Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Impact of titanium dioxide (TiO2) nanoparticle and liquid leachate of mushroom compost on agronomic and biochemical response of marigold (Tagetes erecta L.) under saline stress

The cultivation of ornamental horticultural crops under salinity stress has been a challenge for growers all over the world. In this study, an attempt was made for pot cultivation of Marigold (Tagetes erecta L. var. Pusa Basanti Gainda) in salt-stressed (SS) soil (150 mM) with the combined use of mushroom compost leachate (CL) and foliar application of titanium dioxide nanoparticles (TiO2-NPs). For this purpose, a total of six pot treatments, i.e., borewell water (BW; control), T1 (BW with SS), T2 (BW with SS and TiO2-NPs), T3 (CL supplemented), T4 (CL with SS), and T5 (CL with SS and TiO2-NPs) were conducted in triplicate. The results of this study showed that CL supplementation significantly (p < 0.05) improved the physicochemical i.e., pH (14.5%), electrical conductivity (32.9%), total nitrogen (27.4%), total phosphorus (247.6%)), and nutrient (organic matter: 119.6%) profiles of soil which later helped in higher growth (30-35%) and yield (5.4-40.7%) of T. erecta. In CL-based treatments, the biochemical constituents were significantly (p < 0.05) higher than those in BW-irrigated ones. Also, the levels of selected stress defense enzymes were significantly increased under SS treatment but reduced under TiO2-NP application. Overall, it was observed that the combined application of CL and TiO2-NPs (T5 treatment) was the most helpful treatment for enhanced germination, growth, yield, biochemical parameters, and better plant enzymatic activities to cope with saline stress. This study provides a mechanistic understanding of T. erecta plants under saline stress which is crucial for the development of targeted interventions aimed at improving plant tolerance to saline conditions.

Identification of bacterial community in a rapid composting method using 16SrDNA genes sequencing

Composting is a process of microbial degradation of organic waste and is commonly applied for waste management. This is a slow process and requires a lot of land and human resources. The present study investigated mechanical augmentation with required microbial culture for composting municipal solid waste (MSW). Thirty isolates were subjected to 16S rDNA PCR amplification and gene sequencing. The isolates' sequencing from the compost samples was processed on BLASTn. Fourteen strains were identified for further experiments. The results divulge that Empedobacter (04), Bacillus (02), Proteus (02), Lactiplantibacillus (01), Klebsiella (01), Citrobacter (01), Brevibacillus (01), E. coli (01) and one unidentified strain were growing during composting. Eleven combinations of bacterial consortium and respective additives were applied for the organic waste decomposition in the next stage, resulting in varied completion periods ranging from 3 to 14 days. Two combinations were completed within 3 days, which are considered ideal combinations for composting. The microbial consortium was significantly diverse, which is a reason for rapid biodegradation. The present study reveals that the technology will be highly feasible for municipal solid waste management in tropical/subtropical countries.

Effect of different bulking agents on fed-batch composting and microbial community profile

The current study focused on analyzing the effect of different types of bulking agents and other factors on fed-batch composting and the structure of microbial communities. The results indicated that the introduction of bulking agents to fed-batch composting significantly improved composting efficiency as well as compost product quality. In particular, using green waste as a bulking agent, the compost products would achieve good performance in the following indicators: moisture (3.16%), weight loss rate (85.26%), and C/N ratio (13.98). The significant difference in moisture of compost products (p < 0.05) was observed in different sizes of bulking agent (green waste), which was because the voids in green waste significantly affected the capacity of the water to permeate. Meanwhile, controlling the size of green waste at 3-6 mm, the following indicators would show great performance from the compost products: moisture (3.12%), organic matter content (63.93%), and electrical conductivity (EC) (5.37 mS/cm). According to 16S rRNA sequencing, the relative abundance (RA) of thermophilic microbes increased as reactor temperature rose in fed-batch composting, among which Firmicutes, Proteobacteria, Basidiomycota, and Rasamsonia were involved in cellulose and lignocellulose degradation.

Antagonistic effect of Bacillus and Pseudomonas combinations against Fusarium oxysporum and their effect on disease resistance and growth promotion in watermelon

AIMS

We aimed to develop an effective bacterial combination that can combat Fusarium oxysporum infection in watermelon using in vitro and pot experiments.

METHODS AND RESULTS

In total, 53 strains of Bacillus and 4 strains of Pseudomonas were screened. Pseudomonas strains P3 and P4 and Bacillus strains XY-2-3, XY-13, and GJ-1-15 exhibited good antagonistic effects against F. oxysporum. P3 and P4 were identified as Pseudomonas chlororaphis and Pseudomonas fluorescens, respectively. XY-2-3 and GJ-1-15 were identified as B. velezensis, and XY-13 was identified as Bacillus amyloliquefaciens. The three Bacillus strains were antifungal, promoted the growth of watermelon seedlings and had genes to synthesize antagonistic metabolites such as bacilysin, surfactin, yndj, fengycin, iturin, and bacillomycin D. Combinations of Bacillus and Pseudomonas strains, namely, XY-2-3 + P4, GJ-1-15 + P4, XY-13 + P3, and XY-13 + P4, exhibited a good compatibility. These four combinations exhibited antagonistic effects against 11 pathogenic fungi, including various strains of F. oxysporum, Fusarium solani, and Rhizoctonia. Inoculation of these bacterial combinations significantly reduced the incidence of Fusarium wilt in watermelon, promoted plant growth, and improved soil nutrient availability. XY-13 + P4 was the most effective combination against Fusarium wilt in watermelon with the inhibition rate of 78.17%. The number of leaves; aboveground fresh and dry weights; chlorophyll, soil total nitrogen, and soil available phosphorus content increased by 26.8%, 72.12%, 60.47%, 16.97%, 20.16%, and 16.50%, respectively, after XY-13 + P4 inoculation compared with the uninoculated control. Moreover, total root length, root surface area, and root volume of watermelon seedlings were the highest after XY-13 + P3 inoculation, exhibiting increases by 265.83%, 316.79%, and 390.99%, respectively, compared with the uninoculated control.

CONCLUSIONS

XY-13 + P4 was the best bacterial combination for controlling Fusarium wilt in watermelon, promoting the growth of watermelon seedlings, and improving soil nutrient availability.

