Biochar and Rhizobacteria Amendments Improve Several Soil Properties and Bacterial Diversity

Response of soil microbial ecological functions and biological characteristics to organic fertilizer combined with biochar in dry direct-seeded paddy fields

Biochar and organic fertilizer are commonly used to maintain soil health and sustainable agroecosystems, and the alternate wet-dry management of soil moisture in dry direct-seeded paddy fields can complicate the effects of biochar and organic fertilizer on soil microhabitats. Therefore, this study used chicken manure organic fertilizer to replace some of the inorganic fertilizer and applied biochar to explore the ability of biochar and organic fertilizer to regulate the functions of the soil microhabitat in dry direct-seeded paddy fields. The coupling effect of organic fertilizer and biochar increased the diversity and richness of soil bacteria but had no significant effect on soil fungi. Biochar and organic fertilizer affected the distribution and composition of soil bacteria and fungi, and the total number of soil bacteria and fungi increased by 1365 and -71 (5 t/hm2 biochar and no organic fertilizer), 660 and 79 (10 t/hm2 biochar and no organic fertilizer), 3121 and 7 (no biochar and 20 % organic fertilizer substitution), 1873 and -72 (5 t/hm2 biochar and 20 % organic fertilizer substitution), and -544 and -65 (10 t/hm2 biochar and 20 % organic fertilizer substitution), respectively, compared with that of the control treatment. Compared with the application of biochar alone, the coupling effect of biochar and organic fertilizer increased the average degree (0.95 and 0.16), links (190 and 32), and ratio of fungal positive links (1.651 %), and decreased the modularity (0.034 and 0.052) and ratio of bacterial positive links (6.482 %) of bacterial and fungal networks. In addition, the coupling effect resulted in a more complex association between soil microbial diversity and richness and microbial ecological functions. Random forest predictions indicated that, organic fertilizer as a random factor, changes in the abundance of bacterial Bacteroidetes and Nitrospirae and fungal Monoblepharomycota were the main factors driving the differences in soil microbial ecological functions.

Effects of biochar and compost on microbial community assembly and metabolic processes in glyphosate, imidacloprid and pyraclostrobin polluted soil under freezethaw cycles

Biochar and organic compost are widely used in agricultural soil remediation as soil immobilization agents. However, the effects of biochar and compost on microbial community assembly processes in polluted soil under freezingthawing need to be further clarified. Therefore, a freezethaw cycle experiment was conducted with glyphosate (herbicide), imidacloprid (insecticide) and pyraclostrobin (fungicide) polluted to understand the effect of biochar and compost on microbial community assembly and metabolic behavior. We found that biochar and compost could significantly promote the degradation of glyphosate, imidacloprid and pyraclostrobin in freezethaw soil decrease the half-life of the three pesticides. The addition of immobilization agents improved soil bacterial and fungal communities and promoted the transformation from homogeneous dispersal to homogeneous selection. For soil metabolism, the combined addition of biochar and compost alleviated the pollution of glyphosate, imidacloprid and imidacloprid to soil through up-regulation of metabolites (DEMs) in amino acid metabolism pathway and down-regulation of DEMs in fatty acid metabolism pathway. The structural equation modeling (SEM) results showed that soil pH and DOC were the main driving factors affecting microbial community assembly and metabolites. In summary, the combined addition of biochar and compost reduced the adverse effects of pesticides residues.

Less is more: A new strategy combining nanomaterials and PGPB to promote plant growth and phytoremediation in contaminated soil

Novel combination strategies of nanomaterials (NMs) and plant growth-promoting bacteria (PGPB) may facilitate soil remediation and plant growth. However, the efficiency of the NM-PGPB combination and interactions among NMs, PGPB, and plants are still largely unknown. We used multiwalled carbon nanotubes (MWCNTs) and zero-valent iron (nZVI) combined with Bacillus sp. PGP5 to enhance the phytoremediation efficiency of Solanum nigrum on heavy metal (HM)-contaminated soil. The NM-PGPB combination showed the best promoting effect on plant growth, which also had synergistic effects on the bioaccumulation of HMs in S. nigrum. The MWCNT-PGP5 combination increased the Cd, Pb, and Zn removal efficiency of S. nigrum by 62.03%, 69.44%, and 61.31%, respectively. The underlining causes of improved plant growth and phytoremediation by NMs-PGPB combination were further elucidated. NM application promoted PGPB survival in soil. Compared with each single application, the combined application minimized disturbance to plant transcription levels and rhizosphere microbial community, resulting in the best performance on soil remediation and plant growth. The NM-PGPB-induced changes in the microbial community and root gene expression were necessary for plant growth promotion. This work reveals the "less is more" advantage of the NM-PGPB combination in soil remediation, providing a new strategy for soil management.

