Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

Does fresh farmyard manure introduce surviving microbes into soil or activate soil-borne microbiota?

Manure inputs into soil strongly affect soil microbial communities leading to shifts in microbial diversity and activity. It is still not clear whether these effects are caused mainly by the survival of microbes introduced with manure or by activation of the soil-borne microbiome. Here, we investigated how the soil microbiome was changed after the introduction of fresh farmyard cattle manure, and which microorganisms originating from manure survived in soil. Manure addition led to a strong increase in soil microbial biomass, gene copies abundances, respiration activity, and diversity. High-throughput sequencing analysis showed that higher microbial diversity in manured soil was caused mainly by activation of 113 soil-borne microbial genera which were mostly minor taxa in not-fertilized soil. Two weeks after manure input, 78% of the manure-associated genera were not detected anymore. Only 15 of 237 prokaryotic genera that originated from manure survived for 144 days in soil, and only 8 of them (primarily representatives of Clostridia class) were found in manured soil after winter. Thus, an increase in microbial biomass and diversity after manure input is caused mainly by activation of soil-borne microbial communities, while most exogenous microbes from manure do not survive in soil conditions after few months.

Adaptation of Soil Fungal Community Structure and Assembly to Long- Versus Short-Term Nitrogen Addition in a Tropical Forest

Soil fungi play critical roles in ecosystem processes and are sensitive to global changes. Elevated atmospheric nitrogen (N) deposition has been well documented to impact on fungal diversity and community composition, but how the fungal community assembly responds to the duration effects of experimental N addition remains poorly understood. Here, we aimed to investigate the soil fungal community variations and assembly processes under short- (2 years) versus long-term (13 years) exogenous N addition (∼100 kg N ha^–1 yr^–1) in a N-rich tropical forest of China. We observed that short-term N addition significantly increased fungal taxonomic and phylogenetic α-diversity and shifted fungal community composition with significant increases in the relative abundance of Ascomycota and decreases in that of Basidiomycota. Short-term N addition also significantly increased the relative abundance of saprotrophic fungi and decreased that of ectomycorrhizal fungi. However, unremarkable effects on these indices were found under long-term N addition. The variations of fungal α-diversity, community composition, and the relative abundance of major phyla, genera, and functional guilds were mainly correlated with soil pH and NO₃^––N concentration, and these correlations were much stronger under short-term than long-term N addition. The results of null, neutral community models and the normalized stochasticity ratio (NST) index consistently revealed that stochastic processes played predominant roles in the assembly of soil fungal community in the tropical forest, and the relative contribution of stochastic processes was significantly increased by short-term N addition. These findings highlighted that the responses of fungal community to N addition were duration-dependent, i.e., fungal community structure and assembly would be sensitive to short-term N addition but become adaptive to long-term N enrichment.

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.

Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils

Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.

Biological Indicators of Soil Quality under Different Tillage Systems in Retisol

Soil microorganism diversity has a close relation with soil function, and the changes in the composition of the soil microbial population can directly affect it. The aim of this study was to identify the bacterial community composition and determine the main soil chemical and physical properties formed by the different tillage systems. In the experiment, we analyzed the combination of three tillage systems and four organic fertilizers. Soil samples were taken from the two layers of the soil profile: the upper 0–10 cm and the lower 10–20 cm. The composition and diversity of soil bacterial communities were assessed by the sequencing of 16S rRNA genes. Results revealed that the highest biodiversity was found in the soil with shallow ploughless tillage and enriched with farmyard manure. Actinobacteria and Proteobacteria were the dominant bacterial species across all treatments. Their total abundance varied between 26% and 36% in the different analyzed agroecosystems. For the Dystric Bathygleyic Glossic Retisol, shallow ploughless tillage is the most suitable tillage system, as it creates favorable conditions for the accumulation of organic carbon in the soil under the Western Lithuania climate conditions.

Integrated Application of Composted Agricultural Wastes, Chemical Fertilizers and Biofertilizers as an Avenue to Promote Growth, Yield and Quality of Maize in an Arid Agro-Ecosystem

Formulating new integrated plant nutrient management (IPNM) strategies in order to sustain crop production and protect the environment has become an important issue in the present agricultural system. Therefore, a field study was carried out in the two seasons 2016 and 2017 to formulate the best IPNM strategies for improving the growth, yield, and quality of maize grown in an arid agro-ecosystem. The IPNM comprised full-dose NPK (T1); composted agricultural wastes based on cow manure (T2), poultry manure (T3), and a mixture of sheep and camel manure (T4) as activators at the rate of 5 t ha−1 for each; half-dose NPK was combined with the mixture of the three types of composted agricultural wastes at the rate of 5 t ha−1 (T5) or 10 t ha−1 (T6), and a mixture of the three types of composted agricultural wastes at the rate of 10 t ha−1 (T7), 15 t ha−1 (T8), or 20 t ha−1 (T9), either with or without biofertilizers. The results showed that, as compared to T1, T6 or T9 significantly increased different growth, yield, and quality parameters of maize by 11.4–27.3%, 0.8–31.8%, and 4.6–17.2%, while T2 significantly decreased these parameters by 2.2–17.8%, 3.5–16.7%, and 4.5–9.4%, respectively. Seed inoculation with biofertilizers significantly increased different parameters of maize by 1.8–12.9%, compared to that of the non-inoculation seed treatment. Principal component analysis showed a strong relationship between different parameters of maize and treatments T5, T6, T8, and T9 with seed inoculation. Further, a significant and linear relationship was observed between different parameters of maize and the amount of N (R2 = 0.65–0.77), P (R2 = 0.58–0.71), and K (R2 = 0.63–0.73). These results indicated that any IPNM strategies that manage the NPK status and dynamics in the soil are a promising avenue for improving the growth and productivity of maize grown in the arid agro-ecosystem.