Food waste-based bio-fertilizers production by bio-based fermenters and their potential impact on the environment

Increasing food waste is creating a global waste (and management) crisis. Globally, ∼1.6 billion tons of food is wasted annually, worth ∼$1.2 trillion. By reducing this waste or by turning it into valuable products, numerous economic advantages can be realized, including improved food security, lower production costs, biodegradable products, environmental sustainability, and cleaner solutions to the growing world's waste and garbage management. The appropriate handling of these detrimental materials can significantly reduce the risks to human health. Food waste is available in biodegradable forms and, with the potential to speed up microbial metabolism effectively, has immense potential in improving bio-based fertilizer generation. Synthetic inorganic fertilizers severely affect human health, the environment, and soil fertility, thus requiring immediate consideration. To address these problems, agricultural farming is moving towards manufacturing bio-based fertilizers via utilizing natural bioresources. Food waste-based bio-fertilizers could help increase yields, nutrients, and organic matter and mitigate synthetic fertilizers' adverse effects. These are presented and discussed in the review.

Advances in research and utilization of botanical pesticides for agricultural pest management in Inner Mongolia, China

Traditional Chinese herbal medicines not only cure human diseases, but also play an important role as insecticides. Compared with conventional chemical agents, traditional Chinese herbal medicines are characterized by low toxicity, low residues, and being eco-friendly, and they have become a research hotspot. Traditional Chinese herbal medicines have tremendous flexibility and indefinite potential. Therefore, this paper reviewed the types of insecticides belonging to traditional Chinese herbal medicines in Inner Mongolia, China, including their traditional uses, secondary metabolites, biological activities, action mechanisms, application methods, and development status. In addition, the most relevant issues involved in the development of traditional Chinese herbal medicines was discussed. We believe that traditional Chinese herbal medicines can be better implemented and developed; such that its other advantages, such as an insect repellent, can be promoted. Moreover, this study lays a solid foundation for further research on traditional Chinese herbal medicines in Inner Mongolia, China.

Application of different packing media for the biofiltration of gaseous effluents from waste composting

A pilot-scale experiment was implemented in a waste bioreactor with an inner capacity of 1 m3 in order to simulate a real-scale composting process. The waste underwent composting conditions that are typical of the initial bio-oxidation phase, characterised by a high production of volatile organic compounds (VOCs), hydrogen sulphide (H2S) and odorants. The waste bioreactor was fed with an intermittent airflow rate of 6 Nm3/h. The target of this study was to investigate the air treatment performance of three biofilters with the same size, but filled with different filtering media: (1) wood chips, (2) a two-layer combination of lava rock (50%) and peat (50%), and (3) peat only. The analyses on air samples taken upstream and downstream of the biofilters showed that the combination of lava rock and peat presents the best performance in terms of mean removal efficiency of odour (96%), total VOCs (95%) and H2S (77%) concentrations. Wood chips showed the worst abatement performance, with respective mean removal efficiencies of 90%, 88% and 62%. From the results obtained, it is possible to conclude that the combination of lava rock and peat can be considered as a promising choice for air pollution control in waste composting facilities.

Recent Trends and Advances in Additive-Mediated Composting Technology for Agricultural Waste Resources: A Comprehensive Review

Agriculture waste has increased annually due to the global food demand and intensive animal production. Preventing environmental degradation requires fast and effective agricultural waste treatment. Aerobic digestion or composting uses agricultural wastes to create a stabilized and sterilized organic fertilizer and reduces chemical fertilizer input. Indeed, conventional composting technology requires a large surface area, a long fermentation period, significant malodorous emissions, inferior product quality, and little demand for poor end results. Conventional composting loses a lot of organic nitrogen and carbon. Thus, this comprehensive research examined sustainable and adaptable methods for improving agricultural waste composting efficiency. This review summarizes composting processes and examines how compost additives affect organic solid waste composting and product quality. Our findings indicate that additives have an impact on the composting process by influencing variables including temperature, pH, and moisture. Compost additive amendment could dramatically reduce gas emissions and mineral ion mobility. Composting additives can (1) improve the physicochemical composition of the compost mixture, (2) accelerate organic material disintegration and increase microbial activity, (3) reduce greenhouse gas (GHG) and ammonia (NH3) emissions to reduce nitrogen (N) losses, and (4) retain compost nutrients to increase soil nutrient content, maturity, and phytotoxicity. This essay concluded with a brief summary of compost maturity, which is essential before using it as an organic fertilizer. This work will add to agricultural waste composting technology literature. To increase the sustainability of agricultural waste resource utilization, composting strategies must be locally optimized and involve the created amendments in a circular economy.

Fungal Colonization of the Airways of Patients with Cystic Fibrosis: the Role of the Environmental Reservoirs

Filamentous fungi frequently colonize the airways of patients with cystic fibrosis and may cause severe diseases, such as the allergic bronchopulmonary aspergillosis. The most common filamentous fungi capable to chronically colonize the respiratory tract of the patients are Aspergillus fumigatus and Scedosporium species. Defining the treatment strategy may be challenging, the number of available drugs being limited and some of the causative agents being multiresistant microorganisms. The knowledge of the fungal niches in the outdoor and indoor environment is needed for understanding the origin of the contamination of the patients. In light of the abundance of some of the causative molds in compost, agricultural and flower fields, occupational activities related to such environments should be discouraged for patients with cystic fibrosis (CF). In addition, the microbiological monitoring of their indoor environment, including analysis of air and dust on surfaces, is essential to propose preventive measures aiming to reduce the exposure to environmental molds. Nevertheless, some specific niches were also identified in the indoor environment, in relation with humidity which favors the growth of thermotolerant molds. Potted plants were reported as indoor reservoirs for Scedosporium species. Likewise, Exophiala dermatitidis may be spread in the kitchen via dishwashers. However, genotype studies are still required to establish the link between dishwashers and colonization of the airways of CF patients by this black yeast. Moreover, as nothing is known regarding the other filamentous fungi associated with CF, further studies should be conducted to identify other potential specific niches in the habitat.

Quantitative detection of the Ralstonia solanacearum species complex in soil by qPCR combined with a recombinant internal control strain

IMPORTANCE

DNA-based detection and quantification of soil-borne pathogens, such as the Ralstonia solanacearum species complex (RSSC), plays a vital role in risk assessment, but meanwhile, precise quantification is difficult due to the poor purity and yield of the soil DNA retrieved. The internal sample process control (ISPC) strain RsPC we developed solved this problem and significantly improved the accuracy of quantification of RSSC in different soils. ISPC-based quantitative PCR detection is a method especially suitable for the quantitative detection of microbes in complex matrices (such as soil and sludge) containing various PCR inhibitors and for those not easy to lyse (like Gram-positive bacteria, fungi, and thick-wall cells like resting spores). In addition, the use of ISPC strains removes additional workload on the preparation of high-quality template DNA and facilitates the development of high-throughput quantitative detection techniques for soil microbes.

