Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil

Spent Mushroom Substrate Improves Microbial Quantities and Enzymatic Activity in Soils of Different Farming Systems

Organic fertilizers, such as spent mushroom substrate (SMS), improve soil fertility, but studies comparing their effects on different agricultural soils are limited. In this study, the effects of standard, SMS and composed fertilizers on soils from conventional-integrated, organic and biodynamic farming were investigated. Soil samples were analyzed for microorganisms and the activity of β-glucosidase (β-GLU), β-1,4-N-acetylglucosaminidase (NAG), urease (URE), arylamidase (ARN), phosphatase (PHOS), acid phosphatase (PAC), alkaline phosphatase (PAH) and arylsulphatase (ARS). Biodynamic soil showed the highest microbial counts and enzyme activities, followed by organic and conventional soils. SMS significantly increased the number of microorganisms and enzyme activities, especially in biodynamic and organic soils. Seasonal variations affected all microorganisms and most enzymes in all soils, except NAG in conventional and organic soils. Biodynamic soil showed stable activity of enzymes and microorganisms throughout the year, indicating greater stability. This study concludes that soil microorganisms and enzyme activities respond differently to fertilization depending on the soil type, with SMS demonstrating beneficial effects in all tested soils.

Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'

BACKGROUND

The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.

RESULTS

Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.

CONCLUSIONS

In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

Dispersal of microbes from grassland fire smoke to soils

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.

Combining frass and fatty acid co-products derived from Black soldier fly larvae farming shows potential as a slow release fertiliser

Use of black soldier fly larvae (BSFL) to process large volumes of organic waste is an emerging industry to produce protein. A co-product of this industry, the larval faeces (frass), has potential to be used as an organic fertiliser in a circular economy. However, BSFL frass has a high ammonium (N-NH4+) content which could result in nitrogen (N) loss following its application to land. One solution is to process the frass by combining it with solid fatty acids (FA) that have previously been used to manufacture slow-release inorganic fertilisers. We investigated the slow-releasing effect of N after combining BSFL frass with three FAs - lauric, myristic and stearic acid. Soil was amended with the three forms of FA processed (FA-P) frass, unprocessed frass or a control and incubated for 28 days. The impact of treatments on soil properties and soil bacterial communities were characterised during the incubation. Lower N-NH4+ concentrations occurred in soil treated with FA-P frass compared to unprocessed frass, and N-NH4+ release was slowest for lauric acid processed frass. Initially, all frass treatments caused a large shift in the soil bacterial community towards a dominance of fast-growing r-strategists that were correlated with increased organic carbon levels. FA-P frass appeared to enhance the immobilisation of N-NH4+ (from frass) by diverting it into microbial biomass. Unprocessed and stearic acid processed frass became enriched by slow-growing K-strategist bacteria at the latter stages of the incubation. Consequently, when frass was combined with FAs, FA chain length played an important role in regulating the composition of r-/K- strategists in soil and N and carbon cycling. Modifying frass with FAs could be developed into a slow release fertiliser leading to reduced soil N loss, improved fertiliser use efficiency, increased profitability and lower production costs.

Nitrogen dynamics and biological processes in soil amended with microalgae grown in abattoir digestate to recover nutrients

The use of microalgae for nutrient recovery from wastewater and subsequent conversion of the harvested biomass into fertilizers offers a sustainable approach towards creating a circular economy. Nonetheless, the process of drying the harvested microalgae represents an additional cost, and its impact on soil nutrient cycling compared to wet algal biomass is not thoroughly understood. To investigate this, a 56-day soil incubation experiment was conducted to compare the effects of wet and dried Scenedesmus sp. microalgae on soil chemistry, microbial biomass, CO2 respiration, and bacterial community diversity. The experiment also included control treatments with glucose, glucose + ammonium nitrate, and no fertilizer addition. The Illumina Mi-Seq platform was used to profile the bacterial community and in-silico analysis was performed to assess the functional genes involved in N and C cycling processes. The maximum CO2 respiration and microbial biomass carbon (MBC) concentration of dried microalgae treatment were 17% and 38% higher than those of paste microalgae treatment, respectively. NH4+ and NO3- released slowly and through decomposition of microalgae by soil microorganisms as compared to synthetic fertilizer control. The results indicate that heterotrophic nitrification may contribute to nitrate production for both microalgae amendments, as evidenced by low amoA gene abundance and a decrease in ammonium with an increase in nitrate concentration. Additionally, dissimilatory nitrate reduction to ammonium (DNRA) may be contributing to ammonium production in the wet microalgae amendment, as indicated by an increase in nrfA gene and ammonium concentration. This is a significant finding because DNRA leads to N retention in agricultural soils instead of N loss via nitrification and denitrification. Thus, further processing the microalgae through drying or dewetting may not be favorable for fertilizer production as the wet microalgae appeared to promote DNRA and N retention.