Efficiency of biochar, nitrogen addition, and microbial agent amendments in remediation of soil properties and microbial community in Qilian Mountains mine soils

Lacking systematic evaluations in soil quality and microbial community recovery after different amendments addition limits optimization of amendments combination in coal mine soils. We performed a short-term incubation experiment with a varying temperature over 12 weeks to assess the effects of three amendments (biochar: C; nitrogen fertilizer at three levels: N-N1~N3; microbial agent at two levels: M-M1~M2) based on C/N ratio (regulated by biochar and N level: 35:1, 25:1, 12.5:1) on mine soil properties and microbial community in the Qilian Mountains, China. Over the incubation period, soil pH and MBC/MBN were significantly lower than unamended treatment in N addition and C + M + N treatments, respectively. Soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), available potassium (AK), microbial biomass carbon (MBC), and nitrogen (MBN) contents increased significantly in all amended treatments (p < .001). Higher AP, AK, MBC, MBN, and lower MBC/MBN were observed in N2-treated soil (corresponding to C/N ratio of 25:1). Meanwhile, N2-treated soil significantly increased species richness and diversity of soil bacterial community (p < .05). Principal coordinate analysis further showed that soil bacterial community compositions were significantly separated by N level. C-M-N treatments significantly increased the relative abundance (>1%) of the bacterial phyla Bacteroidetes and Firmicutes, and decreased the relative abundance of fungal phyla Chytridiomycota (p < .05). Redundancy analysis illustrated the importance of soil nutrients in explaining variability in bacterial community composition (74.73%) than fungal composition (35.0%). Our results indicated that N addition based on biochar and M can improve soil quality by neutralizing soil pH and increasing soil nutrient contents in short-term, and the appropriate C/N ratio (25:1) can better promote microbial mass, richness, and diversity of soil bacterial community. Our study provided a new insight for achieving restoration of damaged habitats by changing microbial structure, diversity, and mass by regulating C/N ratio of amendments.

The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics

Biogeochemical cycling of phosphorus in the agro-ecosystem is mediated by soil microbes. These microbes regulate the availability of phosphorus in the soil. Little is known about the response of functional traits of phosphorus cycling microbes in soil fertilized with compost manure (derived from domestic waste and plant materials) or inorganic nitrogen fertilizers at high and low doses. We used a metagenomics investigation study to understand the changes in the abundance and distribution of microbial phosphorus cycling genes in agricultural farmlands receiving inorganic fertilizers (120 kg N/ha, 60 kg N/ha) or compost manure (8 tons/ha, 4 tons/ha), and in comparison with the control. Soil fertilization with high level of compost (Cp8) or low level of inorganic nitrogen (N1) fertilizer have nearly similar effects on the rhizosphere of maize plants in promoting the abundance of genes involved in phosphorus cycle. Genes such as ppk involved in polyphosphate formation and pstSABC (for phosphate transportation) are highly enriched in these treatments. These genes facilitate phosphorus immobilization. At a high dose of inorganic fertilizer application or low compost manure treatment, the phosphorus cycling genes were repressed and the abundance decreased. The bacterial families Bacillaceae and Carnobacteriaceae were very abundant in the high inorganic fertilizer (N2) treated soil, while Pseudonocardiaceae, Clostridiaceae, Cytophagaceae, Micromonosporaceae, Thermomonosporaceae, Nocardiopsaceae, Sphaerobacteraceae, Thermoactinomycetaceae, Planococcaceae, Intrasporangiaceae, Opitutaceae, Acidimicrobiaceae, Frankiaceae were most abundant in Cp8. Pyrenophora, Talaromyces, and Trichophyton fungi were observed to be dominant in Cp8 and Methanosarcina, Methanobrevibacter, Methanoculleus, and Methanosphaera archaea have the highest percentage occurrence in Cp8. Moreover, N2 treatment, Cenarchaeum, Candidatus Nitrososphaera, and Nitrosopumilus were most abundant among fertilized soils. Our findings have brought to light the basis for the manipulation of rhizosphere microbial communities and their genes to improve availability of phosphorus as well as phosphorus cycle regulation in agro-ecosystems.

The Impact of Fertilizer Amendments on Soil Autotrophic Bacteria and Carbon Emissions in Maize Field on the Semiarid Loess Plateau

Soil autotrophic bacteria play a crucial role in regulating CO₂ fixation and crop productivity. However, the information is limited to how fertilization amendments alter soil autotrophic bacterial community, crop yield, and carbon emission efficiency (CEE). Here, we estimated the impact of the structure and co-occurrence network of soil autotrophic bacterial community on maize yield and CEE. A long-term field experiment was conducted with five fertilization treatments in semiarid Loess Plateau, including no amendment (NA), chemical fertilizer (CF), chemical fertilizer plus commercial organic fertilizer (SC), commercial organic fertilizer (SM), and maize straw (MS). The results showed that fertilization amendments impacted the structure and network of soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial community via changing soil pH and NO₃-N. Compared with no amendment, the cbbL-carrying bacterial diversity was increased under the SC, SM, and MS treatments but decreased under the CF treatment. Soil autotrophic bacterial network contained distinct microbial modules that consisted of closely associated microbial species. We detected the higher abundances of soil cbbL-carrying bacterial genus Xanthobacter, Bradyrhizobium, and Nitrosospira. Structural equation modeling further suggested that the diversity, composition, and network of autotrophic bacterial community had strongly positive relationships with CEE and maize yield. Taken together, our results suggest that soil autotrophic bacterial community may drive crop productivity and CEE, and mitigate the atmospheric greenhouse effect.