Next-Generation Sequencing for Evaluating the Soil Nematode Diversity and Its Role in Composting Processes

Biodiversity within composting systems involves a variety of microorganisms including nematodes. In the research, nematode populations were monitored within six simultaneously operating composting processes. These processes involved varying proportions of feedstock materials. The primary objective was to evaluate the consistency of nematode community succession patterns across the composting processes over a time of 3 months. During the study, samples were taken every month to isolate nematodes, determine the population density of the five trophic groups (per genus) and determine the dominant nematode species. It was shown that the bacterial-feeding community maintained dominance, while the fungus-feeding nematodes gradually increased in dominance as the maturation process progressed. The presence of predatory nematodes Mononchoides which were initially absent, along with the total absence of parasitic nematodes in the late stages of waste stabilization, serves as strong evidence for the reliable evaluation of the biodegradable waste processing level. Based on the obtained results, it is evident that the succession of nematode communities holds promise as a reliable method for evaluating compost maturity.

Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting

The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.

Bacterial wilt suppressive composts: Significance of rhizosphere microbiome

Composts are often suppressive to several plant diseases, including the devastating bacterial wilt caused by Ralstonia solanacearum. However, the underlying mechanisms are still unclear. Herein, we carried out an experiment with 38 composts collected from different factories in China to study the interlinking among bacterial wilt suppression, the physicochemical properties and bacterial community of the compost, and bacterial community in the rhizosphere of tomato fertilized by compost. Totally 26 composts were suppressive to bacterial wilt, while six composts stimulated the disease. The control efficiency was neither correlated with physicochemical properties (TC, TN, P and K, pH or GI) nor bacterial community of compost, but with rhizosphere bacterial community (r = 0.17, p = 0.016). The control efficiency was also positive correlated with taxa (Rhizobium, Aeromicrobium) known suppressive to R. solanacearum. The mushroom spent or cow manure, from which the two composts were 100% and 77% in control efficiencies against bacterial wilt respectively were subject to a pilot-scale composting reaction. The reproduced composts from mushroom spent or cow manure were only 57% and 23% effective on the control of bacterial wilt, respectively. The analysis of bacterial communities revealed that the relative abundances of R. solanacearum were 28.4% for the control, but only 7.8%-7.9% for compost fertilized tomatoes. The compost from mushroom spent also exerted a strong effect on rhizosphere bacterial community. Taken together, most composts were suppressive to bacterial wilt possibly also by modifying rhizosphere bacterial community towards inhibiting the colonization of R. solanacearum and selecting for beneficial genera of Proteobacteria, Bacteroidetes and Actinobacteria.

Effect of organic amendments obtained from different pretreatment technologies on soil microbial community

The application of organic amendments (OAs) obtained from biological treatment technologies is a common agricultural practice to increase soil functionality and fertility. OAs and their respective pretreatment processes have been extensively studied. However, comparing the properties of OAs obtained from different pretreatment processes remains challenging. In most cases, the organic residues used to produce OAs exhibit intrinsic variability and differ in origin and composition. In addition, few studies have focused on comparing OAs from different pretreatment processes in the soil microbiome, and the extent to which OAs affect the soil microbial community remains unclear. This limits the design and implementation of effective pretreatments aimed at reusing organic residues and facilitating sustainable agricultural practices. In this study, we used the same model residues to produce OAs to enable meaningful comparisons among compost, digestate, and ferment. These three OAs contained different microbial communities. Compost had higher bacterial but lower fungal alpha diversity than ferment and digestate. Compost-associated microbes were more prevalent in the soil than ferment- and digestate-associated microbes. More than 80% of the bacterial ASVs and fungal OTUs from the compost were detected 3 months after incorporation into the soil. However, the addition of compost had less influence on the resulting soil microbial biomass and community composition than the addition of ferment or digestate. Specific native soil microbes, members from Chloroflexi, Acidobacteria, and Mortierellomycota, were absent after ferment and digestate application. The addition of OAs increased the soil pH, particularly in the compost-amended soil, whereas the addition of digestate enhanced the concentrations of dissolved organic carbon (DOC) and available nutrients (such as ammonium and potassium). These physicochemical variables were key factors that influenced soil microbial communities. This study furthers our understanding of the effective recycling of organic resources for the development of sustainable soils.

Biocontrol Activity of Aromatic and Medicinal Plants and Their Bioactive Components against Soil-Borne Pathogens

Soil-borne phytopathogens can have detrimental effects on both cereal and horticultural crops resulting in serious losses worldwide. Due to their high efficiency and easy applicability, synthetic pesticides are still the primary choice in modern plant disease control systems, but stringent regulations and increasing environmental concerns make the search for sustainable alternatives more pressing than ever. In addition to the incorporation of botanicals into agricultural practices, the diversification of cropping systems with aromatic and medicinal plants is also an effective tool to control plant diseases through providing nutrients and shaping soil microbial communities. However, these techniques are not universally accepted and may negatively affect soil fertility if their application is not thoroughly controlled. Because the biocontrol potential of aromatic and medicinal plants has been extensively examined over the past decades, the present study aims to overview the recent literature concerning the biopesticide effect of secondary metabolites derived from aromatic and medicinal plants on important soil-borne plant pathogens including bacteria, fungi, and nematodes. Most of the investigated herbs belong to the family of Lamiaceae (e.g., Origanum spp., Salvia spp., Thymus spp., Mentha spp., etc.) and have been associated with potent antimicrobial activity, primarily due to their chemical constituents. The most frequently tested organisms include fungi, such as Rhizoctonia spp., Fusarium spp., and Phytophthora spp., which may be highly persistent in soil. Despite the intense research efforts dedicated to the development of plant-based pesticides, only a few species of aromatic herbs are utilized for the production of commercial formulations due to inconsistent efficiency, lack of field verification, costs, and prolonged authorization requirements. However, recycling the wastes from aromatic and medicinal plant-utilizing industries may offer an economically feasible way to improve soil health and reduce environmental burdens at the same time. Overall, this review provides comprehensive knowledge on the efficiency of aromatic herb-based plant protection techniques, and it also highlights the importance of exploiting the residues generated by aromatic plant-utilizing sectors as part of agro-industrial processes.