Organic vs. conventional: impact of cultivation treatments on the soil microbiota in the vineyard

The aim of this study was to compare the effects of two vineyard management practices on the soil and its associated microbiota. The experiments were conducted in two adjacent plots, one completely organically managed and the other conventionally managed in terms of phytosanitary treatments but fertilized with organic amendments. The chemical soil analyses were correlated to the prokaryotic and fungal communities, which were studied using the metabarcoding technique. The main difference between the two treatments was a significantly higher amount of Cu in the organic managed vineyard soil, while conventional managed soil presented higher concentration of Na and Mg and was also associated with higher pH values. Despite these differences, no significant diversities were observed on soil biodiversity and microbial composition considering alpha and beta diversity metrics. However, the percentages of some phyla analyzed individually differed significantly between the two managements. Analyzing the metabolisms of these phyla, it was discovered an increment of species correlated to soils with higher organic matter content or land not used for agricultural purposes in the organic treated soil. The findings indicate that, despite the use of copper-based phytosanitary products, there was no degradation and loss of biodiversity in the organic soil microbial population compared to conventional management with the same type of fertilization, and the observed microbial population was more similar to that of natural soils.

Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes

Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

Soil microbiome response to 2-chlorodibenzo-p-dioxin during bioremediation of contaminated tropical soil in a microcosm-based study

A pristine soil was artificially contaminated with 2-chlorodibenzo-p-dioxin (2-CDD) and separated into three portions. Microcosms SSOC and SSCC were seeded with Bacillus sp. SS2 and a three-member bacterial consortium respectively; SSC was untreated, while heat-sterilized contaminated soil served as overall control. Significant degradation of 2-CDD occurred in all microcosms except for the control where the concentration remained unchanged. Degradation of 2-CDD was highest in SSCC (94.9%) compared to SSOC (91.66%) and SCC (85.9%). There was also a notable reduction in the microbial composition complexity both in species richness and evenness following dioxin contamination, a trend that nearly lasted the study period; particularly in setups SSC and SSOC. Irrespective of the bioremediation strategies, the soil microflora was practically dominated by the Firmicutes and at the genus level, the phylotype Bacillus was the most dominant. Other dominant taxa though negatively impacted were Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria. Overall, this study demonstrated the feasibility of microbial seeding as an effective strategy to cleanup tropical soil contaminated with dioxins and the importance of metagenomics in elucidating the microbial diversities of contaminated soils. Meanwhile, the seeded organisms, owed their success not only to metabolic competence, but survivability, adaptability and ability to compete favourably with autochthonous microflora.

Impacts of Rock Mineral and Traditional Phosphate Fertilizers on Mycorrhizal Communities in Pasture Plants

Intensive fertilizer use can constrain contributions from soil biological processes in pastures, including those associated with arbuscular mycorrhizal (AM) fungi. We evaluated the effect of fertilizers of different P solubility on the colonization of the roots of two common pasture plants by a community of AM fungi in a pasture soil. The treatments were a rock mineral fertilizer, a chemical fertilizer and a microbial inoculant. Subterranean clover and annual ryegrass were grown in pots for 10 weeks. Both fertilizers reduced the proportion and length of roots colonized by naturally occurring AM fungi. However, by 10 weeks, there was a much greater length of mycorrhizal root for annual ryegrass than for subterranean clover. The relative abundance of mycorrhizal fungi in the families Glomeraceae and Acaulosporaceae in roots was not affected by the form of fertilizer, but diversity indices of AM fungi in roots were altered. The chemical fertilizer had a greater negative effect on AM fungal diversity indices in the annual ryegrass roots compared with the subterranean clover roots. The reduction in OTU richness of AM fungi with fertilizer application corresponded with reduced soil pH. Differential effects of P fertilizers on naturally occurring AM fungi in this agricultural soil have the potential to influence the efficacy of P fertilizer use and dominance of plant species in grasslands.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Introduction

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.

Methods

Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.

Results

As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.

Discussion

Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation

Soil aggregates are extremely vulnerable to agricultural intensification and are important drivers of soil health, microbial diversity, and biogeochemical cycling. Despite its importance, there is a dearth of studies revealing how fertilization regimes influence diazotrophic community behind soil aggregates, as well as the potential consequences for crop yields. To do this, a two-decade fertilization of wheat-maize intercropping field experiment was conducted in Loess Plateau of China semiarid area under three treatments: no fertilizer, chemical and organic fertilizer. Moreover, we categorized soil aggregates as large macroaggregates (>2 mm), medium macroaggregates (1-2 mm), small macroaggregates (0.25-1 mm), microaggregates (< 0.25 mm) and rhizosphere soils aggregates. We found that soil aggregates exerted a much more influence on the nifH gene abundance than fertilization practices. Particularly, nifH gene abundance has been promoted with increasing the size of soil aggregates fraction without blank soil in the organic fertilization while its abundance presented contrast patterns in the chemical fertilization. Bipartite association networks indicated that different soil aggregates shaped niche differentiation of diazotrophic community behind fertilization regimes. Additionally, we found that organic fertilization strengthens the robustness of diazotrophic communities as well as increases the complexity of microbial networks by harboring keystone taxa. Mantel test results suggested that specific soil factors exerted more selective power on diazotrophic community and nifH gene abundance in the chemical fertilization. Furthermore, β-diversity and nifH gene abundance of diazotrophic communities in the soil microaggregates jointly determine the crop yields. Collectively, our findings emphasize the key role of functional community diversity in sustaining soil cycling process and crop yields under long-term fertilization, and facilitate our understanding of the mechanisms underlying diazotrophic community in response to agricultural intensification, which could pave the way to sustainable agriculture through manipulating the functional taxa.