Short-Term Effect of Green Waste and Sludge Amendment on Soil Microbial Diversity and Volatile Organic Compound Emissions

Soil amendments with organic waste products (OWPs) have been widely supported in Europe to improve soil fertility, causing wide changes in the microbial community structure and diversity, especially in the short-term period. Those changes are known to affect the volatile organic compound (VOC) emissions by soil. This work aimed to characterize, in terms of quantity and composition, the effect of green waste and sludge (GWS) application on soil VOC emissions and microbial community 49 h after the last GWS application. Two different soil samples were compared to test the effect of the soil history on VOC emissions and microbial communities. For this reason, we chose a soil that received GWS input for 20 years (GWS sample) and one that did not receive any organic input during the same period (CN sample). Furthermore, samples were manipulated to generate three microbial dilution diversity gradients (low, medium, and high). Results showed that Bacteroidetes phyla took advantage of the GWS application in all samples, increasing their relative abundance by 22% after 49 h, while the Proteobacteria phylum was penalized by the GWS amendment, passing from 58% to 49% relative abundance 49 h after the GWS application. Microbial structure differences between microbial diversity dilution levels remained even after the GWS application. GWS amendment induced a change in the emitted VOC profiles, especially in samples used to receiving GWS. GWS amendment doubled the VOC emissions from samples used to receiving GWS after 49 h. Finally, the microbial community was strongly correlated to the VOC emissions. Firmicutes, Proteobacteria, Actinobacteria, and Crenarchaeota were positively correlated (Pearson coefficient > 0.6), while other phyla, such as Bacteroidetes and Verrucomicrobia, were found to be negatively correlated (Pearson coefficient < −0.6) to the VOC emissions. After the addition of GWS, these correlations shifted from positive to negative and from negative to positive.

Expatiating the impact of anthropogenic aspects and climatic factors on long-term soil monitoring and management

This article is an extensive collection of scientific literature related to the impact of fertilizers on soil microbial and enzymatic activity. Due to the significance of technology in quantitative and qualitative evaluation of agricultural production, this is a basic problem for the present and future of mankind, where the scientific data being of utmost importance related to the topic. The comparison, including pedo-enzymological evaluation of minerals along with organic fertilization, highlights significant differences between mineral and organic fertilizers, confirming the superiority of complex mineral-organic fertilization. Enzymatic indicators that describe and define the soil quality resulted from enzymatic activities value and provide valuable information regarding the soil fertility status. Moreover, soil enzyme responds to soil management as well as to environmental pollutants. Changes of environmental conditions and pollutants like heavy metals and other toxic substances result in a shift in the biological activity of the soil. These changes can destabilize the soil system and cause a decrease in the nutrient pools. To ensure the improvement of fertilization techniques, the properties of nanoparticles are exploited that can efficiently release nutrients to plant cells. Numerous researches were performed in order to follow the long-term effects of incorporating nanofertilizers into the soil, obtaining an exhaustive overview of this new technology over the development of sustainable agriculture.

Responses of Soil Fungal Communities to Lime Application in Wheat Fields in the Pacific Northwest

Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq). Our results revealed that the location and liming did not significantly affect soil fungal diversity and richness, and the impact of soil depth on fungal diversity varied among locations. In contrast, location and soil depth had a strong effect on the structure and composition of soil fungal communities, whereas the impact of liming was much smaller, and location- and depth-dependent. Interestingly, families Lasiosphaeriaceae, Piskurozymaceae, and Sordariaceae predominated in the surface soil (0–7.5 cm) and were positively correlated with soil OM and aluminum, and negatively correlated with pH. The family Kickxellaceae which predominated in deeper soil (15–22.5 cm), had an opposite response to soil OM. Furthermore, some taxa in Ascomycota, such as Hypocreales, Peziza and Penicillium, were increased by liming at one of the locations (Moro). In conclusion, these findings suggest that fungal community structure and composition rather than fungal diversity responded to location, soil depth and liming. Compared to liming, location and depth had a stronger effect on the soil fungal community, but some specific fungal taxa shifted with lime application.

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners

Recent studies found that the majority of shrub and tree species are associated with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. However, our knowledge on how different mycorrhizal types interact with each other is still limited. We asked whether the combination of hosts with a preferred association with either AM or EM fungi increases the host tree roots' mycorrhization rate and affects AM and EM fungal richness and community composition.We established a tree diversity experiment, where five tree species of each of the two mycorrhiza types were planted in monocultures, two-species and four-species mixtures. We applied morphological assessment to estimate mycorrhization rates and next-generation molecular sequencing to quantify mycobiont richness.Both the morphological and molecular assessment revealed dual-mycorrhizal colonization in 79% and 100% of the samples, respectively. OTU community composition strongly differed between AM and EM trees. While host tree species richness did not affect mycorrhization rates, we observed significant effects of mixing AM- and EM-associated hosts in AM mycorrhization rate. Glomeromycota richness was larger in monotypic AM tree combinations than in AM-EM mixtures, pointing to a dilution or suppression effect of AM by EM trees. We found a strong match between morphological quantification of AM mycorrhization rate and Glomeromycota richness. Synthesis. We provide evidence that the combination of hosts differing in their preferred mycorrhiza association affects the host's fungal community composition, thus revealing important biotic interactions among trees and their associated fungi.

Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems

Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.

The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil

The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.