Biochar modulating soil biological health: A review

Biochar can be used for multifunctional applications including the improvement of soil health and carbon storage, remediation of contaminated soil and water resources, mitigation of greenhouse gas emissions and odorous compounds, and feed supplementation to improve animal health. A healthy soil preserves microbial biodiversity that is effective in supressing plant pathogens and pests, recycling nutrients for plant growth, promoting positive symbiotic associations with plant roots, improving soil structure to supply water and nutrients, and ultimately enhancing soil productivity and plant growth. As a soil amendment, biochar assures soil biological health through different processes. First, biochar supports habitats for microorganisms due to its porous nature and by promoting the formation of stable soil micro-aggregates. Biochar also serves as a carbon and nutrient source. Biochar alters soil physical and chemical properties, creating optimum soil conditions for microbial diversity. Biochar can also immobilize soil pollutants and reduce their bioavailability that would otherwise inhibit microbial growth. However, depending on the pyrolysis settings and feedstock resources, biochar can be comprised of contaminants including polycyclic aromatic hydrocarbons and potentially toxic elements that can inhibit microbial activity, thereby impacting soil health.

Recent advances in Bacillus-mediated plant growth enhancement: a paradigm shift in redefining crop resilience

The Bacillus genus has emerged as an important player in modern agriculture, revolutionizing plant growth promotion through recent advances. This review provides a comprehensive overview of the critical role Bacillus species play in boosting plant growth and agricultural sustainability. Bacillus genus bacteria benefit plants in a variety of ways, according to new research. Nitrogen fixation, phosphate solubilization, siderophore production, and the production of growth hormones are examples of these. Bacillus species are also well-known for their ability to act as biocontrol agents, reducing phytopathogens and protecting plants from disease. Molecular biology advances have increased our understanding of the complex interplay between Bacillus species and plants, shedding light on the genetic and metabolic underpinnings of these interactions. Furthermore, novel biotechnology techniques have enabled the development of Bacillus-based biofertilizers and biopesticides, providing sustainable alternatives to conventional chemical inputs. Apart from this, the combination of biochar and Bacillus species in current biotechnology is critical for improving soil fertility and encouraging sustainable agriculture through enhanced nutrient retention and plant growth. This review also emphasizes the Bacillus genus bacteria's ability to alleviate environmental abiotic stresses such as drought and salinity, hence contributing to climate-resilient agriculture. Moreover, the authors discuss the challenges and prospects associated with the practical application of Bacillus-based solutions in the field. Finally, recent advances in Bacillus-mediated plant growth promotion highlight their critical significance in sustainable agriculture. Understanding these improvements is critical for realizing the full potential of Bacillus genus microorganisms to address current global food production concerns.

Nitrogen (N) "supplementation, slow release, and retention" strategy improves N use efficiency via the synergistic effect of biochar, nitrogen-fixing bacteria, and dicyandiamide

Irrational nitrogen (N) fertilizer management and application practices have led to a range of ecological and environmental problems that seriously threaten food security. In this study, an effective N fertilizer management strategy was established for improving N fertilizer utilization efficiency (NUE). Biochar, N2-fixing bacteria (Enterobacter cloacae), and a nitrification inhibitor (dicyandiamide, DCD) were simultaneously added to the soil during maize cultivation. The goal was to increase soil ammonium nitrogen content and NUE by regulating the relative abundance, enzyme activity, and functional gene expression of N conversion-related soil microbes. Biochar combined with E. cloacae and DCD significantly increased soil N content, and the NUE reached 46.69 %. The relative abundance of Burkholderia and Bradyrhizobium and the activity of nitrogenase increased significantly during biological N2 fixation. Further, the abundance of the nifH gene was significantly up-regulated. The relative abundance of Sphingomonas, Pseudomonas, Nitrospira, and Castellaniella and the activities of ammonia monooxygenase and nitrate reductase decreased significantly during nitrification and denitrification. Moreover, the abundance of the genes amoA and narG was significantly down-regulated. Correlation analyses showed that the increase in soil N2 fixation and the suppression of nitrification and denitrification reactions were the key contributors to the increase in soil N content and NUE. Biochar combined with E. cloacae and DCD synergistically enabled the supplementation, slow release, and retention of N, thus providing adequate N for maize growth. Thus, the combination of biochar, E. cloacae, and DCD is effective for mitigating the irrational application of N fertilizers and reducing N pollution.