Soil microbial community structure dynamics shape the rhizosphere priming effect patterns in the paddy soil

Microbial community structure plays a crucial part in soil organic carbon (SOC) decomposition and variation of rhizosphere priming effects (RPEs) during plant growth. However, it is still uncertain how bacterial community structure regulates RPEs in soil and how RPE patterns respond to plant growth. Therefore, we conducted an experiment to examine the RPE response to plant growth and nitrogen (N) addition (0 (N0), 150 (N150), and 300 (N300) kg N ha^-1) using the ¹³C natural abundance method in a C₃ soil (paddy soil) - C₄ plant (maize, Zea mays L.) system; we then explored the underlying biotic mechanisms using 16S rRNA sequencing techniques. Networks were constructed to identify keystone taxa and to analyze the correlations between network functional modules of bacterial community and C decomposition. The results indicated that negative and positive RPEs occurred on Day 30 and Day 75 after maize planting, respectively. Bacterial community structure significantly changed and tended to shift from r-strategists toward K-strategists with changing labile C: N stoichiometry and soil pH during plant growth stages. The different network modules of bacterial community were aggregated in response to RPE pattern variation. Caulobacteraceae, Bacillus, and Chitinophagaceae were keystone taxa on Day 30, while Gemmatimonas, Candidatus Koribacter, and Xanthobacteraceae were keystone taxa on Day 75. Moreover, keystone taxa with different C utilization strategies were significantly different between the two growth stages and related closely to different RPE patterns. This study provides deeper insights into the network structure of bacterial communities corresponding to RPE patterns and emphasizes the significance of keystone taxa in RPE variation.

The characterization of microbial communities and associations in karst tiankeng

The karst tiankeng is a special and grand negative terrain on the surface, that maintains a unique ecosystem. However, knowledge about bacterial and fungal communities in karst tiankengs is still limited. Therefore, soil samples from five karst tiankengs were collected and subjected to high-throughput sequencing of 16S rRNA and ITS genes, and multivariate statistical analysis. The results showed abundant and diversified bacterial and fungal communities in karst tiankeng. The bacterial communities were dominated by Proteobacteria and Acidobacteria, and the fungal communities were dominated by Ascomycota and Basidiomycota. Statistical analysis revealed significant differences in bacterial and fungal communities among the five karst tiankengs, which may indicate that the distribution of bacterial and fungal communities was driven by separate karst tiankengs. The co-occurrence network structure was characterized by highly modularized assembly patterns and more positive interactions. The keystone taxa were mainly involved in nutrient cycling and energy metabolism. The null model analysis results showed that the stochastic process, especially dispersal limitation, tended to be more important in controlling the development of bacterial and fungal communities in karst tiankeng. The bacterial community structure was significantly associated with soil properties (SWC, TN, AN, and BD), while the fungal community structure was significantly associated with soil properties (SWC and TP) and plant diversity. These results can expand our knowledge of the karst tiankeng microbiome.

Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems

Despite the central role of microorganisms in soil fertility, little understanding exists regarding the impact of management practices and soil microbial diversity on soil processes. Strong correlations among soil microbial composition, management practices, and microbially mediated processes have been previously shown. However, limited integration of the different parameters has hindered our understanding of agroecosystem functioning. Multivariate analyses of these systems allow simultaneous evaluation of the parameters and can lead to hypotheses on the microbial groups involved in specific nutrient transformations. In the present study, using a multivariate approach, we investigated the effect of microbial composition (16SrDNA sequencing) and soil properties in carbon mineralization (C_MIN) (BIOLOG™, Hayward, CA, USA) across different management categories on coffee agroecosystems in Mexico. Results showed that (i) changes in soil physicochemical variables were related to management, not to region, (ii) microbial composition was associated with changes in management intensity, (iii) specific bacterial groups were associated with different management categories, and (iv) there was a broader utilization range of carbon sources in non-managed plots. The identification of specific bacterial groups, management practices, and soil parameters, and their correlation with the utilization range of carbon sources, presents the possibility to experimentally test hypotheses on the interplay of all these components and further our understanding of agroecosystem functioning and sustainable management.

Soil Microbial Network Complexity Varies With pH as a Continuum, Not a Threshold, Across the North China Plain

There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequencing on a set of 90 samples across a 1,092 km transect in wheat fields of the North China Plain (NCP). We found that pH was the most important environmental factor driving network topology and relative abundance of keystone taxa. For the metacommunity composed of both bacteria and fungi, and for the bacterial community alone, lower soil pH was associated with a more complex microbial network. However, the network for fungi showed no strong trend with soil pH. In addition, keystone taxa abundance was positively correlated with ecosystem function and stability, and best explained by pH. Our results present new perspectives on impacts of pH on soil microbial network structure across large scales in agricultural environments. This improved knowledge of community processes provides a step toward understanding of functioning and stability of agricultural ecosystems.