Flood Pulse Irrigation of Meadows Shapes Soil Chemical and Microbial Parameters More Than Mineral Fertilization

While mineral fertilization increases agricultural yields, it also bears the risk of contaminating non-target ecosystems and negatively affecting soil chemical parameters and microbial communities. This calls for alternative and more sustainable agricultural practices that reduce the use of fertilizers. Flood pulse irrigation could be an alternative to mineral fertilization of hay meadows, since it increases the yield with little or no application of fertilizer. However, the positive and negative implications of flood pulse irrigation on soil chemical parameters and particularly soil microbial communities are still largely unknown. In this study, we assessed shifts in soil microbial communities (SMC) as a response to changes in soil chemical parameters after flood pulse irrigation and/or fertilization of meadows. We determined soil chemical (Corg, Ntot, water extractable N, P, K, pH) and microbial (phospholipid-derived fatty acids, PLFA) parameters of 12 meadows in a 2 × 2 factorial design, comprising flood pulse irrigation and fertilization. Corg, Ntot, and water content as well as microbial biomass were higher in flood-irrigated than in non-flooded soils. Soil microbial biomass positively correlated with Corg, Ntot, and water extractable N. Gram-negative bacteria significantly increased, whereas the fungi/bacteria ratio significantly decreased in flood-irrigated soils compared to non-flooded soils. Arbuscular mycorrhizal fungi were positively correlated with soil pH. Flood pulse irrigation seemed to promote the build-up of a larger soil carbon and nitrogen pool as well as higher water content and microbial biomass. By this, it potentially mitigated negative mineral fertilization effects such as changed soil pH and reduced carbon use efficiency. We conclude that flood pulse irrigation may represent a sustainable alternative to mineral fertilization.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Effect of Organic Fertilizer on Soil Bacteria in Maize Fields

Soil microorganisms play an important role in agricultural ecosystems, but their response to organic fertilizer application has not been thoroughly elucidated. Thus, high-throughput sequencing was used to investigate the responses of soil bacterial to organic fertilizer amendment (composted from pig manure) in the field during the entire growth cycle of maize plants. Four treatments were studied: treatment with 2 kg·m−2 organic fertilizer application (OF_2), treatment with 4 kg·m−2 organic fertilizer application (OF_4), treatment with 6 kg·m−2 organic fertilizer application (OF_6), and a controlled treatment (CK) without fertilization. The results revealed that the bacterial richness in OF_2 was significantly lower than that of CK (p < 0.05). Soil eutrophication bacteria Bacteroidetes increased effectively in all fertilized soils, relative abundance in OF_2, OF_4, and OF_6 for the entire maize growth cycle was 68.00%, 71.40%, and 77.93% higher than that in CK, respectively. In addition, soil nitrobacteria (Nitrospirae, Nitrospira), were markedly decreased (p < 0.05) with fertilization amount. The relative abundance of the nitrogen-fixing genus Adhaeribacter in OF_6 was 209.28%, 72.8% and 35.66% higher than that in CK, OF_2 and OF_4 at mature stage. The pathogenic genus Flavolibacterium was significantly increased (p < 0.05) in fertilized soil at the seeding stage. The driving factor governing the variations of bacterial community in CK, OF_2, OF_4 and OF_6 were pH value, available phosphorus, available phosphorus, and chromium, respectively. The findings highlight that part of the soil functional or pathogenic bacteria population was susceptible to organic fertilizer application; and the driving factor of bacterial composition change was associated with the rate of fertilization. More targeted experiments are needed to enhance the understanding of functional bacteria and the synergistic effect of soil physicochemical property physical on soil bacteria.

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote^® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.

Changes in soil organic carbon status and microbial community structure following biogas slurry application in a wheat-rice rotation

Biogas slurry is widely used as a crop fertilizer due to its available nitrogen content. However, it remains unclear how biogas slurry application affects soil organic carbon (SOC) status and soil microbial community under typical agricultural systems. Here, under a wheat-rice field experiment, we examined the responses of SOC and soil bacterial and fungal communities to biogas slurry application, both with (BSS) and without (BS) straw return, relative to chemical nitrogen fertilizer with (CFS) and without (CF) straw return. The BS treatment significantly increased total organic carbon (TOC) at all soil depths (0-60 cm), compared to CF. Greater TOC occurred at 20-40 cm depth under BSS relative to all other treatments. However, straw return had no impact on soil TOC content under the CF and CFS treatments. Labile organic carbon (LOC) in the topsoil and recalcitrant organic carbon (ROC) at 20-60 cm depth was significantly greater under BS relative to CF. The bacterial class Gammaproteobacteria and family Hyphomicrobiaceae were found to be specifically abundant under biogas slurry application after one year of wheat-rice double cropping. Network analyses showed that the soil bacterial community under biogas slurry application was more complex than under chemical fertilizer application, while the opposite was true for the fungal community. Correlations between network modules and the SOC fractions indicated that biogas slurry application stimulated soil bacteria and fungi to participate in SOC cycling. The module functionality supports our speculation that soil microorganisms degraded the biogas slurry derived-ROC in the topsoil. Overall, we conclude that substitution of chemical fertilizer with biogas slurry can be beneficial for increasing SOC stocks and, in systems with straw return, enhancing straw decomposition.

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect

Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). Then, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions.

Straw retention efficiently improves fungal communities and functions in the fallow ecosystem

BACKGROUND

Straw retention is a substitute for chemical fertilizers, which effectively maintain organic matter and improve microbial communities on agricultural land. The purpose of this study was to provide sufficient information on soil fungal community networks and their functions in response to straw retention. Hence, we used quantitative real-time PCR (qRT-PCR), Illumina MiSeq (ITS rRNA) and FUNGuild to examine ITS rRNA gene populations, soil fungal succession and their functions under control (CK) and sugarcane straw retention (SR) treatments at different soil layers (0-10, 10-20, 20-30, and 30-40 cm) in fallow fields.

