuse. And to further reveal the fungal involvement in the nitrogen cycling system, laboratory-scale simulated aerated landfill reactors were then constructed. The results in the aerated landfill site showed a significant correlation between fungal community structure and ammonia nitrogen content in the refuse. Dominant fungi in the fungal community included commonly found environmental fungi such as Fusarium, Aspergillus, Gibberella, as well as unique fungi in the aerated system like Chaetomium. In the laboratory-scale aerated landfill simulation experiments, the fungal system was constructed using bacterial inhibitor, and nitrogen balance analysis confirmed the significant role of fungal nitrification in the nitrogen cycling process. When ammonia nitrogen was not readily available, fungi converted organic nitrogen to nitrate, serving as the main nitrification mechanism in the system, with a contribution rate ranging from 62.71 % to 100 % of total nitrification. However, when ammonia nitrogen was present in the system, autotrophic nitrification became the main mechanism, and the contribution of fungal nitrification to total nitrification was only 15.96 %. Additionally, fungi were capable of directly utilizing nitrite for nitrate production with a rate of 4.65 mg L-1 d-1. This research article contributes to the understanding of the importance of fungi in the aerated landfill systems, filling a gap in knowledge.

Manure application maintained the CO2 fixation activity of soil autotrophic bacteria but changed its ecological characteristics in an entisol of China

The response of soil autotrophs to anthropogenic activities has attracted increasing attention against the background of global change. Here, three entisol plots under different fertilizing regimes, including no fertilization (CK), manure (M), and a combined application of chemical fertilizer and manure (NPKM) were selected, and then the soil RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity and cbbl (gene encoding the large subunit of RubisCO) composition were measured to indicate the activity and community of autotrophic bacteria, respectively. The results revealed that the RubisCO activity of CK showed no difference from that of M but was significantly higher than that of NPKM. The CK and M had the lowest and highest soil cbbl abundance, respectively. The α-diversity of soil cbbl-carrying bacteria showed no significant difference among these treatments, whereas they showed significantly different community structures of cbbl-carrying bacteria. Meanwhile, compared with CK, M had significantly lower abundances of bacterial species with the functions of nitrogen fixation (Azoarcus sp.KH32C) or detoxification (Methylibium petroleiphilum), indicating that manure application might have an inhibiting potential to some beneficial autotrophic bacterial species in this entisol.

The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers

Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.

Insight into biofilm formation of wastewater treatment processes: Nitrogen removal performance and biological mechanisms

Biofilm formation affects biological nitrogen (N) removal, and a sequencing batch biofilm reactor (SBBR) was set up to evaluate the changes in N removal and microbial characteristics during biofilm formation. The results indicated that the average effluent concentration of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N) and total nitrogen (TN) in the SBBR were 27.48, 1.41, and 13.52 mg L-1, respectively after biofilm formation. Furthermore, this process increased microbial richness, but reduced microbial diversity. Patescibacteria, Proteobacteria, and Bacteroides were the dominant phyla that did not change after biofilm formation. After biofilm formation, Firmicutes was eliminated while Spirochaetes involved in the interspecies relationship. Biofilm increased the nitrification and denitrification relating coding genes abundance (hao, narG, narZ, nxrA, narH, narY, nxrB, napA, napB, norB, norC and nosZ), and enhanced the processes of N respiration and denitrification, carbohydrate metabolism, amino acid metabolism and membrane transport. Meanwhile, correlation analysis between genera and transcriptome reflected that Zooglea, Micropruina, Aeromonas and Tessaracoccus played essential roles in biofilm formation and N removal. The key enzyme abundance of EC:1.7.99.1, EC:1.7.2.4, and EC:1.1.1.42 of N and tricarboxylic acid (TCA) cycle increased after biofilm formation. This study can reveal the effect of biofilm formation on biological N removal and provide a theoretical foundation for the application of biofilm process.

