Inoculum Concentration and Mineral Fertilization: Effects on the Endophytic Microbiome of Soybean

The process of nitrogen-adaptation root endophytic bacterial rather than phosphorus-adaptation fungal subcommunities construction unveiled the tomato yield improvement under long-term fertilization

Interactions between endophytes (endophytic bacteria and fungi) and plants are crucial in maintaining crop fitness in agricultural systems, particularly in relation to abundant and rare subcommunities involved in community construction. However, the influence of long-term fertilization on heterogeneous rhizosphere nitrogen and phosphorus environments and how these conditions affect the key subcommunities of root endophytes and their community assembly mechanisms remain unclear. We studied the 26th year of a field experiment conducted in a greenhouse with varying levels of nitrogen and phosphorus (CKP0, CKP1, CNP0, CNP1, ONP0, and ONP1) to assess the composition of tomato root endophytes and their impact on yield. We employed 16S rRNA and fungal ITS region amplicon sequencing to investigate the assembly mechanisms of abundant and rare endophytic subcommunities, network correlations, core subcommunity structures, and key species that enhance crop yield. The results indicated that organic manure and phosphorus fertilizers significantly increased the rhizosphere soil nitrogen content, phosphorus content, and phosphorus availability (labile P, moderately labile P, and non-labile P). These fertilizers also significantly affected the composition (based on Bray-Curtis distance) and community assembly processes (βNTI) of endophytic microbial subcommunities. The assembly of both bacterial and fungal subcommunities was primarily governed by dispersal limitation, with community structures being significantly regulated by the content of rhizosphere soil available nitrogen (AN) and moderately labile P (MLP). Rare bacterial and fungal subcommunities complemented the ecological niches of abundant subcommunities in the co-occurrence network, supporting community functions and enhancing network stability. Nitrogen-adapting abundant and rare bacterial subcommunities provided a stronger predictive correlation for tomato yield than phosphorus-adapting fungal subcommunities. Additionally, three core genera of rare endophytic bacteria such as Arthrobacter, Microbacterium, and Sphingobium were identified as potentially involved in improving crop yield improvement. These findings revealed the distinct assembly mechanisms of endophytic microbial subcommunities affected by fertilization, enhancing our understanding of better management practices and controlling endophytes to improve crop yield in intensive agricultural ecosystems.

Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion

Biological pretreatment is a viable method for enhancing biogas production from straw crops, with the improvement in lignocellulose degradation efficiency being a crucial factor in this process. Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil. Subsequently, synthetic microbial communities were constructed for fermentation-enzyme production. The crude enzyme solution obtained was used to pretreat WS and was compared with two commercial enzymes. The synthetic microbial community enzyme-producing pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme solution, followed by anaerobic digestion achieved satisfactory results. SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS, which was 38.79% higher than that observed for WS, 22.15% higher than that of solid-state commercial enzyme pretreatment and 25.41% higher than that of liquid commercial enzyme pretreatment. These results indicate that enzyme-pretreated WS can significantly enhance biogas production. This study represents a solution to the environmental burden and energy use of crop residues.

Construction of a synthetic microbial community based on multiomics linkage technology and analysis of the mechanism of lignocellulose degradation

The efficient degradation of lignocellulose is a bottleneck for its integrated utilization. This research performed species analysis and made functional predictions in various ecosystems using multiomics coupling to construct a core synthetic microbial community with efficient lignocellulose degradation function. The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. The degradation mechanisms were resolved using proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d. Under these conditions, the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, 45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin 1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to lignocellulose degradation. The metabolic pathways involved in lignocellulose degradation and the functional roles of eight strains were obtained. The synthesis of a microbial community via multiomics linkage technology can effectively decompose lignocellulose, which is useful for their further utilization.

Biocontrol of fungal phytopathogens by Bacillus pumilus

Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.