Characterization of the microbiological effects of pomegranate, banana, and mandarin peels on water under laboratory conditions

The protection of natural resources, especially water resources, is attracting international attention by researchers in order to achieve sustainable development. Inadequate treatment of waste from the food industry leads to pollution of ground and surface water through leachate or direct discharge of waste. To understand the impact of inappropriate discharge of these wastes, the microbial groups (bacteria, yeasts, and moulds) of pomegranate peel (PP), banana peel (BP), mandarin peel (MP) and the water in which each waste is decomposed were studied. The microbial groups were isolated, quantified, and purified by elective media at 30 °C. The fungal microbial isolates were identified by their macro and microscopic characteristics. The findings show that the highest density of bacteria (3.95 ± 0.48 × 10⁵ CFU/ml) was obtained in the water in which the BP is decomposed, the highest density of yeasts (4.59 ± 0.52 × 10⁵ CFU/ml) and moulds (4.10 ± 0.34 × 10⁵ CFU/ml) was recorded in the water in which the PP is decomposed compared to the microbial density of the initial and the final control water. The fungal microbial groups were more diverse between the decomposition waters; the waters in which PP and BP are decomposed showed a higher diversity with 9 and 8 species respectively, compared to the water in which MP is decomposed with 7 species, and compared to the initial and the final control water with 3 and 5 species respectively. Conclusively, direct dumping or landfilling of food waste in general, PP, BP, and MP in particular can cause pollution of surface and groundwater by microorganisms that can be harmful.

Effect of Chinese medicinal herbal residues compost on tomato and Chinese cabbage plants: Assessment on phytopathogenic effect and nutrients uptake

Chinese medicinal herbal residues (CMHRs) are known for their antipathogenic properties due to the presence of bioactive compounds. Hence, CMHRs could be used as a potential resource to produce biofertilizer with antipathogenic properties for agricultural applications. In this study, a novel approach was used by utilizing the waste-derived biofertilizer, i.e., CMHRs compost (CMHRC) as a nutrient supplier as well as an organic bioagent against Alternaria solani (A. solani) and Fusarium oxysporum (F. oxysporum) on tomato (Lycopersicon esculentum) and Chinese cabbage (Brassica rapa subsp. Chinensis) plants. The experiments were conducted under greenhouse conditions using locally collected acidic soil wherein 2%, 5% and 10% CMHRC (dry weight) along with 5% food waste compost were used as treatments. In addition, only soil and soil with phytopathogens were used as control treatments. The results suggested that amending the compost into acidic soil significantly increased the pH to a neutral level along with enhanced uptake of nutrients. Among all the treatments, 5% CMHRs compost addition increased the tomato plant biomass production to 4.9 g/pot (dry weight) compared to 2.2 g/pot in control. A similar trend was observed in Chinese cabbage plants and the improved plant biomass production could be attributed to the combined effect of strong nutrient absorption ability by healthy roots and enhanced nutrient supply. At 5% CMHRC application rate, the nitrogen uptake by tomato and Chinese cabbage plants increased by 78% and 62%, respectively, whereas phosphorous uptake increased by 75% and 25%, respectively. The reduction in A. solani by 48% and F. oxysporum by 54% in the post-harvested soil of 5% CMHRC treatment against the control demonstrated the anti-phytopathogenic efficiency of CMHRC compost. Hence, the present study illustrates the beneficiary aspects of utilizing CMHRs to produce biofertilizer with anti-phytopathogenic properties which can be safely used for tomato and Chinese cabbage plant growth.

Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth

Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.

Plant Microbiome Engineering: Hopes or Hypes

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant's second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

Changes in Soil Characteristics, Microbial Metabolic Pathways, TCA Cycle Metabolites and Crop Productivity following Frequent Application of Municipal Solid Waste Compost

The benefit sof municipal solid waste (MSW) compost on soil health and plant productivity are well known, but not its long-term effect on soil microbial and plant metabolic pathways. A 5-year study with annual (AN), biennial (BI) and no (C, control) MSW compost application were carried out to determine the effect on soil properties, microbiome function, and plantgrowth and TCA cycle metabolites profile of green beans (Phaseolus vulgaris), lettuce (Latuca sativa) and beets (Beta vulgaris). MSW compost increased soil nutrients and organic matter leading to a significant (p < 0.05) increase in AN-soil water-holding capacity followed by BI-soil compared to C-soil. Estimated nitrogen release in the AN-soil was ca. 23% and 146% more than in BI-soil and C-soil, respectively. Approximately 44% of bacterial community due to compost. Deltaproteobacteria, Bacteroidetes Bacteroidia, and Chloroflexi Anaerolineae were overrepresented in compost amended soils compared to C-soil. A strong positive association existed between AN-soil and 18 microbial metabolic pathways out of 205. Crop yield in AN-soil were increased by 6−20% compared to the BI-soil, and by 35−717% compared to the C-soil. Plant tricarboxylic acid cycle metabolites were highly (p < 0.001) influenced by compost. Overall, microbiome function and TCA cycle metabolites and crop yield were increased in the AN-soil followed by the BI-soil and markedly less in C-soil. Therefore, MSW compost is a possible solution to increase soil health and plants production in the medium to long term. Future study must investigate rhizosphere metabolic activities.

Effects of organic and chemical nitrogen fertilization and postharvest treatments on the visual and nutritional quality of fresh-cut celery (Apium graveolens L.) during storage