RESULT

The result showed that SR significantly enhanced ITS rRNA gene copy number and Shannon index at 0-10 cm soil depth. Fungi abundance, OTUs number and ACE index decreased with the increasing soil depth. The ANOSIM analysis revealed that the fungal community of SR significantly differed from that of CK. Similarly, significant difference was also observed between topsoil (0-20 cm) and subsoil (20-40 cm). Compared with CK, SR decreased the relative abundance of the pathogen, while increased the proportion of saprotroph. Regarding soil depth, pathogen relative abundance in topsoil was lower than that in subsoil. Besides, both sugarcane straw retention and soil depths (topsoil and subsoil) significantly altered the co-occurrence patterns and fungal keystone taxa closely related to straw decomposition. Furthermore, both SR and topsoil had higher average clustering coefficients (aveCC), negative edges and varied modularity.

CONCLUSIONS

Overall, straw retention improved α-diversity, network structure and fungal community, while reduced soil pathogenic microbes across the entire soil profile. Thus, retaining straw to improve fungal composition, community stability and their functions, in addition to reducing soil-borne pathogens, can be an essential agronomic practice in developing a sustainable agricultural system.

DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

Recent Advances in the Chemistry of Bioactive Compounds from Plants and Soil Microbes: a Review

Bioactive compounds derived from plants and microbial sources are required for the survival of the human race and groundbreaking research must continue in this line. Plants and microbes are the major sources of naturally occurring bioactive compounds for numerous biotechnological applications. Recent progress in the fields of bioactive compounds and soil chemistry in agriculture has since given man a lead to the discovery of potent drugs that combat both human and plant diseases. The soil provides the medium for the growth of medicinal plants, but its contamination greatly affects the quality of drugs, food crops, and other essential elements present in the plants which give strength to the body. This area has attracted the attention of scientists and the drug industry toward developing more potent drugs from medicinal plants grown in different soil. The studies of the effect of various parameters and the properties of soil such as; effect of heavy metals, pH, soil organic matter, and phytoremediation process have given a measure of some quality dependence of the soil producing secondary metabolites and soil containing microbes. The information provided will be useful in determine the action of microbes and their interaction with the soil and all true plants producing drugs. Some active compounds in plants and microbes, their properties, and applications have been described in this review. The soil microbes, activities and their interactions, effects of soil particle size, dispersibility and stability of microbes in the soil, and the future outlook for the development of novel active compounds have been reported.

Soil Microbial Composition and phoD Gene Abundance Are Sensitive to Phosphorus Level in a Long-Term Wheat-Maize Crop System

Microbes associated with phosphorus (P) cycling are intrinsic to soil P transformation and availability for plant use but are also influenced by the application of P fertilizer. Nevertheless, the variability in soil P in the field means that integrative analyses of soil P cycling, microbial composition, and microbial functional genes related to P cycling remain very challenging. In the present study in the North China Plain, we subjected the bacterial and fungal communities to amplicon sequencing analysis and characterized the alkaline phosphatase gene (phoD) encoding bacterial alkaline phosphatase in a long-term field experiment (10 years) with six mineral P fertilization rates up to 200 kg P ha^–1. Long-term P fertilization increased soil available P, inorganic P, and total P, while soil organic P increased until the applied P rate reached 25 kg ha^–1 and then decreased. The fungal alpha-diversity decreased as P rate increased, while there were no significant effects on bacterial alpha-diversity. Community compositions of bacteria and fungi were significantly affected by P rates at order and family levels. The number of keystone taxa decreased from 10 to 3 OTUs under increasing P rates from 0 to 200 kg ha^–1. The gene copy numbers of the biomarker of the alkaline phosphatase phoD was higher at moderate P rates (25 and 50 kg ha^–1) than at low (0 and 12.5 kg ha^–1) and high (100 and 200 kg ha^–1) rates of P fertilization, and was positively correlated with soil organic P concentration. One of the keystone taxa named BacOTU3771 belonging to Xanthomonadales was positively correlated with potential functional genes encoding enzymes such as glycerophosphoryl diester phosphodiesterase, acid phosphatase and negatively correlated with guinoprotein glucose dehydrogenase. Altogether, the results show the systematic effect of P gradient fertilization on P forms, the microbial community structure, keystone taxa, and functional genes associated with P cycling and highlight the potential of moderate rates of P fertilization to maintain microbial community composition, specific taxa, and levels of functional genes to achieve and sustain soil health.

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce

Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.

Functional potential differences between Firmicutes and Proteobacteria in response to manure amendment in a reclaimed soil

Manure amendment generally bolsters soil organisms but not all bacteria equally. To understand why different taxa respond differently, we used shotgun metagenomic approaches to profile functional potentials and correlate them with taxon abundances. A soil originally unproductive was reclaimed using commercial manure and finally became productive. The abundance of Firmicutes in the soil decreased, whereas that of Bacteroidetes and Proteobacteria increased after manure addition. Thirty-nine KEGG modules were significantly different across fertilizer treatments. These modules were mainly associated with the phosphoenolpyruvate-dependent phosphotransferase system (PTS), ATP-binding cassette (ABC) transporters, and two-component signal transduction systems. The Proteobacteria and Firmicutes mainly contributed to these modules. Correlation between the abundances of phyla and orthologs showed two distinctive patterns. One linked the Firmicutes to cell wall biosynthesis, PTS, and ABC transporters, and the other linked the Betaproteobacteria, Bacteroidetes, and Verrucomicrobia to lipopolysaccharide biosynthesis, bacterial motility, and carbon metabolism. Correlation between the abundances of phyla and Carbohydrate-Active Enzyme Database families also showed two distinctive patterns, one of them linking the Betaproteobacteria, Bacteroidetes, and Verrucomicrobia to very high abundances of glycosyltransferases and glycoside hydrolases. Overall, the Proteobacteria and Firmicutes were main drivers of functional potential differences across fertilizer treatments. The Firmicutes were enriched with genes associated with cell wall biosynthesis and membrane transports, while Proteobacteria with lipopolysaccharide biosynthesis and carbohydrate metabolism, which supports our hypothesis that the Firmicutes have a lower potential for utilizing manure-derived carbohydrates, while Proteobacteria have a higher potential. This explains why the Proteobacteria and Firmicutes responded to manure differently.