Optimal K Management Improved Potato Yield and Soil Microbial Community Structure

Optimal potassium (K) fertilizer application in potato cropping systems can effectively increase food production and mitigate soil microbial ecosystem stress. The dynamics and sustainability of potato yield, the dynamics of potato commodity rates (CRs), and microbial community structure were explored under four different K application rates (kg K ha−1 year−1): 0 (control), 75 (low K), 150 (medium K), and 225 (high K). Compared with the low-K application, the medium-K and high-K applications increased potato yields by 8.08% and 11.66%, respectively. The mean CR of potato tubers during 4 years was significantly greater under the medium-K treatment than under the low-K and high-K treatments. Both medium-K and high-K applications significantly enhanced the sustainable yield index (SYI) relative to the Low-K application by 7.93% and 9.34%, respectively. Compared with the zero-K, low-K, and high-K treatments, the medium-K treatment improved the total phospholipid fatty acid (PLFA) contents by 11.91%, 16.84%, and 11.66%, respectively. Moreover, the medium-K application increased the bacterial PFLA, actinomycete PFLA, gram-positive (G+) bacterial PFLA, and gram-negative (G−) bacterial PFLA contents in the soil. Overall, application of 150 kg ha−1 year−1 K fertilizer represents a promising fertilization strategy in potato cropping systems in Southwest China.

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

N Addition Overwhelmed the Effects of P Addition on the Soil C, N, and P Cycling Genes in Alpine Meadow of the Qinghai-Tibetan Plateau

Although human activities have greatly increased nitrogen (N) and phosphorus (P) inputs to the alpine grassland ecosystems, how soil microbial functional genes involved in nutrient cycling respond to N and P input remains unknown. Based on a fertilization experiment established in an alpine meadow of the Qinghai-Tibetan Plateau, we investigated the response of the abundance of soil carbon (C), N, and P cycling genes to N and P addition and evaluated soil and plant factors related to the observed effects. Our results indicated that the abundance of C, N, and P cycling genes were hardly affected by N addition, while P addition significantly increased most of them, suggesting that the availability of P plays a more important role for soil microorganisms than N in this alpine meadow ecosystem. Meanwhile, when N and P were added together, the abundance of C, N, and P cycling genes did not change significantly, indicating that the promoting effects of P addition on microbial functional genes abundances were overwhelmed by N addition. The Mantel analysis and the variation partitioning analysis revealed the major role of shoot P concentration in regulating the abundance of C, N, and P cycling genes. These results suggest that soil P availability and plant traits are key in governing C, N, and P cycling genes at the functional gene level in the alpine grassland ecosystem.

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping

Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.

Network structure of resource use and niche overlap within the endophytic microbiome

Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.

Reduction effect of individual N, P, K fertilization on antibiotic resistance genes in reclaimed water irrigated soil

The transfer of antibiotic resistance genes (ARGs) in soil under reclaimed water irrigation poses a potential environmental risk. Regulation of NPK fertilizer could influence the behavior of bacterial communities, mobile genetic elements (MGEs), and soil properties, which determine the fate of ARGs. To identify the key element in NPK fertilizer and realize efficient regulation, we explored the effect of individual N, P, K fertilization on ARG variation in tomato rhizosphere and bulk soils. Compared with an unfertilized treatment, N fertilization resulted in greater decreases in the abundance of ARGs (decreases of 24.06%-73.09%) than did either P fertilization (increases of up to 35.84%, decreases of up to 58.80%) or K fertilization (decreases of 13.47%-72.47%). The influence of different forms of N (CO(NH₂)₂, NaNO₃, and NH₄HCO₃), P (Ca(H₂PO₄)₂ and CaMgO₄P⁺), and K (KCl and K₂(SO₄)) fertilizers was also investigated in this study, and showed the influence of NaNO₃, CaMgO₄P⁺, and K₂(SO₄) on reducing ARGs abundance was greater in different types of N, P, K fertilizers. Bacterial communities showed the strongest response to N fertilization. The reduced bacterial diversity and abundance of ARG-host and non-host organisms explained the decline of total ARG abundance in soil. In soils fertilized with either P or K, the effect of soil properties, especially total nitrogen and pH, on ARG variation was greater than that of bacterial community and MGEs. These results suggest that N regulation of in NPK fertilizer may be an effective way to reduce the risks of ARGs in soil associated with reclaimed water irrigation.

Engineering the Plant Microenvironment To Facilitate Plant-Growth-Promoting Microbe Association

New technologies that enhance soil biodiversity and minimize the use of scarce resources while boosting crop production are highly sought to mitigate the increasing threats that climate change, population growth, and desertification pose on the food infrastructure. In particular, solutions based on plant-growth-promoting bacteria (PGPB) bring merits of self-replication, low environmental impact, tolerance to biotic and abiotic stressors, and reduction of inputs, such as fertilizers. However, challenges in facilitating PGPB delivery in the soil still persist and include survival to desiccation, precise delivery, programmable resuscitation, competition with the indigenous rhizosphere, and soil structure. These factors play a critical role in microbial root association and development of a beneficial plant microbiome. Engineering the seed microenvironment with protein and polysaccharides is one proposed way to deliver PGPB precisely and effectively in the seed spermosphere. In this review, we will cover new advancements in the precise and scalable delivery of microbial inoculants, also highlighting the latest development of multifunctional rhizobacteria solutions that have beneficial impact on not only legumes but also cereals. To conclude, we will discuss the role that legislators and policymakers play in promoting the adoption of new technologies that can enhance the sustainability of crop production.

Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences

Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.