Effects of nitrogen stress and nitrogen form ratios on the bacterial community and diversity in the root surface and rhizosphere of Cunninghamia lanceolata and Schima superba

Background

The bacterial communities of the root surface and rhizosphere play a crucial role in the decomposition and transformation of soil nitrogen (N) and are also affected by soil N levels and distribution, especially the composition and diversity, which are sensitive to changes in the environment with high spatial and temporal heterogeneity of ammonium N (NH4 +-N) and nitrate N (NO3 --N).

Methods

One-year-old seedlings of Cunninghamia lanceolata and Schima superba were subjected to N stress (0.5 mmol L-1) and normal N supply (2 mmol L-1), and five different N form ratios (NH4 +-N to NO3 --N ratio of 10:0, 0:10, 8:2, 2:8, and 5:5) were created. We analyze the changes in composition and diversity of bacteria in the root surface and rhizosphere of two tree species by high-throughput sequencing.

Results

Differences in the composition of the major bacteria in the root surface and rhizosphere of C.lanceolata and S. superba under N stress and N form ratios were not significant. The dominant bacterial phyla shared by two tree species included Proteobacteria and Bacteroidota. Compared to normal N supply, the patterns of diversity in the root surface and rhizosphere of two tree species under N stress were distinct for each at five N form ratios. Under N stress, the bacterial diversity in the root surface was highest at NH4 +-N to NO3 --N ratio of 10:0 of C. lanceolata, whereas in the root surface, it was highest at the NH4 +-N to NO3 --N ratio of 0:10 of S. superba. The NH4 +-N to NO3 --N ratio of 5:5 reduced the bacterial diversity in the rhizosphere of two tree species, and the stability of the bacterial community in the rhizosphere was decreased in C. lanceolata. In addition, the bacterial diversity in the root surface was higher than in the rhizosphere under the N stress of two tree species.

Conclusion

The bacterial compositions were relatively conserved, but abundance and diversity changed in the root surface and rhizosphere of C. lanceolata and S. superba under N stress and different N form ratios. The heterogeneity of ammonium and nitrate N addition should be considered for N-stressed environments to improve bacterial diversity in the rhizosphere of two tree species.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Short- and long-term effects of continuous compost amendment on soil microbiome community

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R² = 0.15, P < 0.001) and rare (R² = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.05, P < 0.05) and nitrogen (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

The effect of wheat genotype on the microbiome is more evident in roots and varies through time

Crop breeding has traditionally ignored the plant-associated microbial communities. Considering the interactions between plant genotype and associated microbiota is of value since different genotypes of the same crop often harbor distinct microbial communities which can influence the plant phenotype. However, recent studies have reported contrasting results, which led us to hypothesize that the effect of genotype is constrained by growth stages, sampling year and plant compartment. To test this hypothesis, we sampled bulk soil, rhizosphere soil and roots of 10 field-grown wheat genotypes, twice per year, for 4 years. DNA was extracted and regions of the bacterial 16 S rRNA and CPN60 genes and the fungal ITS region were amplified and sequenced. The effect of genotype was highly contingent on the time of sampling and on the plant compartment sampled. Only for a few sampling dates, were the microbial communities significantly different across genotypes. The effect of genotype was most often significant for root microbial communities. The three marker genes used provided a highly coherent picture of the effect of genotype. Taken together, our results confirm that microbial communities in the plant environment strongly vary across compartments, growth stages, and years, and that this can mask the effect of genotype.

Combination of Aspergillus niger MJ1 with Pseudomonas stutzeri DSM4166 or mutant Pseudomonas fluorescens CHA0-nif improved crop quality, soil properties, and microbial communities in barrier soil