In-Depth Observation on the Microbial and Fungal Community Structure of Four Contrasting Tomato Cultivation Systems in Soil Based and Soilless Culture Systems

As soil and soilless culture systems are highly dynamic environments, the structure of rhizosphere microbial communities is consistently adapting. There is a knowledge gap between the microbial community structure of soil based and soilless culture systems and thus we aimed at surveying their impact on diversity and composition of bacterial communities across a 10-month period in a tomato cultivation system. We compared community metrics between an soil based culture system fertilized with malt sprouts and blood meal, known for its slow and high mineralization rate, respectively and a soilless culture system fertilized with fish effluent or supplemented with an liquid organic fertilizer. Bacterial and fungal community composition was followed over time using two complementary techniques, phospholipid fatty acid analysis and 16S rRNA amplicon sequencing. Nitrogen dynamics and plant performance were assessed to provide insight on how bacterial diversity of soil and soilless microbial communities ultimately impacts productivity. Similar plant performance was observed in soilless culture systems and soil based system and yield was the highest with the aquaponics-derived fertilizer. Soil and soilless cultivating systems supplemented with different nitrogen-rich fertilizers differed on its characteristics throughout the experimental period. Fast-paced fluctuations in pH(H₂O) and nutrient cycling processes were observed in growing medium. Physicochemical characteristics changed over time and interacted with bacterial community metrics. Multivariate analysis showed that plant length, pH, Flavisolibacter, phosphorus, chloride, ammonium, potassium, calcium, magnesium, sodium, electrical conductivity, nitrate, sulfate, and the bacterial genera Desulfotomaculum, Solirubrobacter, Dehalococcoides, Bythopirellula, Steroidobacter, Litorilinea, Nonomuraea were the most significant factors discriminating between natural soils supplemented with animal and plant by-products. Long-term fertilizer regimes significantly changed the PLFA fingerprints in both the soilless culture and soil based culture system. The use of these by-products in the soil was positively associated with arbuscular mycorrhizal fungi (AMF), which may influence rhizosphere communities through root exudates and C translocation. Community structure was distinct and consistently different over time, despite the fertilizer supplementation. The fungal microbial community composition was less affected by pH, while the composition of the bacterial communities (Actinomycetes, Gram-negative bacteria, and Gram-positive bacteria) was closely defined by soil pH, demonstrating the significance of pH as driver of bacterial community composition. Fertilizer application may be responsible for variations over time in the ecosystem. Knowledge about the microbial interactions in tomato cultivating systems opens a window of opportunity for designing targeted fertilizers supporting sustainable crop production.

Characterising the effect of crop species and fertilisation treatment on root fungal communities

Information about the root mycobiome may improve the overall quality of the plants and contribute to a valuable strategy to enhance sustainable agriculture. Therefore, we assessed differences in fungal community diversity and composition in the roots of potato, wheat and barley grown under mineral nitrogen fertilisation at five rates, with and without farmyard manure amendment. The same factorial combination of treatments has been used since 1989. Species richness and diversity, as well as community composition, of different fungal guilds were characterised using Illumina MiSeq sequencing of the ITS2 region. Crop species was the main factor determining overall fungal richness and diversity, with wheat showing the highest, and potato the lowest, richness and diversity. Pathogen diversity indices were highest in wheat plots amended with farmyard manure, whereas the lowest values were observed for potato roots. Fertilisation treatments and the interaction between crop species and fertilisation had the strongest impact on arbuscular mycorrhiza and saprotroph diversity. Crop species also determined the composition of the overall fungal community and that of fungal guilds, whereas fertilisation treatment had only a minor effect. This study highlights crop species as the main driver in shaping root fungal diversity and composition under the same environmental conditions.

Spatial variation of the soil bacterial community in major apple producing regions of China

AIMS

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality.

METHODS AND RESULTS

Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids.

CONCLUSIONS

Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

Biochar-fertilizer interaction modifies N-sorption, enzyme activities and microbial functional abundance regulating nitrogen retention in rhizosphere soil

The impact of the excessive use of N fertilizer remains an environmental problem of global concern. The effect of biochar on soil N retention is still unclear, and knowledge on how a mixture of biochar and fertilizer (B-F) influence N-sorption, N-cycling enzymes activities, diversity and functional abundance of organisms regulating N-retention in rhizosphere soil is poorly understood. Therefore, biochars derived from bamboo, rice straw, cow and pig manure were characterized, and their interactions with NPK fertilizer were evaluated. Results showed that while the effect of biochar on N retention varied among biochar types, such variations increased after B-F. Unlike NH₄⁺ retention, NO₃^- retention by biochar in fertilized soil was poor (<8 weeks), but were however increased after longer periods (15 weeks) in B-F due to plant uptake, sorption and stimulation of N-cycling enzymes activities. This stimulation proved that N-fertilizer provided substrates for N-cycling organisms which was confirmed by the dominance of Proteobacteria, Chloroflexi, Actinobacteria, and Gemmatimonadetes which are important in soil N-cycling, despite the reductions in total diversity, class, phyla and genera abundance of bacterial 16SrRNA genes by B-F. This suggested that B-F induced specific organisms involved in N-cycling, which out-competed other organisms not involved in N-cycling. The provision of substrates by N-fertilizer in B-F for bacterial groups involved in N-cycling modified the rhizosphere microbial structure. The abundance of N-cycling organisms was regulated by the persistence among dominant groups, soil pH, total N, and microbial colonization induced by different biochars interacting with fertilizer which led to enhanced N-retention.