The shelf life of horticultural commodities depends on pre- and postharvest factors, such as soil fertilization and postharvest handling. The current study aimed to evaluate fresh-cut celery's postharvest quality as affected by the rate and type (organic and chemical) of nitrogen (N) fertilizer and postharvest treatments. Celery ('Tall Utah') crop was grown in a field in Karaj, Iran. The experimental design was a randomized complete block with three replications and seven preharvest (fertilizer), and five postharvest treatments. Organic fertilizers were vermicompost (VER) and bio-organic fertilizer [farmyard and livestock manure plus Trichoderma harzianum (COM)]. Chemical fertilizers were urea (46% N) at high rate [322 kg·ha¹ N (UREA_HIGH)], optimal rate [196 kg·ha^-1 N (UREA_OPT)], and low rate [138 kg·ha^-1 N (UREA_LOW)]; ammonium nitrate [35% N (AN)] at 196 kg·ha^-1 N; and treatment without fertilization was used as a control. Postharvest treatments included plastic packaging (PP), hydrocooling (HC), blanching (B), and edible coating of psyllium seed mucilage (EC). After postharvest treatments, celery petioles were stored (0-2°C, 85%-90% RH) for 4 weeks and evaluated weekly for quality attributes. Organic fertilizers and UREA_LOW were the most effective treatments in reducing the changes in color, weight loss, titratable acidity (TA), pH, and total soluble solids (TSS) of fresh-cut celery. Organic fertilizers enhanced the vitamin C content, total phenols, and antioxidant activity in celeries. As postharvest treatments, hydrocooling, plastic packaging, and blanching maintained chroma and hue values. Blanching had the greatest effect on the L* value. Hydrocooling increased celery's TA, TSS, and vitamin C content and reduced weight loss and pH during storage. Thus, celery quality was improved when grown under low or adequate N fertilization. Hydrocooling was an effective postharvest treatment for preserving fresh-cut celery quality during storage.

Critical evaluation of biochar utilization effect on mitigating global warming in whole rice cropping boundary

Biochar and compost were accepted as a stable organic amendment to increase soil C stock as well as to decrease greenhouse gas (GHG) emissions in rice paddy soils. However, in most studies, their effect on GHG flux was evaluated only within the cropping boundary without considering industrial processes. To compare the net effect of these organic amendment utilizations on global warming within the whole rice cropping system boundary from industrial process to cropping, fresh, compost, and biochar manures were applied at a rate of 12 Mg ha^-1 (dry weight) in a rice paddy, and total GHG fluxes were evaluated. Compared with fresh manure, compost utilization decreased net global warming potential (GWP) which summated GHG fluxes and soil C stock change with CO₂ equivalent by 43% within rice cropping boundary, via a 25% decrease of CH₄ flux and 39% increase of soil C stock. However, 34 Mg CO₂-eq. of GHGs were additionally emitted during composting to make 12 Mg of compost and then increased the net GWP by 34% within the whole system boundary. In comparison, biochar changed paddy soil into a GHG sink, via 56% decrease of CH₄ flux and 13% increase of soil C stock. However, pyrolysis emitted a total of 0.08 and 19 Mg CO₂-eq. of GHGs under with and without syngas recycling system, respectively, to make 12 Mg of biochar. As a result, biochar utilization decreased net GWP by approximately 28-70% over fresh manure within the whole system boundary. Rice grain productivity was not discriminated between biochar and compost manures, but compost considerably increased grain yield over fresh manure. Consequently, biochar utilization significantly decreased GHG intensity which indicates net GWP per grain by 33-72% over fresh manure, but compost increased by 22%. In conclusion, biochar could be a sustainable organic amendment to mitigate GHG emission impact in the rice paddy, but compost should be carefully selected.

Vermicompost and Its Derivatives against Phytopathogenic Fungi in the Soil: A Review

Synthetic chemicals, such as fertilizers and pesticides, are abundantly used in agriculture to enhance soil fertility and prevent the occurrence of diseases, respectively. Many studies have reported a negative influence of these chemicals on the soil environment. Natural sources from earthworms and their products, as a result of vermicomposting, may be considered better alternatives. The aim of this review was to reveal the source of antifungal efficiency of vermicompost and its derivatives, such as vermiwash, coelomic fluid, skin secretion of earthworms, and metabolites from decomposer bacteria in vermicompost, in order to highlight their application in agriculture. The synergistic activity of bioactive compounds present in coelomic fluid, mucus, skin secretion, and metabolites from associated bacteria (decomposer) assisted crop plants for effective action against various soil pathogenic fungi, such as Rhizoctoniasolani, Alternaria solani, Aspergillus niger, A.flavus, Fusariumoxysporum, and F. graminearum. Thus, these bioactive metabolites can be recommended to suppress plant fungal diseases. Vermicompost and its derivatives should be considered for use in agricultural fields to control harmful soil fungi and increase crop productivity.

Impact of bamboo sphere amendment on composting performance and microbial community succession in food waste composting

The purpose of this study was to find an economical and effective amendment for improving composting performance and product quality, as well as to analyze the microbial community succession in the whole phase of composting. Therefore, the effect of reusable amendment bamboo sphere on composting performance and microbial community succession during food waste composting was investigated. The results showed that 6% bamboo sphere treatment had the highest degree of polymerization (3.7) and humification index (0.18). Compared with control, 6% bamboo sphere amendment increased total nitrogen (TN), phosphorus (TP) and potassium (TK) contents by 13.61%, 19% and 17.42%, respectively. Furthermore, bamboo sphere enhanced bacterial-fungal diversity and improved microbial community composition by enhancing the relative abundance of thermo-tolerance and lignocellulolytic bacteria and fungi. The five most abundant genera in bamboo sphere composting comprised Bacillus (0-71.47%), Chloroplast-norank (0-47.17%), Pusillimonas (0-33.24%), Acinetobacter (0-27.98%) and unclassified Sphingobacteriaceae (0-22.62%). Linear discriminant analysis effect size showed that Firmicutes, Thermoascaceae and Actinobacteriota, which have a relationship with the decomposition of soluble organic matter and lignocellulose, were significantly enriched in bamboo sphere treatment. Canonical correspondence analysis illustrated that total organic carbon (TOC), TK, and TP were the most important environmental factors on microbial community succession in the two composting systems. Together these results suggest that bamboo sphere as a reusable amendment can shorten maturity period, improve humification degree, increase the contents of nutrient and contribute to the succession of microbial community during food waste composting. These findings provide a theoretical basis for improving the efficiency of food waste composting.

Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness

Composting is an advantageous and efficient process for recycling organic waste and producing organic fertilizers, and many kinds of microorganisms are involved in obtaining quality compost with suppressive activity against soil-borne pathogens. The aim of this work was to evaluate the main differences in the effects of three composting piles on the whole bacterial and fungal communities of baby-leaf lettuce crops and to determine the specific communities by high-throughput sequencing related to suppressiveness against the soil-borne plant pathogen Pythium irregulare- (P. irregulare). Compost pile A was composed of 47% vineyard pruning waste, 34% tomato waste and 19% leek waste; pile B was composed of 54% vineyard pruning waste and 46% tomato waste; and pile C was composed of 42% vineyard pruning waste, 25% tomato waste and 33% olive mill cake. The temperature and the chemical properties of the piles were monitored throughout the composting process. In addition, the potential suppressive capacity of the three composts (C_A, C_B and C_C) against P. irregulare in baby-leaf lettuce was assessed. We found that the bacterial community changed according to the composting phases and composting pile and was sensitive to chemical changes throughout the composting process. The fungal community, on the other hand, did not change between the composting piles and proved to be less influenced by chemical properties, but it did change, principally, according to the composting phases. All composts obtained were considered stable and mature, while compost C_C showed higher maturity than composts C_A and C_B. During composting, the three piles contained a greater relative abundance of Bacterioidetes, Proteobacterias and Actinobacterias related to the suppression of soil-borne pathogens such as Pythium irregulare. Composts C_A and C_B, however, showed higher suppressiveness against P. irregulare than compost C_C. Deeper study showed that this observed suppressiveness was favored by a higher abundance of genera that have been described as potential suppressive against P. irregulare, such as Aspergillus, Penicillium, Truepera and Luteimonas.

Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Inactivation and risk control of pathogenic microorganisms in municipal sludge treatment: A review

The rapid global spread of coronavirus disease 2019 (COVID-19) has promoted concern over human pathogens and their significant threats to public health security. The monitoring and control of human pathogens in public sanitation and health facilities are of great importance. Excessive sludge is an inevitable byproduct of sewage that contains human and animal feces in wastewater treatment plants (WWTPs). It is an important sink of different pollutants and pathogens, and the proper treatment and disposal of sludge are important to minimize potential risks to the environment and public health. However, there is a lack of comprehensive analysis of the diversity, exposure risks, assessment methods and inactivation techniques of pathogenic microorganisms in sludge. Based on this consideration, this review summarizes the control performance of pathogenic microorganisms such as enterovirus, Salmonella spp., and Escherichia coli by different sludge treatment technologies, including composting, anaerobic digestion, aerobic digestion, and microwave irradiation, and the mechanisms of pathogenic microorganism inactivation in sludge treatment processes are discussed. Additionally, this study reviews the diversity, detection methods, and exposure risks of pathogenic microorganisms in sludge. This review advances the quantitative assessment of pathogenic microorganism risks involved in sludge reuse and is practically valuable to optimize the treatment and disposal of sludge for pathogenic microorganism control.

Evaluation of the Potential of Agro-Industrial Waste-Based Composts to Control Botrytis Gray Mold and Soilborne Fungal Diseases in Lettuce

Composts are widely used in horticulture as organic amendments to improve the properties of soils. Composts have also been reported to enhance the disease suppressive potential of soils and, therefore, could be used as a strategy for managing plant diseases. The aim of this study was to test the ability of soils amended with four different agro-industrial waste-based composts (chestnut peels and shells, spent coffee grounds, grape marc, and olive leaves) to inhibit the growth and activity of Botrytis cinerea and several soilborne pathogens. First, the capacity of aqueous compost extracts to inhibit the growth of Botrytis cinerea and five soilborne fungi was evaluated in vitro using a broth macrodilution method. Second, lettuce plants were grown on soils amended with composts and inoculated either with B. cinerea or the soilborne fungus Fusarium oxysporum Schlechtendahl isolated from lamb’s lettuce. The determination of minimal inhibitory concentrations indicated that none of the composts inhibited the mycelium growth of the selected fungal pathogens. However, the pathogens did not cause any damage on plants grown on the chestnut- and olive-based composts. Lettuce yields were also highest for plants grown with composts made from chestnut and olive, irrespective of the amount of compost incorporated into soils (5% or 10%, weight basis). The grape-based compost also exhibited a fertilization effect, although the effect was associated with increased Fusarium wilt severity. Both N immobilization and symbiosis with the compost’s microflora were used to explain the pathogenicity of F. oxysporum Schlechtendahl in response to amendment with composts made from grape and coffee wastes. The beneficial effects of the chestnut- and olive-based composts reported in this study could be exploited in strategies aimed at reducing reliance on synthetic pesticides for the control of fungi in lettuce cultivation.

Bioprospecting of cowdung microflora for sustainable agricultural, biotechnological and environmental applications

The review aims at highlighting the manifold applications of cow dung (CD) and CD microflora covering agricultural, biotechnological and environmental applications. The update research on CD microflora and CD in agricultural domain such as biocontrol, growth promotion, organic fertilizer, sulfur oxidation, phosphorus solubilization, zinc mobilization and underlying mechanisms involved in these processes are discussed. The significance of CD applications in tropical agriculture in context to climate change is briefly emphasized. The advances on genomics and proteomics of CD microflora for enhanced yield of enzymes, organic acids, alternative fuels (biomethane and biohydrogen) and other biocommodities, and environmental applications in context to biosorption of heavy metals, biodegradation of xenobiotics, etc. have been given critical attention.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Co-composting of cotton residues with olive mill wastewater: process monitoring and evaluation of the diversity of culturable microbial populations

With the aim to recommend an integrated alternative for the combined treatment of olive mill wastewater (OMW) and cotton residues (CR), and the production of high value and environmentally friendly products, two compost piles were set up. The first pile (control, pile 1) consisted of ginned CR, whereas the second (pile 2) was made of CR with the addition of OMW. A series of physicochemical parameters and the culturable microbial diversity in both piles were assessed. Co-composting (pile 2) displayed higher temperatures during the whole process, a prolonged second thermophilic phase and temperature values higher than 40 °C even after the thermophilic stage. Comparing the physicochemical parameters of the pile 2 with those of the pile 1, it was deduced that pH in the former was more acidic during the onset of the process; the EC values were higher throughout the process, while the levels of ammonium and nitrate nitrogen, as well as the NH₄⁺/NO₃^- ratios, were lower at most of the sampling dates. By evaluating the abovementioned results, it was estimated that the co-composting process headed sooner toward stability and maturity, Isolated microorganisms from both piles were identified as members of the genera Brevibacillus, Serratia, Klebsiella, and Aspergillus, whereas active thermotolerant diazotrophs were detected in both piles at the 2nd thermophilic phase emerging a promising prospect upon further evaluation for enhancing the end-product quality. Our findings indicate that co-composting is an interesting approach for the exploitation of large quantities of agro-industrial residues with a final product suitable for improving soil fertility and health.