Influences of phosphorus-modified biochar on bacterial community and diversity in rhizosphere soil

Root-associated bacteria play a vital role in the soil ecosystem and plant productivity. Previous studies have reported the decline of bacterial community and rhizosphere soil quality in the cultivation of some medicinal plants (i.e., Pseudostellaria heterophylla). Phosphorus (P)-modified biochar has the potential to improve soil health and quality. However, its influence on the bacterial community and diversity in the rhizosphere of medicinal plants is not well understood. Therefore, this study aims to investigate the effects of P-modified biochar on the bacterial community and diversity in the rhizosphere of P. heterophylla. Soil samples were collected from the rhizosphere of 4-month P. heterophylla under control (no biochar), 3% unmodified and 3% P-modified biochar treatments, respectively. Compared with control and unmodified biochar treatment, P-modified biochar significantly increased the relative abundance of plant-beneficial bacteria (P < 0.05), particularly Firmicutes, Nitrospirae and Acidobacteria. The relative abundance of Bacillus, belonging to Firmicutes, was dramatically raised from 0.032% in control group to 1.723% in P-modified biochar-treated group (P < 0.05). These results indicate the potential enhancement of soil quality for the growth of medicinal plants. The application of biochar significantly increased bacterial richness and bacterial diversity (P < 0.05). P modification of biochar did not have significant effects on soil bacterial richness (P > 0.05), while it reduced Shannon and increased Simpson diversity index of soil bacterial communities significantly (P < 0.05). It indicates a decrease in bacterial diversity. This research provides a new perspective for understanding the role of P-modified biochar in the rhizosphere ecosystem.

Role of plant metabolites in the formation of bacterial communities in the rhizosphere of Tetrastigma hemsleyanum

Tetrastigma hemsleyanum Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of Actinomadura, Streptomyces and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.

Effects of biochar on soil microbial communities: A meta-analysis

Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.

High resilience of soil bacterial communities to large wildfires with an important stochastic component

Wildfires alter the structure and functioning of ecosystems through changes in their biotic and abiotic components. A deeper understanding recovery process concerning diverse communities and properties within these components can provide valuable insights into the ecological effects of wildfires. Therefore, it is appropriate to enhance our understanding of the resilience of bacterial communities after wildfires within Mediterranean ecosystems. In this research, soil bacterial community resilience was evaluated in three types of ecosystems for two fire severities, two years after a large wildfire in Mediterranean ecosystems. The resilience of the soil bacterial community refers to its ability to return to original state after disturbance. This capacity can be estimated by the study of its recovery over time. In this study we evaluated the resilience using the variables: alpha diversity, beta diversity and the changes in abundance of both OTUs (Operational Taxonomic Units) and principal bacterial taxa (phyla, classes or orders). Our results showed that resilience depends on fire severity and type of ecosystem. We studied three ecosystems with different stage in the secondary succession: low maturity shrublands and heathlands, and high maturity oak forests. In general, high resilience in the soil bacterial community was observed in heathlands under low and high fire severity conditions. The other two ecosystems were resilient only under low fire severity. Stochastic replacement of the abundance of the OTUs was observed in all three ecosystems, with a notable impact on oak forests, under during high-severity conditions.