Effects of fertilization and reclamation time on soil bacterial communities in coal mining subsidence areas

Land impaired by mining activity can be restored to a productive and healthy state through a variety of reclamation methods. Fertilization is one effective method to improve soil fertility and microbial activity. However, the effects of fertilization and reclamation time on bacterial communities in reclaimed soil remain unclear. Here, we hypothesized that both fertilization and reclamation time could promote restoration of reclaimed soil. To test this, soil properties and bacterial communities in a reclaimed coal mining subsidence area were investigated under different fertilizer regimes and different reclamation times. Compared with no fertilization treatment, fertilization rapidly improved the soil nutrients and bacterial α-diversity, both of which exhibited no significant differences between chemical fertilizer and organic fertilizer. With increasing of reclamation time, the soil nutrient levels (soil organic matter, available nitrogen, available phosphorus, available potassium) and the bacterial diversity increased. Meanwhile, the relative abundances of Proteobacteria, Actinobacteria and Bacteroidetes increased, and the relative abundances of Acidobacteria, Chloroflexi and Nitrospirae decreased. Compared with the 1-year and 3-year reclaimed soils, the soil nutrients and bacterial community structure in the 7-year reclaimed soils were more similar to those in the undisturbed soils. In conclusion, reclamation time is the main driving force for the restoration of soil properties and bacterial communities in mining areas, and fertilization can shorten the recovery time of the reclaimed soil.

The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates

Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha^-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha^-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha^-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha^-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha^-1) and excess Zn (34.1 kg ha^-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers.

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.

A consecutive 4-year elevated air temperature shaped soil bacterial community structure and metabolic functional groups in the rhizosphere of black locust seedlings exposed to lead pollution

Global warming may influence the bioavailability and mobility of heavy metals by stimulating or inhibiting plant growth, thereby influencing rhizosphere soil chemistry and microbial characteristics. Black locust has been widely planted in China as a promising species for afforestation programs, farmland shelterbelt projects, and soil restoration in mined areas because of its rapid growth and adaptability to environmental stressors. Here, we examined soil bacterial community structure and predicted bacterial metabolic function in the rhizosphere of black locust exposed to elevated temperature (+1.99 °C) and Pb for 4 years. Elevated temperature significantly (p < 0.05) reduced total carbon (TC), total nitrogen (TN), and total sulfur (TS) contents in above-ground parts but increased TC and TN contents in roots and seedling height under Pb exposure. Elevated temperature significantly (p < 0.05) increased Pb availability and raised pH, TC, TN, TS and water-soluble organic carbon (WSOC) contents, and the C:H ratio in rhizosphere soils under Pb exposure. The interactive effects between Pb and temperature on pH, TC, TH, TS, WSOC, and the C:H ratio were significant (p < 0.05). Elevated temperature significantly (p < 0.05) reduced the diversity and the richness of bacterial community, altered genus-level bacterial community composition, and improved (p < 0.05) the relative abundances of some bacteria involving in terpenoids and polyketides and xenobiotics biodegradation metabolism under Pb exposure. Canonical correspondence analysis indicated that pH, WSOC, C:N ratio, and soluble Pb were significant (p < 0.05) factors on the relative abundance of bacterial genera, such as Ochrobactrum and Sphingomnas. Overall, long-term elevated temperature resulted in changes in rhizosphere soil characteristics and Pb availability, thus affecting the bacterial community structure and metabolic functional groups. The conclusion helps us understand the response mechanism of soil bacteria in the rhizosphere to heavy metals under global warming scenarios.

Effects of inorganic and organic treatments on the microbial community of maize rhizosphere by a shotgun metagenomics approach

Purpose

The main drivers of biogeochemical cycling of nutrients, plant growth promotion, and disease suppression are microbes. Organic manure increases soil quality and plant productivity; the same is true of inorganic fertilizer. In this study, we explored shotgun metagenomics study to investigate how maize (Zea mays everta) rhizosphere microbial community diversity is shaped following the application of both compost manure and inorganic fertilizer.

Methods

We used high throughput next-generation sequencing—metagenomics studies to examine the rhizosphere microbial community of maize plants grown in an organic compost manure (8 tons/ha and 4 tons/ha) and inorganic (120 kg/ha NPK and 60 kg/ha NPK chemical) fertilized soils. An unfertilized soil was used as a control.

Results

The taxonomic analysis of the soil revealed that regardless of the fertilization regimes, Proteobacteria and Bacteroidetes are distributed across all the samples, but in varying populations. Higher quantities of organic manure (8 tons/ha) and lower (60 kg/ha) nitrogen fertilizer, as well as the untreated control, supports the selection and enrichment of Proteobacteria and Actinobacteria, while lower quantities of organic compost (4 tons/ha) manure boost the population of Bacteroidetes. Firmicutes, on the other hand, were most abundant in low organic manure (4 tons/ha) and higher inorganic (120 kg/ha) fertilized soil. Fungi were selected and enriched by higher (8 tons/ha) and lower (4 tons/ha) compost manure, while archaea were mostly supported by higher doses of inorganic fertilizers (120 kg/ha) and high compost manure (8 tons/ha) treatments.

Conclusion

Therefore, comprehending the effects of compost and chemical fertilizers (NPK—20% nitrogen, 7% phosphorus, 3% potassium) on the community structure, dynamics, and abundance of rhizosphere microbiome will help in the manipulation of soil microbial community to increase microbial diversity in the agroecosystem.