Mitigation of carbon and nitrogen losses during pig manure composting: A meta-analysis

Composting is a reliable way to recycle manure for use on croplands in sustainable agriculture. Poor management of the composting process can result in a decrease in the final compost quality and negative environmental impacts. Optimization technologies during composting have varied effects on the mitigation of carbon (C) and nitrogen (N) losses. To determine the feasibility and effectiveness of mitigation options, a meta-analysis was performed based on 68 studies in which C and/or N losses were investigated during pig manure composting. The results indicated that 48.7% of the total C (TC) was lost with 34.8% as CO₂-C and 0.9% as CH₄-C, and 27.5% of the total N (TN) was lost with 17.1% as NH₃-N and 1.5% as N₂O-N. The composting method and bulking agent type obviously influenced the C and N losses. CO₂-C and CH₄-C emission was significantly influenced by the initial C/N ratio and moisture, respectively. At the same time, NH₃-N and N₂O-N emissions were remarkably affected by the initial pH and composting duration, respectively. The results of the meta-analysis showed that TC and TN losses were reduced by 12.4% and 27.5%, respectively. Controlling feedstock, including the C/N ratio and moisture, could be regarded as N conservation technology. Controlling aeration, including turning frequency and ventilation rate, would be reliable in reducing greenhouse gas emissions. Applying additives, especially biochar and superphosphate, was found to be an effective method for synergistically mitigating C and N losses. Therefore, the production of high-quality compost products and minimization of environmental pollution will be achieved by a combination of adjusting the initial substrate properties, controlling the composting process conditions and applying additives.

Role of soil in the regulation of human and plant pathogens: soils' contributions to people

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Pepper root rot resistance and pepper yield are enhanced through biological agent G15 soil amelioration

Pepper root rot is a serious soil-borne disease that hinders pepper production, and efforts are being made to identify biological agents that can prevent and control pepper root rot. Our group recently discovered and produced a biological agent, named G15, which reduces the diversity and richness of fungi and bacteria when applied to pepper fields. In the soil of the G15-treatment condition, the pathogenic fungus Fusarium was inhibited, while the richness of beneficial bacteria Rhodanobacter was increased. Also, the ammonia nitrogen level was decreased in the G15-treatment soil, and the pH, total carbon, and total potassium levels were increased. Compared to the control condition, pepper yield was increased in the treatment group (by 16,680 kg acre^-1). We found that G15 could alter the microbial community structure of the pepper rhizosphere. These changes alter the physical and chemical properties of the soil and, ultimately, improve resistance to pepper root rot and increase pepper yield.

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media

Three characteristics are considered key for optimal use of composts in growing media: maturity, pH and organic matter content. Maturation is a critical step in the processing of composts contributing to compost quality. Blending of composts with chopped heath biomass, sieving out the larger fraction of composts and acidification of composts by adding elemental sulfur may be used either to increase organic matter content or to reduce pH for a better fit in growing media. While several studies have shown the effectiveness of these treatments to improve the use of composts in growing media, the effect of these treatments on the compost microbiome has merely been assessed before. In the present study, five immature composts were allowed to mature, and were subsequently acidified, blended or sieved. Bacterial and fungal communities of the composts were characterized and quantified using 16S rRNA and ITS2 gene metabarcoding and phospholipid fatty acid analysis. Metabolic biodiversity and activity were analyzed using Biolog EcoPlates. Compost batch was shown to be more important than maturation or optimization treatments to determine the compost microbiome. Compost maturation increased microbial diversity and favored beneficial microorganisms, which may be positive for the use of composts in growing media. Blending of composts increased microbial diversity, metabolic diversity, and metabolic activity, which may have a positive effect in growing media. Blending may be used to modify the microbiome to a certain degree in order to optimize microbiological characteristics. Acidification caused a decrease in bacterial diversity and microbial activity, which may be negative for the use in growing media, although the changes are limited. Sieving had limited effect on the microbiome of composts. Because of the limited effect on the microbiome, sieving of composts may be used flexible to improve (bio)chemical characteristics. This is the first study to assess the effects of maturation and optimization treatments to either increase organic matter content or lower pH in composts on the compost microbiome.

Vermiwash: An agent of disease and pest control in soil, a review

Vermiwash is a liquid extract produced from vermicompost in a medium where earthworms are richly populated. It comprises a massive decomposer bacteria count, mucus, vitamins, different bioavailable minerals, hormones, enzymes, different antimicrobial peptides, etc. This paper aimed to assess how these natural products in vermiwash suppressed the pathogen and pests. Thus, we have reviewed the importance of vermiwash/vermicompost in disease control, the mechanism of disease suppression, the components of vermiwash applied in disease suppression, and pest control to use the scientific facts in agriculture to enhance the productivity of the crops. The bioactive macromolecules from the skin secretion of earthworm, coelomic fluid, and mucus directly able to defend pathogenic soil microbes against the worm and thereby freed the environment from the disease. Earthworms establish symbiotic relations with microbes, produce an essential product that supports the growth of plants, and suppress plant's root disease. It is recomended that earthworm should be inoculated in an agricultural field, or prepare and apply its vermiwash/vermicompost as a spray or as additive bio-fertilizer in the soil to enhance the productivities of the crops.

Effect of microbial transformation induced by metallic compound additives and temperature variations during composting on suppression of soil-borne pathogens

Agricultural wastes can be modified by composting and reused in soil to suppress soil-borne pathogens, which was proved to be closely related with microbial parameters. However, the microbial community in compost can be directly altered by temperature variations and metallic compound additives during composting process. The present study collected samples in various stages of the 35-day composting process, in which a study control (no additives) and different metallic compound additives, including magnesium oxide (MgO), alum (AlK(SO₄)₃), calcium oxide (CaO) and ferrous sulfate (FeSO₄), were set in the bespoke compost with cow dung and corn stalk. The results showed that the additives prolonged the composting maturity process, whereas no consistent influence on the temperature variation and microbial community was observed. Temperature variations during composting significantly varied the bacteria and fungi diversity and community, especially the bacteria phyla of Firmicutes and Proteobacteria, while the bacteria were shown similar in Day 14 and Day 35 by PCA analysis. Meanwhile the samples from Day 14 and Day 35 showed stable suppressive effects on R. solani. and F. oxysporum, especially in D14 shown as 73.12%-88.16% and 30.95-58.55%, respectively, which were significantly related with the phyla of Firmicutes and Proteobacteria. In conclusion, temperature variations during composting process had a more significant impact than metallic compound additives on the microbial community and diversity, which resulted in significantly influence on the pathogen suppression. Suitable composting duration could produce effective suppressive products on soil-borne pathogens, for which further study was needed.