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.

Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus

Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.

Applications of food waste-derived black soldier fly larval frass as incorporated compost, side-dress fertilizer and frass-tea drench for soilless cultivation of leafy vegetables in biochar-based growing media

Black soldier fly (BSF) larval bioconversion can recycle nutrients in organic wastes into larval biomass and frass. While the frass has been commonly marketed as a soil amendment, its usefulness in soilless cultivation remains largely unexplored. Growth experiments were conducted to investigate the effectiveness of surplus food-derived and okara-derived BSF larval frass as an incorporated compost, side-dress fertilizer and frass-tea drench for the cultivation of pak choi and lettuce in waste-wood derived biochar growing media. Pak choi yields from treatments with surplus food-derived frass and biochar at a 10:90 (v/v) ratio and inorganic fertilizer were comparable to those of the control which consisted of soil, peat-based compost and inorganic fertilizer. However, yields decreased with increasing frass incorporation rates owing to high salinity and potentially low oxygen conditions in the growing media. When used as a fertilizer on biochar-coir growing media, the direct application of frass as a side-dress fertilizer was 1.6-6.8 times more effective in promoting lettuce growth than the application as a frass-tea drench. Frass fertilizers derived from surplus food outperformed those derived from okara by 1.3-5.3 times. Lettuce yields were not significantly different between the treatment with surplus food-derived frass applied as a side-dress fertilizer and the control of liquid inorganic fertilizer. Variations in fertilizing potential were attributed to nutrient availability and the presence of plant growth promoting microbes in the growing media. BSF larval frass derived from food waste shows promise in partially replacing unsustainable agricultural inputs for leafy vegetable cultivation, including soil and inorganic fertilizers.

Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application

Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.

Evaluating the potential of okara-derived black soldier fly larval frass as a soil amendment

Bioconversion of organic waste by the black soldier fly (BSF) larva yields a by-product commonly known as 'frass'. Although BSF larval frass has often been marketed as a biofertilizer, few studies have evaluated this claim. In this study, BSF larvae reared on a pure okara diet achieved an 85% waste reduction in the fresh weight of the okara. Subsequently, the frass was mixed with soil at concentrations of 10, 20, and 30% (vol/vol), and used to cultivate lettuce plants. At 10% concentration, the lettuce plants had biomasses comparable to those of the controls. Higher frass concentrations stunted the growth of the lettuce, likely because of the low C:N ratio of larval frass resulting from the rapid mineralization of nutrients. Larval frass was also found to be able to provide sufficient nutrients for lettuce growth as fertilizer application was only necessary after the first growth cycle, suggesting its suitability as a soil amendment. Analyses of the microbial community of all the growing media showed that the growth medium treatments with BSF larval frass tended to have a lower number of microbial species than the controls. Inherently higher micronutrient levels present in the frass resulted in the growth of lettuce plants. More importantly, the microbial analysis revealed that common foodborne pathogens were absent in the BSF larval frass and elemental analysis also indicated no heavy metal pollutants present. Overall, BSF larval frass was found to be a suitable soil amendment and more in-depth studies could facilitate its sensible use in agriculture.

Plant Diversity Enhances Soil Fungal Diversity and Microbial Resistance to Plant Invasion

Interactions and feedbacks between aboveground and belowground biomes are fundamental in controlling ecosystem functions and stability. However, the relationship between plant diversity and soil microbial diversity is elusive. Moreover, it remains unknown whether plant diversity loss will cause the stability of soil microbial communities to deteriorate. To shed light on these questions, we conducted a pot-based experiment to manipulate the plant richness gradient (1, 2, 4, or 8 species) and plant [Symphyotrichum subulatum (Michx.) G. L. Nesom] invasion status. We found that, in the noninvasion treatment, soil fungal diversity significantly and positively correlated with plant diversity, while the relationship between bacterial and plant diversity was not significant. Under plant invasion conditions, the coupling of plant-fungal alpha diversity relationship was enhanced, but the plant-fungal beta diversity relationship was decoupled. We also found significant positive relationships between plant diversity and soil microbial resistance. The observed positive relationships were determined by turnover (species substitution) and nestedness (species loss) processes for bacterial and fungal communities, respectively. Our study demonstrated that plant diversity enhanced soil fungal diversity and microbial resistance in response to plant invasion. This study expands our knowledge about the aboveground-belowground diversity relationship and the diversity-stability relationship.IMPORTANCE Our study newly showed that plant invasion significantly altered relationships between aboveground and belowground diversity. Specifically, plant richness indirectly promoted soil fungal richness through the increase of soil total carbon (TC) without plant invasion, while plant richness had a direct positive effect on soil fungal richness under plant invasion conditions. Our study highlights the effect of plant diversity on soil fungal diversity, especially under plant invasion conditions, and the plant diversity effect on microbial resistance in response to plant invasion. These novel findings add important knowledge about the aboveground-belowground diversity relationship and the diversity-stability relationship.

Urbanization pressures alter tree rhizosphere microbiomes

The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban-rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural-urban gradient indicate pH, Ca⁺, and organic matter are largely responsible for driving relative abundance of specific SMC members.

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.

High soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

Soil functions and processes are driven by complex microbial interactions. It is, therefore, critical to understand the coexistence patterns of soil microbiota, especially in fragile alpine ecosystems. We identified biogeographic patterns in the network-level topological features of the soil microbial co-occurrence network in the Tibetan alpine grasslands, based on high-throughput sequencing. We verified that soil pH was the most important environmental variable for predicting network-level topological features of soil microbial co-occurrence networks. Associations among soil microbiota were enhanced with increasing pH (5.17-8.92), and the network was the most stable at neutral pH. Moreover, node-level topological features suggested that the archaeal operational taxonomic units, compared with bacterial operational taxonomic units, hold a central role in the co-occurrence network. Network-level topological features revealed closer connections among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Therefore, our study demonstrated that soil pH served as a critical environmental filter that influenced the potential associations and ecological signature of soil microbiota in the Tibetan alpine grasslands. These findings provide a new perspective on the distinct biogeographic patterns of co-occurrence networks, to explore the ecological role of soil microbiota and thus help manage soil bacterial and archaeal communities for provisioning alpine ecosystem services.

Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota

Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.

Response of Horticultural Soil Microbiota to Different Fertilization Practices

Environmentally friendly agricultural production necessitates manipulation of microbe-plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.

Effect of Different Grain for Green Approaches on Soil Bacterial Community in a Karst Region

Soil bacteria participate in nutrient cycling above and below ground to promote ecosystem stability and health. However, the relationship of soil bacteria and environmental factors following the Grain for Green (GfG) program remains poorly understood in southwest China. Soil samples were collected from seven Grain for Green sites that had been revegetated for 15 years. Four of these sites were afforested with a different tree species: Zenia insignis (ZI), Toona sinensis (TS), Castanea mollissima (CM), and Citrus reticulate (CR). One site was revegetated with Zenia insignis and Guimu-1 elephant grass (ZG), and one with only Guimu-1 elephant grass (GM). The remaining site, abandoned cropland (AC), was left to regenerate naturally. Here, we used Illumina sequencing of 16S rRNA genes to explore how the Grain for Green project affected soil bacterial community. We found that Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these soils. The dominant genera at each revegetation site were also different. The CM, ZI, TS, and AC sites were dominated by Micromonospora, ZG was dominated by Streptomyces, and CR and GM were dominated by Subgroup 6. The bacterial structure was most similar in AC and TS. Correlation analysis showed that the ratio of C:P had positive effects on KD4-96, Intrasporangiaceae, and Gaiella. The ratio of soil N:P was significantly positively correlated with Cupriavidus and Kribbella. The combination of planting Zenia insignis and Guimu-1 elephant grass had the best edaphic benefits, and the approach of planting Citrus reticulate and Toona sinensis needs to be improved. Redundancy analysis (RDA) revealed that plant Simpson index, and soil N:P contributed to 16 and 15.7% of the total variations in the soil bacterial community composition, respectively. Our results suggested that plant diversity (Simpson index) and soil stoichiometric ratio (N:P) were the important factors affecting the bacterial community, and phosphorus was the limiting factor of the bacterial community in the Grain for Green karst region. In the future, revegetation should be accompanied with phosphorus fertilizer and polycultures should be considered.

Quasi-steady uptake and bacterial community assembly in a mathematical model of soil-phosphorus mobility

We mathematically model the uptake of phosphorus by a soil community consisting of a plant and two bacterial groups: copiotrophs and oligotrophs. Four equilibrium states emerge, one for each of the species monopolising the resource and dominating the community and one with coexistence of all species. We show that the dynamics are controlled by the ratio of chemical adsorption to bacterial death permitting either oscillatory states or quasi-steady uptake. We show how a steady state can emerge which has soil and plant nutrient content unresponsive to increased fertilization. However, the additional fertilization supports the copiotrophs leading to community reassembly. Our results demonstrate the importance of time-series measurements in nutrient uptake experiments.

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations?

Water stress and nutrient supply are two of the most ubiquitous global changes that surely drive substantial variations not only in agricultural productivity but also extend to alert soil living organisms. The present study aims to understand the intrinsic changes in the composition of soil populations and their functions due to the interaction between long-term fertilization and rainfall fluctuations, seeing whether fertilization history would render the soil microbial communities and their activities more resistant to water stress or not. The experiment was established in 1988 on a typical meadow soil (Vertisols) as a rainfed maize monoculture receiving six elevated rates of NPK annually. The 30-year average annual precipitation of the growing season in this region is 345.1 mm. However, in 2010 rainfall was 106.1% greater than the average, while in 2011 it was 26.5% lower. The results show that long-term NPK fertilization has made the soil microbes more tolerant to changes in soil moisture content resulting from rainfall fluctuations. Soil microbes and their activities, however, did not follow a dose-response relationship of NPK as soil moisture content was the main driving factor. Numbers of total fungi, cellulose decomposing bacteria, and nitrifying bacteria increased as rainfall in 2010 increased. Moreover, microbial biomass carbon in 2010 was almost 2-fold higher than in 2009. Soil respiration in 2010 was 11 and 35% higher than in 2009 and 2011, respectively. Otherwise, high rainfall in 2010 significantly diminished soil NO₃^- content and nitrification rate. Soil enzyme activity showed a higher response to soil moisture than the rate of NPK. The highest activity of phosphatase, dehydrogenase, and saccharase was measured in the driest year (2011), while urease displayed its highest activity in 2010. High rates of NPK significantly reduced soil dehydrogenase activity. These results illustrate how important it is for fertilizer programs to be flexible to match expected climate change in order to improve productivity and reduce environmental pollution.

Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances

Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.

Emerging priorities for microbial metagenome research

Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings

Remediation of gold tailings is often difficult due to their extremely barren nature and highly heavy metal concentrations. Returning green manure and applying sewage sludge compost have the beneficial effects of providing nutrients and improving the soil environment. The effects of green manure plants, alfalfa (Medicago sativa L.), ryegrass (Lolium perenne Linn.), and tall fescue (Festuca arundinacea), returning in situ on nutrients, bioavailability of trace metals, and community structure of microorganism in gold tailings amended with 0%, 5%, and 10% (weight/weight) sewage sludge compost on the top 4 cm of tailings (SSC-5, SSC-10) were investigated in a pot experiment. The results showed that the plant biomass and microbial biomass carbon in tailings significantly increased in the treatments with sewage sludge compost. The available N and available P and the availability of Zn decreased markedly with the returning of alfalfa and ryegrass. Moreover, through high-throughput sequencing, it was found that the returning of alfalfa had positive effects on the bacterial community richness but a negative impact on the fungal community richness. The microbial community diversity was reduced in the treatment without sewage sludge compost amendment and with alfalfa returning. However, the microbial community diversity was enriched in the treatment of alfalfa returning with sewage sludge compost. In each plant species, 9 dominant bacterial phyla and 10 dominant fungi phyla could be detected. Returning alfalfa green manure and applying sewage sludge compost led to a relative increase in the abundance of Proteobacteria and Ascomycota. These results demonstrated that returning alfalfa and applying sewage sludge compost could be effective in the ecological restoration of gold tailings.

Spatial patterning of soil microbial communities created by fungus-farming termites

Spatially overdispersed mounds of fungus-farming termites (Macrotermitinae) are hotspots of nutrient availability and primary productivity in tropical savannas, creating spatial heterogeneity in communities and ecosystem functions. These termites influence the local availability of nutrients in part by redistributing nutrients across the landscape, but the links between termite ecosystem engineering and the soil microbes that are the metabolic agents of nutrient cycling are little understood. We used DNA metabarcoding of soils from Odontotermes montanus mounds to examine the influence of termites on soil microbial communities in a semi-arid Kenyan savanna. We found that bacterial and fungal communities were compositionally distinct in termite-mound topsoils relative to the surrounding savanna, and that bacterial communities were more diverse on mounds. The higher microbial alpha and beta diversity associated with mounds created striking spatial patterning in microbial community composition, and boosted landscape-scale microbial richness and diversity. Selected enzyme assays revealed consistent differences in potential enzymatic activity, suggesting links between termite-induced heterogeneity in microbial community composition and the spatial distribution of ecosystem functions. We conducted a large-scale field experiment in which we attempted to simulate termites' effects on microbes by fertilizing mound-sized patches; this altered both bacterial and fungal communities, but in a different way than natural mounds. Elevated levels of inorganic nitrogen, phosphorus and potassium may help to explain the distinctive fungal communities in termite-mound soils, but cannot account for the distinctive bacterial communities associated with mounds.

Long-term fertilization alters soil properties and fungal community composition in fluvo-aquic soil of the North China Plain

Different fertilization regimes can substantially influence soil fungal community composition, yet fewer studies try to control for the effects of nitrogen input. Here, we investigated the impact of fertilization with equal nitrogen upon soil properties and soil fungal diversity and community composition in the North China Plain in a long-term field experiment. Long-term (32 years) fertilization regimes were applied with equal amounts of nitrogen: no chemical fertilizer or organic manure; chemical fertilization only; organic manure fertilization only, and; combination of 1/2 chemical fertilizer and 1/2 organic manure. Then we investigated the influence of these four fertilization regimes to soil properties, fungal diversity and community composition. The results showed that applying organic manure significantly influenced soil properties. Illumina MiSeq sequencing and its analysis revealed that organic manure fertilization significantly changed soil fungal alpha diversity, but chemical fertilization did not. Although soil fungal community composition did not differ significantly among all the fertilization regimes at the phylum and class levels, they did show differences in the abundance of dominant fungi. Yet at the genus level, soil fungal community composition, abundance, and beta diversity was affected by all fertilization regimes. Application of organic manure also reduced the abundance of soil-born fungal pathogens such as Fusarium. Our results suggest that long-term application of organic manure could markedly improve soil properties, altering soil fungal community composition and its diversity. Moreover, organic manure fertilization could limit soil-born fungal diseases, to further contribute to soil ecosystem sustainability.