Different fertilization treatments in coal mining-affected soils change bacterial populations and enable soil reclamation

Purpose

Coal mining activities result in large-scale soil degradation and ecosystem imbalances in many countries. Fertilization is an effective way to improve soil fertility and microbial activity. However, the effect of different fertilizers and remediation time on the subsided soil is not clear. The aim of this study is to explore the effects on soil fertility and the bacterial community.

Methods

In this study, we compared three fertilization regimes (inorganic, organic, and combined) applied over a 5-year period for the purpose of rehabilitating subsoil through measurement of soil’s chemical properties and microbial biomass. Bacterial diversity was evaluated in different reclaimed soils via high-throughput 16S rDNA sequencing; 1,938,561 total sequences were obtained.

Results

The results showed that fertilization improved various soil properties, including the concentrations of available phosphorus, available potassium, and alkali-hydrolysable nitrogen, therefore, increasing microbial biomass. A significant increase in soil microbial diversity was observed in fertilized soils compared to the initial conditions. A positive correlation between microbial diversity and soil properties was observed. Regarding an improvement in soil properties and crop yields, the organic fertilizer demonstrated significantly more effectiveness compared to the inorganic fertilizer. Meanwhile, the relative abundance of Proteobacteria, Bacteroidetes, and Verrucomicrobia increased, but the relative abundance of Chloroflexi and Nitrospirae decreased. More specifically, we found that several Proteobacteria subgroups, such as Rhizobiales, Myxococcales, Sphingomonadales, Rhodospirillales, Xanthomonadales, and Burkholderiales, increased after the restoration. Additionally, the composition of the bacterial community in the 5-year groups (M5, O5, and MO5) was similar to the composition of the FS group, and the yield of the maize test crop following the 5-year restoration period was close to the average in China.

Conclusion

This result indicates that soil reclamation via fertilization can contribute to soil recovery over time. Therefore, we concluded that fertilization is an effective strategy for the restoration of soil properties and bacterial communities in mining soil.

Bioremediation of PAH-contaminated shooting range soil using integrated approaches

Serious contamination of polycyclic aromatic hydrocarbons (PAHs) occurs at outdoor shooting ranges due to the accumulation of clay target fragments containing coal tar or petroleum pitch. These contaminated sites are characterized with high-molecular-weight PAHs that are low in bioavailability and recalcitrant to bioremediation. We evaluated the effectiveness of different remediation strategies, used individually or in combinations, to decontaminate PAHs in a shooting range soil. The treatments included vegetation with bermudagrass [Cynodon dactylon (L.) Pers] or switchgrass [Panicum virgatum]), bioaugmentation of Mycobacterium vanbaalenii PYR-1, and addition of surfactants (Brij-35, rhamnolipid biosurfactant, or Brij-35/sodium dodecyl sulfate mixture). The initial total PAH concentration in the shooting range soil was 373 mg/kg and consisted of primarily high-molecular-weight PAHs (84%). Planting of bermudagrass and switchgrass resulted in 36% and 27% ∑₁₆PAH reduction compared to the non-vegetated control, respectively. Bermudagrass enhanced soil dehydrogenase activity and both vegetation treatments also increased polyphenol oxidase activity. Bioaugmentation of M. vanbaalenii PYR-1 had a significant effect only on the dissipation of high-molecular-weight PAHs, leading to a 15% decrease (∑₁₀PAH) compared to the control. In the non-vegetated soil, Brij-35/sodium dodecyl sulfate mixture increased PAH degradation compared to the no surfactant control. The increased PAH biodegradation in the vegetated and bioaugmented treatments improved lettuce [Lactuca sativa] seed germination, suggesting reduced toxicity in the treated soils. Phytoremediation using bermudagrass or switchgrass with bioaugmentation of M. vanbaalenii PYR-1 was an effective in situ remediation option for shooting range soils with heavy PAH contamination.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.

Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil

P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.

This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens. Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.

IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.)

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha⁻¹ to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.

Effects of Epichloë gansuensis Endophyte on the Root and Rhizosphere Soil Bacteria of Achnatherum inebrians Under Different Moisture Conditions

This study was conducted to explore effects of the systemic fungal endophyte Epichloë gansuensis on root and rhizosphere soil bacterial diversity of Achnatherum inebrians host plants growing under different moisture conditions. Soil properties of different treatments were compared using standard techniques. A total of 4371379 16S rRNA gene sequences were obtained and assigned to 5025 operational taxonomic units (OTUs). These OTUs in roots and rhizosphere soil were divided into 13 and 17 phyla, respectively, and the Actinobacteria and Proteobacteria were the most abundant phyla both in roots and rhizosphere soil. Shannon diversity and Chao1 richness index of bacteria in rhizosphere soil was significantly higher than in roots. E. gansuensis decreased the Shannon diversity of the root-associated bacterial community, and increased Shannon diversity and Chao1 richness index of the rhizosphere soil bacterial community of A. inebrians. Meanwhile, Chao1 richness of the rhizosphere soil bacterial community of A. inebrians significantly increased with the increase of the soil moisture level. Structural equation modeling also emphasized that E. gansuensis decreased the diversity of the root-associated bacterial community and increased the diversity of the rhizosphere soil bacterial community through decreasing soil available N. Additionally, soil moisture increased the diversity of the rhizosphere soil bacterial community through increased soil pH, C/N, and NN, and decreased soil AP. The E. gansuensis endophyte and soil moisture effects on root and rhizosphere soil bacterial diversity were likely to be from responses to modifications of the rhizosphere soil properties.

Reduced microbial diversity induces larger volatile organic compound emissions from soils

Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.