Plant Growth Promotion Using Bacillus cereus

Plant growth-promoting bacteria (PGPB) appear to be a sensible competitor to conventional fertilization, including mineral fertilizers and chemical plant protection products. Undoubtedly, one of the most interesting bacteria exhibiting plant-stimulating traits is, more widely known as a pathogen, Bacillus cereus. To date, several environmentally safe strains of B. cereus have been isolated and described, including B. cereus WSE01, MEN8, YL6, SA1, ALT1, ERBP, GGBSTD1, AK1, AR156, C1L, and T4S. These strains have been studied under growth chamber, greenhouse, and field conditions and have shown many significant traits, including indole-3-acetic acid (IAA) and aminocyclopropane-1-carboxylic acid (ACC) deaminase production or phosphate solubilization, which allows direct plant growth promotion. It includes an increase in biometrics traits, chemical element content (e.g., N, P, and K), and biologically active substances content or activity, e.g., antioxidant enzymes and total soluble sugar. Hence, B. cereus has supported the growth of plant species such as soybean, maize, rice, and wheat. Importantly, some B. cereus strains can also promote plant growth under abiotic stresses, including drought, salinity, and heavy metal pollution. In addition, B. cereus strains produced extracellular enzymes and antibiotic lipopeptides or triggered induced systemic resistance, which allows indirect stimulation of plant growth. As far as biocontrol is concerned, these PGPB can suppress the development of agriculturally important phytopathogens, including bacterial phytopathogens (e.g., Pseudomonas syringae, Pectobacterium carotovorum, and Ralstonia solanacearum), fungal phytopathogens (e.g., Fusarium oxysporum, Botrytis cinerea, and Rhizoctonia solani), and other phytopathogenic organisms (e.g., Meloidogyne incognita (Nematoda) and Plasmodiophora brassicae (Protozoa)). In conclusion, it should be noted that there are still few studies on the effectiveness of B. cereus under field conditions, particularly, there is a lack of comprehensive analyses comparing the PGP effects of B. cereus and mineral fertilizers, which should be reduced in favor of decreasing the use of mineral fertilizers. It is also worth mentioning that there are still very few studies on the impact of B. cereus on the indigenous microbiota and its persistence after application to soil. Further studies would help to understand the interactions between B. cereus and indigenous microbiota, subsequently contributing to increasing its effectiveness in promoting plant growth.

Analysis on methane production from various coal slime fermentations based on metagenomics

Metagenomic sequencing technology was applied to evaluate differences in the anaerobic fermentation process of coal slimes by analyzing microbial diversity, functional activity structure, and cooperative relationship during the anaerobic fermentation of coal slimes with different coal ranks. The obtained results showed that the production of biomethane from coal slime was decreased by increasing metamorphism degree. Internal reason was higher abundance of microbial community in low rank coal slimes compared to that in high rank coal which had higher activity in the gene expression of key steps such as hydrolysis and acidification, methanation and the production of hydrogen and acetic acid. Acetic acid decarboxylation and CO₂ reduction are two key pathways of methanation process. At the same time, K11261 (formylmethanofuran dehydrogenase subunit) and K01499 (methenyltetrahydromethanopterin cyclohydrolase) genes were further enriched in low rank slime systems, which enhanced the proportion of CO₂ reduction in methanation pathway and was beneficial to biomethane production. Research revealed the roles of different coal slime ranks in biomethane production process and is considered as an important reference significance for further exploration of coal slime resource utilization.

Potential of Bacillus pumilus to directly promote plant growth

Plant Growth-Promoting Bacteria (PGPB) are a promising alternative to conventional fertilization. One of the most interesting PGPB strains, among the spore-forming bacteria of the phylum Firmicutes, is Bacillus pumilus. It is a bacterial species that inhabits a wide range of environments and shows resistance to abiotic stresses. So far, several PGPB strains of B. pumilus have been described, including B. pumilus LZP02, B. pumilus JPVS11, B. pumilus TUAT-1, B. pumilus TRS-3, and B. pumilus EU927414. These strains have been shown to produce a wide range of phytohormones and other plant growth-promoting substances. Therefore, they can affect various plant properties, including biometric traits, substance content (amino acids, proteins, fatty acids), and oxidative enzymes. Importantly, based on a study with B. pumilus WP8, it can be concluded that this bacterial species stimulates plant growth when the native microbiota of the inoculated soil is altered. However, there is still a lack of research with deeper insights into the structure of the native microbial community (after B. pumilus application), which would provide a better understanding of the functioning of this bacterial species in the soil and thus increase its effectiveness in promoting plant growth.

The bacterial world inside the plant

Sustainable agriculture requires the recruitment of bacterial agents to reduce the demand for mineral fertilizers and pesticides such as bacterial endophytes. Bacterial endophytes represent a potential alternative to the widespread use of synthetic fertilizers and pesticides in conventional agriculture practices. Endophytes are formed by complex microbial communities and microorganisms that colonize the plant interior for at least part of their life. Their functions range from mutualism to pathogenicity. Bacterial endophytes colonize plant tissues, and their composition and diversity depend on many factors, including the plant organ, physiological conditions, plant growth stage, and environmental conditions. The presence of endophytes influences several vital activities of the host plant. They can promote plant growth, elicit a defense response against pathogen attack, and lessen abiotic stress. Despite their potential, especially with regard to crop production and environmental sustainability, research remains sparse. This review provides an overview of the current research, including the concept of endophytes, endophytes in plant organs, endophyte colonization, nutrient efficiency use, endophytes and crop nutrition, inoculation with synergistic bacteria, the effect of inoculum concentration on plant root microbiota and synthetic communities. It also examines the practical opportunities and challenges when utilizing endophytes in the field of sustainable agriculture. Finally, it explores the importance of these associations with regard to the future of agriculture and the environment.