Biochar-biofertilizer combinations enhance growth and nutrient uptake in silver maple grown in an urban soil

Declining tree health status due to pollutant impacts and nutrient imbalance is widespread in urban forests; however, chemical fertilizer use is increasingly avoided to reduce eutrophication impacts. Biochar (pyrolyzed organic waste) has been advocated as an alternative soil amendment, but biochar alone generally reduces plant N availability. The combination of biochar and either organic forms of N or Plant Growth Promoting Microbes (PGPMs) as biofertilizers may address these challenges. We examined the effects of two wood biochar types with Bacillus velezensis and an inactivated yeast (IY) biofertilizer in a three-month factorial greenhouse experiment with Acer saccharinum L. (silver maple) saplings grown in a representative urban soil. All treatments combining biochars with biofertilizers significantly increased sapling growth, with up to a 91% increase in biomass relative to controls. Growth and physiological responses were closely related to nutrient uptake patterns, with nutrient vector analyses indicating that combined biochar and biofertilizer treatments effectively addressed nutrient limitations of both macronutrients (N, P, K, Mg, Ca), and micronutrients (B, Fe, Mn, Mo, Na, S, and Zn). Biochar-biofertilizer treatments also reduced foliar concentrations of Cu, suggesting potential to mitigate toxic metal impacts common in urban forestry. We conclude that selected combinations of biochar and biofertilizers have substantial promise to address common soil limitations to tree performance in urban settings.

Effect of biochar and bioorganic fertilizer on the microbial diversity in the rhizosphere soil of Sesbania cannabina in saline-alkaline soil

Introduction

Biochar and bioorganic fertilizer (BOF) application in agriculture has garnered increasing interest recently. However, the effects of biochar and BOF on rhizosphere soil microecology, especially in a region with saline-alkaline soil, remain largely unexplored.

Methods

In this study, we performed Illumina-based 16S rRNA sequencing to investigate the effects of biochar with or without BOF addition, as well as at different addition rates and particles sizes, on the microecology of saline-alkaline rhizosphere soil.

Results

In the field experiment, biochar and BOF application altered the rhizosphere soil microecology. Actinobacteriota, Proteobacteria, and Chloroflexi accounted for >60% of the total bacterial population in each treatment. In the different treatments, Actinobacteria and Alphaproteobacteria were the predominant classes; Micromonosporales and Vicinamibacterales were the dominant orders; norank_f__Geminicoccaceae and Micromonosporaceae were the most abundant families; and Micromonospora and norank_f_Geminicoccaceae were the predominant genera. Application of biochar with or without BOF decreased soil electrical conductivity (EC) by 7% -11.58% only at the depth of 10 cm below the surface, again, soil EC can be significantly reduced by an average of 4% at 10 cm depth soil after planting Sesbania cannabina. Soil organic carbon, organic matter, available potassium, and available phosphorus contents had significant effects on the soil bacterial community structure.

Conclusion

Co-application of biochar and BOF resulted in the greatest improvement of rhizosphere soil microecology, either by promoting plant growth or improving the nutrition and physicochemical properties of soil, followed by BOF alone and biochar alone. Additionally, higher application rate of biochar was better than lower application rate, and fine biochar had a stronger effect than coarse biochar. These results provide guidance for the development of new saline-alkaline soil remediation strategies.

Effects of biochar and freeze‒thaw cycles on the bacterial community and multifunctionality in a cold black soil area

Global climate change has altered soil freeze‒thaw cycle events, and little is known about soil microbe response to and multifunctionality regarding freeze‒thaw cycles. Therefore, in this study, biochar was used as a material to place under seasonal freeze-thaw cycling conditions. The purpose of this study was to explore the ability of biochar to regulate the function of freeze-thaw soil cycles to ensure spring sowing and food production. The results showed that biochar significantly increased the richness and diversity of soil bacteria before and after freezing-thawing. In the freezing period, the B50 treatment had the greatest improvement effect (2.6% and 5.5%, respectively), while in the thawing period, the B75 treatment had the best improvement effect. Biochar changed the composition and distribution characteristics of the bacterial structure and enhanced the multifunctionality of freeze-thaw soil and the stability of the bacterial symbiotic network. Compared with the CK treatment, the topological characteristics of the bacterial ecological network of the B50 treatment increased the most. They were 0.89 (Avg.degree), 9.79 (Modularity), 9 (Nodes), and 255 (Links). The freeze-thaw cycle decreased the richness and diversity of the bacterial community and changed the composition and distribution of the bacterial community, and the total bacterial population decreased by 658 (CK), 394 (B25), 644 (B50) and 86 (B75) during the thawing period compared with the freezing period. The soil multifunctionality in the freezing period was higher than that during the thawing period, indicating that the freeze-thaw cycle reduced soil ecological function. From the perspective of abiotic analysis, the decrease in soil multifunctionality was due to the decrease in soil nutrients, enzyme activities, soil basic respiration and other singular functions. From the perspective of bacteria, the decrease in soil multifunctionality was mainly due to the change in the Actinobacteriota group. This work expands the understanding of biochar ecology in cold black soil. These results are conducive to the sustainable development of soil ecological function in cold regions and ultimately ensure crop growth and food productivity.