Soil salinization and acidification seriously damage soil health and restricts the sustainable development of planting. Excessive application of chemical fertilizer and other reasons will lead to soil acidification and salinization. This study focus on acid and salinized soil, investigated the effect of phosphate-solubilizing bacteria, Aspergillus niger MJ1 combined with nitrogen-fixing bacteria Pseudomonas stutzeri DSM4166 or mutant Pseudomonas fluorescens CHA0-nif on crop quality, soil physicochemical properties, and microbial communities. A total of 5 treatments were set: regular fertilization (T1), regular fertilization with MJ1 and DSM4166 (T2), regular fertilization with MJ1 and CHA0-nif (T3), 30%-reducing fertilization with MJ1 and DSM4166 (T4), and 30%-reducing fertilization with MJ1 and CHA0-nif (T5). It was found that the soil properties (OM, HN, TN, AP, AK, and SS) and crop quality of cucumber (yield production, protein, and vitamin C) and lettuce (yield production, vitamin C, nitrate, soluble protein, and crude fiber) showed a significant response to the inoculated strains. The combination of MJ1 with DSM4166 or CHA0-nif influenced the diversity and richness of bacterial community in the lettuce-grown soil. The organismal system-, cellular process-, and metabolism-correlated bacteria and saprophytic fungi were enriched, which were speculated to mediate the response to inoculated strains. pH, OM, HN, and TN were identified to be the major factors correlated with the soil microbial community. The inoculation of MJ1 with DSM4166 and CHA0-nif could meet the requirement of lettuce and cucumber growth after reducing fertilization in acid and salinized soil, which provides a novel candidate for the eco-friendly technique to meet the carbon-neutral topic.

Effects of nitrogen input on soil bacterial community structure and soil nitrogen cycling in the rhizosphere soil of Lycium barbarum L

Lycium barbarum L., goji berry, is a precious traditional Chinese medicine and it is homology of medicine and food. Its growth is heavily dependent on nitrogen. The use of chemical fertilizers has significantly promoted the yield of goji berry and the development of the L. barbarum L. industry. However, crop plants are inefficient in the acquisition and utilization of applied nitrogen, it often leads to excessive application of nitrogen fertilizers by producers, which cause negatively impact to the environment ultimately. The exploration of an interaction model which deals with crops, chemical fertilizers, and rhizosphere microbes to improve nitrogen use efficiency, is, therefore, an important research objective to achieve sustainable development of agriculture greatly. In our study, we explored the effects of nitrogen input on soil microbial community structure, soil nitrogen cycling, and the contents of nutrients in L. barbarum fruits. The structure and composition of the bacterial community in the rhizosphere soil of L. barbarum were significantly different under different nitrogen supply conditions, and high nitrogen addition inhibited the diversity and stability of bacterial communities. Low nitrogen input stimulated the relative abundance of ammonia-oxidizing bacteria (AOB), such as Nitrosospira, catalyzing the first step of the ammonia oxidation process. The results of the GLMM model showed that the level of nitrogen fertilizer (urea) input, the relative abundance of AOB, the relative abundance of Bradyrhizobium, and their combinations had significant effects on the soil nitrogen cycling and contents of nutrients in L. barbarum fruits. Therefore, we believe that moderately reducing the use of urea and other nitrogen fertilizers is more conducive to improving soil nitrogen use efficiency and Goji berry fruit quality by increasing the nitrogen cycling potential of soil microorganisms.

The neglected role of micronutrients in predicting soil microbial structure

Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9-17% in predicting the structure of soil microbial communities with up to 69-78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.

Soil microbes and associated extracellular enzymes largely impact nutrient bioavailability in acidic and nutrient poor grassland ecosystem soils

Understanding the role of soil microbes and their associated extracellular enzymes in long-term grassland experiments presents an opportunity for testing relevant ecological questions on grassland nutrient dynamics and functioning. Veld fertilizer trials initiated in 1951 in South Africa were used to assess soil functional microbial diversity and their metabolic activities in the nutrient-poor grassland soils. Phosphorus and liming trials used for this specific study comprised of superphosphate (336 kg ha⁻¹) and dolomitic lime (2250 kg ha⁻¹) (P + L), superphosphate (336 kg ha⁻¹) (+ P) and control trials. These soils were analyzed for their nutrient concentrations, pH, total cations and exchange acidity, microflora and extracellular enzyme activities. The analysed soil characteristics showed significant differences except nitrogen (N) and organic carbon (C) concentrations showing no significant differences. P-solubilizing, N-cycling and N-fixing microbial diversity varied among the different soil treatments. β-glucosaminidase enzyme activity was high in control soils compared to P-fertilized and limed soils. Alkaline phosphatase showed increased activity in P-fertilized soils, whereas acid phosphatase showed increased activity in control soils. Therefore, the application of superphosphate and liming influences the relative abundance of bacterial communities with nutrient cycling and fixing functions which account for nutrient bioavailability in acidic and nutrient stressed grassland ecosystem soils.