Bacterial Community Structure and Predicted Function in Wheat Soil From the North China Plain Are Closely Linked With Soil and Plant Characteristics After Seven Years of Irrigation and Nitrogen Application

The influence of water and nitrogen (N) management on wheat have been investigated, but studies on the impact of long-term interactive water and N management on microbial structure and function are limited. Soil chemical properties and plants determine the soil microbial communities whose functions involved in nutrient cycling may affect plant productivity. There is an urgent need to elucidate the underlying mechanisms to optimize these microbial communities for agricultural sustainability in the winter wheat production area of the North China Plain. We performed high-throughput sequencing and quantitative PCR of the 16S rRNA gene on soil from a 7-year-old stationary field experiment to investigate the response of bacterial communities and function to water and N management. It was observed that water and N management significantly influenced wheat growth, soil properties and bacterial diversity. N application caused a significant decrease in the number of operational taxonomic units (OTUs), and both Richness and Shannon diversity indices, in the absence of irrigation. Irrigation led to an increase in the relative abundance of Planctomycetes, Latescibacteria, Anaerolineae, and Chloroflexia. In addition, most bacterial taxa were correlated with soil and plant properties. Some functions related to carbohydrate transport, transcription, inorganic ion transport and lipid transport were enriched in irrigation treatment, while N enriched predicted functions related to amino acid transport and metabolism, signal transduction, and cell wall/membrane/envelope biogenesis. Understanding the impact of N application and irrigation on the structure and function of soil bacteria is important for developing strategies for sustainable wheat production. Therefore, concurrent irrigation and N application may improve wheat yield and help to maintain those ecosystem functions that are driven by the soil microbial community.

Coupling ammonia nitrogen adsorption and regeneration unit with a high-load anoxic/aerobic process to achieve rapid and efficient pollutants removal for wastewater treatment

In this study, an ammonium nitrogen (NH₄⁺-N) adsorption and regeneration (AAR) was constructed by a zeolite-packed column and NaClO-NaCl regeneration unit, and coupled with an anoxic/aerobic (AO) system to achieve efficient removal of carbon, nitrogen and phosphorus under short hydraulic retention time (HRT) and sludge retention time (SRT). Compared to conventional anaerobic/anoxic/aerobic (AAO) process, the proposed AO-AAR process achieved more efficient and stable nitrogen removal with greatly shorter HRT (5.6 h) and SRT (8 d) at 10.4 °C, with NH₄⁺-N and total nitrogen in the effluent below 1.5 and 8.0 mg/L, respectively. The AO-AAR also obtained efficient phosphorus removal (<0.5 mg/L) by dosing aluminum in aerobic tank. High load and short SRT deteriorated sludge settleability and dewaterability, but enhanced methane production by improving sludge biodegradability. Dosing aluminum made the AO operating module more stable with improved settleability and dewaterability, and further enhanced methane production. Short HRT and SRT also resulted in the thriving of filamentous bacteria (Thiothrix) and heterotrophic nitrifiers (Acinetobacter, Pseudomonas and Rhodobacter) in the AO module, which helped in enhancing denitrification potential and nitrification efficiency under low temperature. Long-term operation showed that exchange capacity and physicochemical properties of zeolite were unchanged under NaClO-NaCl regeneration by introducing the tail gas from aerobic tank into the used regenerant to remove Ca²⁺ and Mg²⁺ exchanged from effluent of the AO module. Techno-economic analysis showed that the AO-AAR process is attractive and sustainable for municipal wastewater treatment by significantly improving nitrogen removal, greatly reducing land occupancy, enhancing methane production and achieving efficient reduction of carbon dioxide emission.

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

Plant-Dependent Soil Bacterial Responses Following Amendment With a Multispecies Microbial Biostimulant Compared to Rock Mineral and Chemical Fertilizers

Biostimulants are gaining momentum as potential soil amendments to increase plant health and productivity. Plant growth responses to some biostimulants and poorly soluble fertilizers could increase soil microbial diversity and provide greater plant access to less soluble nutrients. We assessed an agricultural soil amended with a multispecies microbial biostimulant in comparison with two fertilizers that differed in elemental solubilities to identify effects on soil bacterial communities associated with two annual pasture species (subterranean clover and Wimmera ryegrass). The treatments applied were: a multispecies microbial biostimulant, a poorly soluble rock mineral fertilizer at a rate of 5.6 kg P ha^-1, a chemical fertilizer at a rate of 5.6 kg P ha^-1, and a negative control with no fertilizer or microbial biostimulant. The two annual pasture species were grown separately for 10 weeks in a glasshouse with soil maintained at 70% of field capacity. Soil bacteria were studied using 16S rRNA with 27F and 519R bacterial primers on the Mi-seq platform. The microbial biostimulant had no effect on growth of either of the pasture species. However, it did influence soil biodiversity in a way that was dependent on the plant species. While application of the fertilizers increased plant growth, they were both associated with the lowest diversity of the soil bacterial community based on Fisher and Inverse Simpson indices. Additionally, these responses were plant-dependent; soil bacterial richness was highly correlated with soil pH for subterranean clover but not for Wimmera ryegrass. Soil bacterial richness was lowest following application of each fertilizer when subterranean clover was grown. In contrast, for Wimmera ryegrass, soil bacterial richness was lowest for the control and rock mineral fertilizer. Beta diversity at the bacterial OTU level of resolution by permanova demonstrated a significant impact of soil amendments, plant species and an interaction between plant type and soil amendments. This experiment highlights the complexity of how soil amendments, including microbial biostimulants, may influence soil bacterial communities associated with different plant species, and shows that caution is required when linking soil biodiversity to plant growth. In this case, the microbial biostimulant influenced soil biodiversity without influencing plant growth.