Functional characterization and molecular fingerprinting of potential phosphate solubilizing bacterial candidates from Shisham rhizosphere

Phosphate solubilizing bacteria (PSB) are important role players in plant growth promotion. In the present study, we aimed to screen the functionally active phosphate solubilizing bacteria (PSB) associated with Dalbergia sissoo Roxb. (Shisham) from different provenances. Screening for phosphate solubilization was done on Pikovskaya's agar, and 18 bacteria positive for the tri-calcium phosphate (Ca₃(PO₄)₂ solubilization showing visible dissolution halo zones were identified. All 18 isolates showed zinc solubilization, indole acetic acid (IAA), siderophore, and hydrogen cyanide (HCN) production. The morphological and biochemical characterization with 16S rDNA gene-based phylogenetic analysis identified bacterial strains as belonging to the genus Pseudomonas, Klebsiella, Streptomyces, Pantoea, Kitasatospora, Micrococcus, and Staphylococcus. Among all the isolates, one of the isolates named L4, from Lacchiwala region was the most efficient P solubilizer with a high P solubilization index (4.75 ± 0.06) and quantitative P solubilization activity (891.38 ± 18.55 μg mL^-1). The validation of phosphate solubilization activity of PSB isolates was done by amplification of the Pyrroloquinoline quinone (PQQ) genes, pqqA and pqqC. Based on this study, we have selected the bacterial strains which are efficient phosphate solubilizers and could be economical and eco-friendly in plant growth promotion, disease suppression, as an antioxidant, and for subsequent enhancement of yield.

The combined action of biochar and nitrogen-fixing bacteria on microbial and enzymatic activities of soil N cycling

This study aims to investigate the positive effects of the combined use of Enterobacter cloacae and biochar on improving nitrogen (N) utilization. The greenhouse pots experimental results showed the synergy of biochar and E. cloacae increased soil total N content and plant N uptake by 33.54% and 15.1%, respectively. Soil nitrogenase (NIT) activity increased by 253.02%. Ammonia monooxygenase (AMO) and nitrate reductase (NR) activity associated with nitrification and denitrification decreased by 10.94% and 29.09%, respectively. The relative abundance of N fixing microorganisms like Burkholderia and Bradyrhizobium significantly increased. Sphingomonas and Ottowia, two bacteria involved in the nitrification and denitrification processes, were found to be in lower numbers. The E. cloacae's ability to fix N₂ and promote the growth of plants allow the retention of N in soil and make more N available for plant development. Biochar served as a reservoir of N for plants by adsorbing N from the soil and providing a shelter for E. cloacae. Thus, biochar and E. cloacae form a synergy for the management of agricultural N and the mitigation of negative impacts of pollution caused by excessive use of N fertilizer.

Effects of continuous cropping Jiashi muskmelon on rhizosphere microbial community

Introduction

The continuous cropping of crops can result in the deterioration of the soil environment and cause a decline in plant health and yield, which complicates agricultural production. However, the effects of continuous melon cropping on rhizospheric microbial communities remain poorly understood.

Methods

In this study, high-throughput absolute quantification 16S rRNA gene amplicon sequencing was employed to analyze the bacterial community structure of greenhouse rhizosphere soil from Jiashi muskmelon replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively).

Results

The results showed that long- term continuous cropping caused significant changes in soil physicochemical properties. The bacterial absolute abundances increased, but the bacterial community richness and diversity were significantly lost (p < 0.05). The composition of bacterial community was more similar after 2 and 3 years of continuous cropping. The longer the continuous cropping years were, the greater the shift in the bacterial diversity and abundance. Analysis of potential functional components revealed that different bacterial groups were enriched in different continuous cropping years. The significant reduction of the taxa associated with nitrate reduction may be responsible for the loss of soil nitrogen in continuous cropping soil.