Impact of Drip Irrigation and Nitrogen Fertilization on Soil Microbial Diversity of Spring Maize

Given the shortage of water resources and excessive application of nitrogen fertilizers in irrigated areas, we explored the effect of water−nitrogen coupling on soil microbial diversity in maize fields irrigated using shallow buried droppers. A field experiment (split-plot design) was used with irrigation amounts set at 40%, 50%, and 60% of the conventional amount; furthermore, 13 water and nitrogen coupling treatments were designed. The secondary area was the nitrogen application level, corresponding to 50%, 70%, and the original conventional application amounts. The results showed that the effect of irrigation amount on bacterial community composition was greater than that of nitrogen, whereas the effect of nitrogen on fungi was greater than that on bacteria. No significant difference was detected in the α diversity index or species richness of bacteria and fungi. Available phosphorus and organic carbon contents significantly correlated with the community structure of soil bacteria (p < 0.05). The relative abundances of bacteria and fungi were stable with the decrease of nitrogen application rate at the irrigation rate of 2000 m3 ha−1. With the decrease of irrigation amount, the relative abundance of bacteria and fungi was stable under the treatment of 210 kg ha−1 nitrogen fertilizer. Moreover, the relative abundance of nitrogen-fixing bacteria related to the nitrogen cycle was increased by irrigation of 2000 m3 ha−1 and nitrogen application of 210 kg ha−1. Moderate reduction of subsequent N supply should be as a prior soil management option in a high N input agroecosystem.

High-resolution shotgun metagenomics: the more data, the better?

In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.

Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens

During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.

Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils

The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH₄ ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH₄ emissions from paddy fields.

Landscape Composition and Soil Physical-Chemical Properties Drive the Assemblages of Bacteria and Fungi in Conventional Vegetable Fields

The soil microbiome is crucial for improving the services and functioning of agroecosystems. Numerous studies have demonstrated the potential of soil physical–chemical properties in driving the belowground microbial assemblages in different agroecosystems. However, not much is known about the assemblage of bacteria and fungi in response to soil physical–chemical properties and the surrounding landscape composition in different vegetable fields of a highly intensive agricultural system. Here, we investigated the effects of soil physical–chemical properties and landscape composition on the community trends of bacteria and fungi in two different soil compartments (bulk and rhizospheric soils) of two different brassica crop types (Chinese cabbage and flower cabbage). The results revealed that bulk soil had a higher alpha diversity of both bacteria and fungi than rhizospheric soil. Each of the soil physical–chemical properties and landscape compositions contributed differently to driving the community structure of distinct bacterial and fungal taxa in both soil compartments and crop types. The higher proportions of forest, grassland, and cultivated land, along with the higher amount of soil calcium in flower cabbage fields, promote the assemblage of Gammaproteobacteria, Actinobacteria, Oxyophotobacteria, Agaricomycetes, and Eurotiomycetes. On the other hand, in Chinese cabbage fields, the increased amounts of iron, zinc, and manganese in the soil together with higher proportions of non-brassica crops in the surrounding landscape strongly support the assemblage of Deltaproteobacteria, Gemmatimonadetes, Bacilli, Clostridia, Alphaproteobacteria, an unknown bacterial species Subgroup-6, Mortierellomycetes, Rhizophlyctidomycetes, and Chytridiomycetes. The findings of this study provide the most comprehensive, comparative, and novel insights related to the bacterial and fungal responses in a highly intensive vegetable growing system for the improvement of the soil fertility and structure. These are important clues for the identification of key bacteria and fungi contributing to the plant–environment interactions and are of a practical significance for landscape-based ecological pest management.

Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.

Phosphorus Fertilizers from Sewage Sludge Ash and Animal Blood as an Example of Biobased Environment-Friendly Agrochemicals: Findings from Field Experiments

Wastes of biological origin from wastewater treatment systems and slaughterhouses contain substantial amounts of phosphorus (P) with high recovery potential and can contribute to alleviating the global P supply problem. This paper presents the performance of fertilizer (AF) and biofertilizer (BF) from sewage sludge ash and animal blood under field conditions. BF is AF incorporated with lyophilized cells of P-solubilizing bacteria, Bacillus megaterium. In the experiments with spring or winter wheat, the biobased fertilizers were compared to commercial P fertilizer, superphosphate (SP). No P fertilization provided an additional reference. Fertilizer effects on wheat productivity and on selected properties of soil were studied. BF showed the same yield-forming efficiency as SP, and under poorer habitat conditions, performed slightly better than AF in increasing yield and soil available P. Biobased fertilizers applied at the P rate up to 35.2 kg ha^-1 did not affect the soil pH, did not increase As, Cd, Cr, Ni, and Pb content, and did not alter the abundance of heterotrophic bacteria and fungi in the soil. The findings indicate that biobased fertilizers could at least partially replace conventional P fertilizers. Research into strain selection and the proportion of P-solubilizing microorganisms introduced into fertilizers should be continued.

Microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows

Unbalanced fertilization of nutritional elements is a potential threat to environmental quality and agricultural productivity in acid soil. Harnessing keystone taxa in soil microbiome represents a promising strategy to enhance crop productivity as well as reducing the adverse environmental effects of fertilizers, with the goal of agricultural sustainability. However, there is a lack of information on which and how soil microbial keystone taxa contribute to sustainable crop productivity in acid soil. Here, we examined soil microbial communities (including bacteria, fungi, and archaea) and soil nutrients, and the mineral nutrition and yield of maize subjected to different inorganic and organic fertilization treatments over 35 years in acid soil. The application of organic fertilizer alone or in combination with inorganic fertilizers sustained high maize yield when compared with the other fertilization treatments. Microbial abundances and community structures rather than their alpha diversities explained the main variation in maize yield among different treatments. Sixteen soil keystone taxa (a fungal operational taxonomic unit and 15 bacterial operational taxonomic units) were identified from the microbial co-occurrence network. Among them, five keystone taxa (in Hypocreales, Bryobacter, Solirubrobacterales, Thermomicrobiales, and Roseiflexaceae) contributed to high maize yield through increasing phosphorus flow and inhibiting toxic aluminum and manganese flow from soils to plants. However, the remaining eleven keystone taxa (in Conexibacter, Acidothermus, Ktedonobacteraceae, Deltaproteobacteria, Actinobacteria, Elsterales, Ktedonobacterales, and WPS-2) exerted the opposite effects. As a result, maize productivity varied among different fertilization treatments because of the altered maize mineral element flows by microbial keystone taxa. We conclude that microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows in acid soil. This study highlights the importance of microbial keystone taxa for sustainable crop productivity in acid soil and provides deep insights into the relationships between soil microbial keystone taxa, crop mineral nutrition, and productivity.

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha⁻¹ and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH₄)₂SO₄ (300 kg N ha⁻¹) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO₂ emission, mineral N and the bacterial community were monitored. Application of NH₄⁺ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH₄⁺ and NO₂⁻ was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH₄⁺ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.