Discussion

In summary, continuous cropping had a significant impact on the bacterial community structure of Jiashi muskmelon rhizospheric soil, and these results will provide a reference for soil management and scientific fertilization of melon and other crops under a continuous cropping regime.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

INTRODUCTION

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

METHODS

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

RESULTS

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

DISCUSSION

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Effects of Two Bacillus Velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana

Microbial inoculants, as harmless, efficient, and environmentally friendly plant growth promoters and soil conditioners, are attracting increasing attention. In this study, the effects of Bacillus velezensis YH-18 and B. velezensis YH-20 on Prunus davidiana growth and rhizosphere soil bacterial community in continuously cropped soil were investigated by inoculation tests. The results showed that in a pot seedling experiment, inoculation with YH-18 and YH-20 resulted in a certain degree of increase in diameter growth, plant height, and leaf area at different time periods of 180 days compared with the control. Moreover, after 30 and 90 days of inoculation, the available nutrients in the soil were effectively improved, which protected the continuously cropped soil from acidification. In addition, high-throughput sequencing showed that inoculation with microbial inoculants effectively slowed the decrease in soil microbial richness and diversity over a one-month period. At the phylum level, Proteobacteria and Bacteroidetes were significantly enriched on the 30th day. At the genus level, Sphingomonas and Pseudomonas were significantly enriched at 15 and 30 days, respectively. These bacterial phyla and genera can effectively improve the soil nutrient utilization rate, antagonize plant pathogenic bacteria, and benefit the growth of plants. Furthermore, inoculation with YH-18 and inoculation with YH-20 resulted in similar changes in the rhizosphere microbiome. This study provides a basis for the short-term effect of microbial inoculants on the P. davidiana rhizosphere microbiome and has application value for promoting the cultivation and production of high-quality fruit trees.

Enhancing N uptake and reducing N pollution via green, sustainable N fixation-release model

The overuse of N fertilizers has caused serious environmental problems (e.g., soil acidification, excessive N₂O in the air, and groundwater contamination) and poses a serious threat to human health. Improving N fertilizer utilization efficiency and plant uptake is an alternative for N fertilizers overuses. Enterobacter cloacae is an opportunistic pathogen, also used as plant growth-promoting rhizobacteria (PGPR), has been widely presented in the fields of bioremediation and bioprotection. Here we developed a new N fixation-release model by combining biochar with E. cloacae. The efficiency of the model was evaluated using a greenhouse pot experiment with maize (Zea mays L.) as the test crop. The results showed that biochar combined with E. cloacae significantly increased the N content. The application of biochar combined with E. cloacae increased total N in soil by 33% compared with that of N fertilizers application. The N-uptake and utilization efficiency (NUE) in plant was increased 17.03% and 14.18%, respectively. The activities of urease, dehydrogenase and fluorescein diacetate hydrolase (FDA) was improved, the catalase (CAT) activity decreased. Analysis of the microbial community diversity revealed the abundance of Proteobacteria, Actinobacteria, Firmicutes, and Gemmatimonadetes were significantly improved. The mechanism under the model is that E. cloacae acted as N-fixation by capturing N₂ from air. Biochar served as carrier, supporting better living environment for E. cloacae, also as adsorbent adsorbing N from fertilizer and from fixed N by E. cloacae, the adsorption in turn slower the N release. Altogether, the model promotes N utilization by plants, improves the soil environment, and reduces N pollution.

Effects of saline-alkali stress on bacterial and fungal community diversity in Leymus chinensis rhizosphere soil

The salinization of grassland in arid and semi-arid areas is a serious environmental issue in China. Halophytes show extreme salt tolerance and are grown in saline-alkaline environments. Their rhizosphere microorganisms contribute significantly to plant stress tolerance. To study bacterial and fungal community structure changes in Chinese ryegrass (Leymus chinensis) rhizosphere soil under salt and alkali stress, pot experiments were conducted with different salt and alkali stress intensities. High-throughput sequencing was conducted, and the microbial diversity, community structure, and driving factors were analyzed in rhizosphere soil. The salinization of grassland in arid and semi-arid areas is a serious environmental issue in China. Halophytes show extreme salt tolerance and grow in saline-alkaline environments. A total of 549 species of bacteria from 28 phyla and 250 species from 11 phyla of fungi were detected in the rhizosphere soil of Leymus chinensis with different saline-alkali gradients. Alpha diversity analysis along saline-alkali gradients showed that bacterial community richness and diversity were the highest in the moderate saline-alkali group (pH = 8.28, EC = 160.4 μS·cm^-1), while fungi had high richness and diversity in the control group (pH = 7.35, EC = 134.5 μS·cm^-1). The bacteriophyta Proteobacteria, Acidobacteria, Plantomycetes, and the eumycota Ascomycota, Basidiomycota, and Glomeromycota were found with relative abundances of more than 10%. Saline-alkali gradients had significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. The distribution of bacterial colony structure was not significant at the species level (P > 0.05). However, there were significant differences in the distribution of fungal structure and considerable differences in the composition of fungal species among the moderate saline-alkali group, severe saline-alkali group, and control group (P < 0.05). Correlation analysis showed that the bacterial phylum Gemmatimonadetes had a highly significant positive correlation with pH and EC (P < 0. 01). Saline-alkali stress significantly inhibited the abundance of the bacteria Latescibacteria, Cyanobacteria, and Bacteroides, and the fungi Zoopagomycota, Mortierllomycota, and Cryptomycota (P < 0. 05). Compared with fungi, bacterial community composition was most closely correlated with soil salinization. This report provided new insights into the responses of relationships between rhizosphere soil microorganisms and salt and alkali tolerance of plants.

Unlocking the potential of co-applied biochar and plant growth-promoting rhizobacteria (PGPR) for sustainable agriculture under stress conditions

Sustainable food security is a major challenge in today's world, particularly in developing countries. Among many factors, environmental stressors, i.e., drought, salinity and heavy metals are major impediments in achieving sustainable food security. This calls for finding environment-friendly and cheap solutions to address these stressors. Plant growth-promoting rhizobacteria (PGPR) have long been established as an environment-friendly means to enhance agricultural productivity in normal and stressed soils and are being applied at field scale. Similarly, pyrolyzing agro-wastes into biochar with the aim to amend soils is being proposed as a cheap additive for enhancement of soil quality and crop productivity. Many pot and some field-scale experiments have confirmed the potential of biochar for sustainable increase in agricultural productivity. Recently, many studies have combined the PGPR and biochar for improving soil quality and agricultural productivity, under normal and stressed conditions, with the assumption that both of these additives complement each other. Most of these studies have reported a significant increase in agricultural productivity in co-applied treatments than sole application of PGPR or biochar. This review presents synthesis of these studies in addition to providing insights into the mechanistic basis of the interaction of the PGPR and biochar. Moreover, this review highlights the future perspectives of the research in order to realize the potential of co-application of the PGPR and biochar at field scale.

Graphical Abstract

Application of Indigenous Rhizospheric Microorganisms and Local Compost as Enhancers of Lettuce Growth, Development, and Salt Stress Tolerance

This study aimed to mitigate salt stress effects on lettuce by using native biostimulants (arbuscular mycorrhizal fungi (M, consortium), plant growth-promoting rhizobacteria (R, Z2, and Z4 strains), and compost (C)) applied alone or in combination under salinity stress (0, 50, and 100 mM NaCl). Physiological, biochemical, nutritional, mycorrhizal, growth, and soil characteristics were evaluated. Results revealed that growth and physiological traits were negatively affected by salinity. However, mycorrhizal colonization was enhanced under 100 mM NaCl after compost application. The applied biostimulants, particularly M and/or R improved the salinity tolerance of lettuce by increasing the dry biomass by 119% and 113% under 100 mM NaCl, respectively, for M and MR treatments. Similarly, MR enhanced stomatal conductance (47%), water content (260%), total chlorophyll (130%), phosphorus content (363%), and reduced the malondialdehyde (54%) and hydrogen peroxide (78%) compared to the control. Moreover, peroxidase activity (76%) and sugar content (36%) were enhanced by CM treatment, while protein (111%) and proline (104%) contents were significantly boosted by R treatment under 100 mM NaCl. Furthermore, glomalin content was enhanced by MR treatment under severe salinity. In conclusion, the applied biostimulants alone or in combination might help lettuce to tolerate salt stress and enhance its production in degraded areas.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.