Impacts of corn stover management and fertilizer application on soil nutrient availability and enzymatic activity

Corn stover is a global resource used in many industrial sectors including bioenergy, fuel, and livestock operations. However, stover removal can negatively impact soil nutrient availability, especially nitrogen (N) and phosphorus (P), biological activity, and soil health. We evaluated the effects of corn stover management combined with N and P fertilization on soil quality, using soil chemical (nitrate, ammonium and Bray-1 P) and biological parameters (β-glucosidase, alkaline phosphatase, arylsulfatase activities and fluorescein diacetate hydrolysis—FDA). The experiment was performed on a Mollisol (Typic Endoaquoll) in a continuous corn system from 2013 to 2015 in Minnesota, USA. The treatments tested included six N rates (0 to 200 kg N ha⁻¹), five P rates (0 to 100 kg P₂O₅ ha⁻¹), and two residue management strategies (residue removed or incorporated) totalling 60 treatments. Corn stover management significantly impacted soil mineral-N forms and enzyme activity. In general, plots where residue was incorporated were found to have high NH₄⁺ and enzyme activity compared to plots where residue was removed. In contrast, fields where residue was removed showed higher NO₃⁻ than plots where residue was incorporated. Residue management had little effect on soil available P. Soil enzyme activity was affected by both nutrient and residue management. In most cases, activity of the enzymes measured in plots where residue was removed frequently showed a positive response to added N and P. In contrast, soil enzyme responses to applied N and P in plots where residue was incorporated were less evident. Soil available nutrients tended to decrease in plots where residue was removed compared with plots where residue was incorporated. In conclusion, stover removal was found to have significant potential to change soil chemical and biological properties and caution should be taken when significant amounts of stover are removed from continuous corn fields. The residue removal could decrease different enzymes related to C-cycle (β-glucosidase) and soil microbial activity (FDA) over continuous cropping seasons, impairing soil health.

Effects of agrochemicals on the beneficial plant rhizobacteria in agricultural systems

Conventional agriculture relies heavily on chemical pesticides and fertilizers to control plant pests and diseases and improve production. Nevertheless, the intensive and prolonged use of agrochemicals may have undesirable consequences on the structure, diversity, and activities of soil microbiomes, including the beneficial plant rhizobacteria in agricultural systems. Although literature continues to mount regarding the effects of these chemicals on the beneficial plant rhizobacteria in agricultural systems, our understanding of them is still limited, and a proper account is required. With the renewed efforts and focus on agricultural and environmental sustainability, understanding the effects of different agrochemicals on the beneficial plant rhizobacteria in agricultural systems is both urgent and important to deduce practical solutions towards agricultural sustainability. This review critically evaluates the effects of various agrochemicals on the structure, diversity, and functions of the beneficial plant rhizobacteria in agricultural systems and propounds on the prospects and general solutions that can be considered to realize sustainable agricultural systems. This can be useful in understanding the anthropogenic effects of common and constantly applied agrochemicals on symbiotic systems in agricultural soils and shed light on the need for more environmentally friendly and sustainable agricultural practices.

Impact of dimethylpyrazole-based nitrification inhibitors on soil-borne bacteria

Nitrogen (N) input from fertilizers modifies the properties of agricultural soils as well as bacterial community diversity, composition and relationships. This can lead to negative impacts such as the deterioration of system multifunctionality, whose maintenance is critical to normal nutrient cycling. Synthetic nitrification inhibitors (NIs) can be combined with fertilizers to improve the efficiency of N use by reducing N losses. However, analysis of their effects on non-target bacteria are scarce. This study aimed to analyze the effect of applying the NIs DMPP and DMPSA on the whole bacterial community. Through 16S rRNA amplicon sequencing we determined the differences between samples in terms of microbial diversity, composition and co-occurrence networks. The application of DMPP and DMPSA exerted little impact on the abundance of the dominant phyla. Nevertheless, several significant shifts were detected in bacterial diversity, co-occurrence networks, and the abundance of particular taxa, where soil water content played a key role. For instance, the application of NIs intensified the negative impact of N fertilization on bacterial diversity under high water-filled pore spaces (WFPS) (>64%), reducing community diversity, whereas alpha-diversity was not affected at low WFPS (<55%). Interestingly, despite NIs are known to inhibit ammonia monooxygenase (AMO) enzyme, both NIs almost exclusively inhibited Nitrosomonas genera among AMO holding nitrifiers. Thus, Nitrosomonas showed abundance reductions of up to 47% (DMPP) and 66% (DMPSA). Nonetheless, non-target bacterial abundances also shifted with NI application. Notably, DMPSA application partially alleviated the negative effect of fertilization on soil multifunctionality. A remarkable increase in populations related to system multifunctionality, such as Armatimonadetes (up to +21%), Cyanobacteria (up to +30%) and Fibrobacteres (up to +25%) was observed when DMPSA was applied. NI application substantially influenced microbial associations by decreasing the complexity of co-occurrence networks, decreasing the total edges and node connectivity, and increasing path distances.

Comparative Effect of Fertilization Practices on Soil Microbial Diversity and Activity: An Overview

Continuously increasing human population demands increased food production, which needs greater fertilizer's input in agricultural lands to enhance crop yield. In this respect, different fertilization practices gained acceptance among farmers. We reviewed effect of three main fertilization practices (Conventional-, Organic-, and Bio-fertilization) on soil microbial diversity, activity, and community composition. Studies reported that over application of inorganic fertilizers decline soil pH, change soil osmolarity, cause soil degradation, disturb taxonomic diversity and metabolism of soil microbes and cause accumulation of extra nutrients into the soil such as phosphorous (P) accumulation. On the contrary, organic fertilizers increase organic carbon (OC) input in the soil, which strongly encourage growth of heterotrophic microbes. Organic fertilizer vermicompost application provides readily available nutrients to both plants as well as microbes and encourage overall microbial number in the soil. Most recently, role of beneficial bacteria in long-term sustainable agriculture attracted attention of scientists towards their use as biofertilizer in the soil. Studies documented favorable effect of biofertilization on microbial Shannon, Chao and ACE diversity indices in the soil. It is concluded from intensive review of literature that all the three fertilization practices have their own way to benefit the soil with nutrients, but biofertilization provides long-term sustainability to crop lands. When it is used in integration with organic fertilizers, it makes the soil best for microbial growth and activity and increase microbial diversity, providing nutrients to soil for a longer time, thus improving crop productivity.

Conservation management improves agroecosystem function and resilience of soil nitrogen cycling in response to seasonal changes in climate

Understanding how conservation agricultural management improves soil nitrogen (N) stability in the face of climate change can help increase agroecosystem productivity and mitigate runoff, leaching and downstream water quality issues. We conducted a 2-year field study in a 36-year-old rain-fed cotton production system to evaluate the impacts of changing climatic factors (temperature and precipitation) on soil N under conservation management, including moderate inorganic N fertilizer application (0 and 67 kg N ha^-1), winter cover crops (fallow; winter wheat, Triticum aestivum L.; hairy vetch, Vicia villosa Roth), and reduced tillage (no-till; disk tillage). Structural equation modeling (SEM) was used to quantify and compare the effects of conservation management and climatic factors on soil N concentrations. Fertilizer and vetch cover crops increased soil total N concentration by 16% and 18%, respectively, and also increased microbial N transformation rate by 41% and 168%. In addition, vetch cover crops also increased soil labile N concentrations by 57%, 21%, and 79%, i.e., extractable organic N, ammonium, and nitrate, respectively. The highest soil δ¹⁵N value (6.4 ± 0.3‰) was observed under the 67 kg N ha^-1 fertilizer-wheat-disk tillage treatment, and the lowest value (4.8 ± 0.3‰) under the zero-fertilizer-wheat-no-till treatment, indicating fertilizer and tillage might accelerate microbial N transformation. The SEM showed positive effects of temperature and precipitation on labile N concentrations, suggesting destabilization of soil N and the potential for soil N loss under increased temperature and intensified precipitation. Fertilizer and vetch use might mitigate some of the effects of temperature by accelerating microbial N transformations, with vetch having a larger effect than fertilizer (0.35 vs. 0.15, Table 1). No-till can reduce some of the effects of precipitation on soil labile N by maintaining soil structure. Our study suggests that fertilizer, vetch cover crop, and no-till might help improve function and resilience of agroecosystems in relation to soil N cycling. Soil N stabilization in cropping systems can be enhanced by adjusting agricultural management.

Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements

Rice cultivation usually involves high water and fertilizer application rates leading to the nonpoint pollution of surface waters with phosphorus (P) and nitrogen (N). Here, a 10-year field experiment was conducted to investigate N and P losses and their impact factors under different irrigation and fertilization regimes. Results indicated that T2 (Chemical fertilizer of 240 kg N ha-1, 52 kg P ha-1, and 198 kg K ha-1 combined with shallow intermittent irrigation) decreased N loss by 48.9% compared with T1 (Chemical fertilizer of 273 kg N ha-1, 59 kg P ha-1, and 112 kg K ha-1 combined with traditional flooding irrigation). The loss ratio (total N loss loading/amount of applied N) of N was 9.24-15.90%, whereas that of P was 1.13-1.31% in all treatments. Nitrate N (NO3--N) loss was the major proportion accounting for 88.30-90.65% of dissolved inorganic N loss through surface runoff. Moreover, the N runoff loss was mainly due to high fertilizer input, soil NO3--N, and ammonium N (NH4+-N) contents. In addition, the N loss was accelerated by Bacteroidetes, Proteobacteria, Planotomycetes, Nitrospirae, Firmicutes bacteria and Ascomycota fungi, but decreased by Chytridiomycota fungi whose contribution to the N transformation process. Furthermore, T2 increased agronomic N use efficiency (AEN) and rice yield by 32.81% and 7.36%, respectively, in comparison with T1. These findings demonstrated that T2 might be an effective approach to ameliorate soil chemical properties, regulate microbial community structure, increase AEN and consequently reduce N losses as well as maintaining rice yields in the present study.

Impact of Olive Saplings and Organic Amendments on Soil Microbial Communities and Effects of Mineral Fertilization

Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroResp^TM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N₂-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

Response of soil fungal communities to continuous cropping of flue-cured tobacco

Fungal communities are considered to be critically important for crop health and soil fertility. However, our knowledge of the response of fungal community structure to the continuous cropping of flue-cured tobacco is limited, and the interaction of soil fungal communities under different cropping systems remains unclear. In this study, we comparatively investigated the fungal abundance, diversity, and community composition in the soils in which continuous cropping of flue-cured tobacco for 3 years (3ys), 5 years (5ys), and cropping for 1 year (CK) using quantitative polymerase chain reaction and high-throughput sequencing technology. The results revealed that continuous cropping of flue-cured tobacco changed the abundance of soil fungi, and caused a significant variation in fungal diversity. In particular, continuous cropping increased the relative abundance of Mortierellales, which can dissolve mineral phosphorus in soil. Unfortunately, continuous cropping also increased the risk of potential pathogens. Moreover, long-term continuous cropping had more complex and stabilize network. This study also indicated that available potassium and available phosphorous were the primary soil factors shifting the fungal community structure. These results suggested that several soil variables may affect fungal community structure. The continuous cropping of flue-cured tobacco significantly increased the abundance and diversity of soil fungal communities.

Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops.

Chemical fertilization: a short-term solution for plant productivity?

The effect of long-term chemical fertilization on plant-microorganisms and microbe-microbe interactions.

Indicators for assessment of soil quality: a mini-review

Soil quality is the competence of soil to perform necessary functions that are able to maintain animal and plant productivity of the soil. Soil consists of various physical, chemical, and biological parameters, and all these parameters are involved in the critical functioning of soil. There is a need for continuous assessment of soil quality as soil is a complex and dynamic constituent of Earth's biosphere that is continuously changing by natural and anthropogenic disturbances. Any perturbations in the soil cause disturbances in the physical (soil texture, bulk density, etc.), chemical (pH, salinity, organic carbon, etc.), and biological (microbes and enzymes) parameters. These physical, chemical, and biological parameters can serve as indicators for soil quality assessment. However, soil quality assessment cannot be possible by evaluating only one parameter out of physical, chemical, or biological. So, there is an emergent need to establish a minimum dataset (MDS) which shall include physical, chemical, and biological parameters to assess the quality of the given soil. This review attempts to describe various physical, chemical, and biological parameters, combinations of which can be used in the establishment of MDS.