Bio-Fermentation Improved Rumen Fermentation and Decreased Methane Concentration of Rice Straw by Altering the Particle-Attached Microbial Community

Bio-fermentation technology has been successfully developed for ensiling rice straw; however, its effects on the particle-attached microbial community remains unknown. Therefore, rice straw (RS) and bio-fermented rice straw (BFRS) were used as substrates for in vitro rumen fermentation to investigate the effect of bio-fermentation on particle-attached microbial community, as well as their effects on gas and methane production, fermentation products, and fiber degradation. Our results have shown that total gas production, fiber degradation, and in vitro fermentation products were significantly higher (p < 0.05) for the BFRS than the RS, while methane concentration in total gas volume was significantly lower (p < 0.05) for the BFRS than RS. Linear discriminant effect size (LefSe) analysis revealed that the relative abundance of the phyla Bacteroidetes, Fibrobacteres, Proteobacteria, and Lantisphaerae, as well as the genera Fibrobacter, Saccharofermentans, and [Eubacterium] ruminantium groups in the tightly attached bacterial community, was significantly higher (p < 0.05) for the BFRS than the RS, whereas other microbial communities did not change. Thus, bio-fermentation altered the tightly attached bacterial community, thereby improving gas production, fiber degradation, and fermentation products. Furthermore, bio-fermentation reduced methane concentration in total gas volume without affecting the archaeal community.

Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis

Fusarium oxysporum f.sp. cubense (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustris, and Methylobacterium nodulans were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed Pseudomonas, Burkholderia, and Streptomyces were present in the suppressive soils, while Bacillus and more Streptomyces were found in the conducive soils. Furthermore, the relative abundance of Pseudomonas, Burkholderia, Bacillus, and Streptomyces was performed. The analysis showed that the relative abundance of Pseudomonas and Burkholderia was higher in the suppressive than conducive soils. Therefore, it assumed Pseudomonas and Burkholderia play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of Pseudomonas and Burkholderia showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.

Daucus carota L. Seed Inoculation with a Consortium of Bacteria Improves Plant Growth, Soil Fertility Status and Microbial Community

The present work aimed to study suitability of a consortium of Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria as biofertilizers. Strains were assayed for plant growth-promoting characteristics (i.e., auxins production, phosphate solubilizing capability, and 1-aminocyclopropane-1-carboxylate deaminase activity). The consortium of four bacteria was then inoculated on carrot seeds and tested in an open field experiment. During the open field experiment, plant growth (morphological parameters, chlorophylls, and carotenoids), soil chemical analysis, and molecular and physiological profiles of soils were investigated. Each strain produced different amounts of indole-3acetic acid and several indole-derivates molecules. All strains showed phosphate solubilization capability, while 1-aminocyclopropane-1-carboxylate deaminase activity was only detected in H. seropedicae and B. ambifaria. The bacterial consortium of the four strains gave interesting results in the open field cultivation of carrot. Plant development was positively affected by the presence of the consortium, as was soil fertility and microbial community structure and diversity. The present work allowed for deepening our knowledge on four bacteria, already known for years for having several interesting characteristics, but whose interactions were almost unknown, particularly in view of their use as a consortium in a valid fertilization strategy, in substitution of agrochemicals for a sustainable agriculture.

Allium cepa L. Inoculation with a Consortium of Plant Growth-Promoting Bacteria: Effects on Plants, Soil, and the Autochthonous Microbial Community

The present work was aimed at investigating the effects of a four bacterial strain consortium—Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria—on Allium cepa L. and on soil health. The bacterial consortium was inoculated on seeds of two different onion varieties; inoculated and Control seeds (treated with autoclaved inoculum) were sown in an open-field and followed until harvest. Plant growth development parameters, as well as soil physico–chemical and molecular profiles (DNA extraction and 16S community sequencing on the Mi-Seq Illumina platform), were investigated. The results showed a positive influence of bacterial application on plant growth, with increased plant height (+18%), total chlorophylls (+42%), crop yields (+13%), and bulb dry matter (+3%) with respect to the Control. The differences between Control and treatments were also underlined in the bulb extracts in terms of total phenolic contents (+25%) and antioxidant activities (+20%). Soil fertility and microbial community structure and diversity were also positively affected by the bacterial inoculum. At harvest, the soil with the presence of the bacterial consortium showed an increase in total organic carbon, organic matter, and available phosphorus, as well as higher concentrations of nutrients than the Control. The ecological indexes calculated from the molecular profiles showed that community diversity was positively affected by the bacterial treatment. The present work showed the effective use of plant growth-promoting bacteria as a valid fertilization strategy to improve yield in productive landscapes whilst safeguarding soil biodiversity.

Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.