The Soil Nutrient Environment Determines the Strategy by Which Bacillus velezensis HN03 Suppresses Fusarium wilt in Banana Plants

Biological control agents (BCAs) are considered as one of the most important strategies for controlling Fusarium wilt, and bioorganic fertilizer, in particular, has been extensively investigated. However, little is known regarding how a biocontrol microorganism affects the suppression mechanisms when combined with different amendments. In this study, a pot experiment was performed using banana plants to investigate the different mechanisms by which the biocontrol bacterium Bacillus velezensis HN03 (isolated from our laboratory) and amendments suppress Fusarium wilt. The incidence of banana wilt was decreased under HN03 and was reduced further when HN03 was combined with compost, particularly wormcast. In the suppression of Fusarium wilt, HN03 was found to influence the soil environment in various ways. HN03 increased the peroxidase level, which improves plant defense, and was highest when combined with wormcast, being 69 times higher than when combined with cow dung compost. The high accumulation of Mg and P in the "HN03 + wormcast" and Zn and Mn in the "HN03 + cow dung" treatments was negatively correlated with disease incidence. Furthermore, HN03 re-established the microbial community destroyed by the pathogen and further increased the level of suppression in the wormcast. HN03 also enhanced the functional traits of the soil, including defensive mechanism-related traits, and these traits were further enhanced by the combination of HN03 + wormcast.

Biocontrol and plant growth-promoting potentiality of bacteria isolated from compost extract

The use of compost extracts is steadily increasing, offering an attractive way for plant growth enhancement and disease management replacing chemical pesticides. In this study, potential mechanisms involved in plant growth promotion and suppressive activity against fungal diseases, of a compost extract produced from poultry manure/olive husk compost, were investigated. Results of physico-chemical and microbiological investigations showed high ability to reduce Fusarium oxysporum, Alternaria alternata, Aspergillus niger and Botrytis cinerea growth. The suppressive ability detected using confrontation test and the phytostimulatory effect tested on tomato seeds were related mainly to its microbial population content. Among 150 bacterial strains, isolated from the compost extract, 13 isolates showed antifungal activity against the four tested plant pathogenic fungi. Their identification based on 16S rRNA gene sequence revealed they belonged to different species of the genus Bacillus, Alcaligenes, Providencia and Ochrobactrum. When tested for their ability to produce cell wall degradation enzymes using specific media, the majority of the 13 isolates were shown to synthesize proteases, lipases and glucanases. Similarly, the best part of them showed positive reaction for plant growth promoting substances liberation, biosurfactant production and biofilm formation. In vivo tests were carried out using tomato seeds and fruits and proved that 92% of strains improved tomato plants vigor indexes when compared to the control and 6 among them were able to reduce decay severity caused by B. cinerea over 50%. Principal component analysis showed an important correlation between in vitro and in vivo potentialities and that Bacillus siamensis CEBZ11 strain was statistically the most effective strain in protecting tomato plants from gray mould disease. This study revealed the selected strains would be useful for plant pathogenic fungi control and plant growth promotion.

Biofertilizers as Strategies to Improve Photosynthetic Apparatus, Growth, and Drought Stress Tolerance in the Date Palm

Rainfall regimes are expected to shift on a regional scale as the water cycle intensifies in a warmer climate, resulting in greater extremes in dry versus wet conditions. Such changes are having a strong impact on the agro-physiological functioning of plants that scale up to influence interactions between plants and microorganisms and hence ecosystems. In (semi)-arid ecosystems, the date palm (Phoenix dactylifera L.) -an irreplaceable tree- plays important socio-economic roles. In the current study, we implemeted an adapted management program to improve date palm development and its tolerance to water deficit by using single or multiple combinations of exotic and native arbuscular mycorrhizal fungi (AMF1 and AMF2 respectively), and/or selected consortia of plant growth-promoting rhizobacteria (PGPR: B1 and B2), and/or composts from grasses and green waste (C1 and C2, respectively). We analyzed the potential for physiological functioning (photosynthesis, water status, osmolytes, mineral nutrition) to evolve in response to drought since this will be a key indicator of plant resilience in future environments. As result, under water deficit, the selected biofertilizers enhanced plant growth, leaf water potential, and electrical conductivity parameters. Further, the dual-inoculation of AMF/PGPR amended with composts alone or in combination boosted the biomass under water deficit conditions to a greater extent than in non-inoculated and/or non-amended plants. Both single and dual biofertilizers improved physiological parameters by elevating stomatal conductance, photosynthetic pigments (chlorophyll and carotenoids content), and photosynthetic efficiency. The dual inoculation and compost significantly enhanced, especially under drought stress, the concentrations of sugar and protein content, and antioxidant enzymes (polyphenoloxidase and peroxidase) activities as a defense strategy as compared with controls. Under water stress, we demonstrated that phosphorus was improved in the inoculated and amended plants alone or in combination in leaves (AMF2: 807%, AMF1+B2: 657%, AMF2+C1+B2: 500%, AMF2+C2: 478%, AMF1: 423%) and soil (AMF2: 397%, AMF1+B2: 322%, AMF2+C1+B2: 303%, AMF1: 190%, C1: 188%) in comparison with controls under severe water stress conditions. We summarize the extent to which the dual and multiple combinations of microorganisms can overcome challenges related to drought by enhancing plant physiological responses.

Dynamic bacterial assembly driven by Streptomyces griseorubens JSD-1 inoculants correspond to composting performance in swine manure and rice straw co-composting

The effect of Streptomyces griseorubens JSD-1 inoculant on composting performance and bacterial community assembly during the swine manure and rice straw co-composting was studied by a high-throughput pyrosequencing technology. The JSD-1 inoculant contributed to a higher temperature (maximum 66.8 °C), a longer thermophilic phase (46 days), and a lower bacterial diversity in JSD-1 compost. The principle component analysis confirmed that JSD-1 inoculant significantly reshaped the microbial communities. The difference in genera significantly increased during both composting processes. The predominant biomarkers were members of Bacteroidetes in JSD-1 composting. The network analysis also showed different chief "connecting" genera in both composts. Moreover, JSD-1 inoculant increased the total nitrogen, phosphorus, and potassium content in composts. The redundancy analysis showed that the bacterial community was mainly influenced by temperature; additionally, the nutrient contents were positively correlated with temperature. These results demonstrated that JSD-1 inoculant drove the bacterial assembly to induce physicochemical property changes in co-composting.

Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.

Evaluation of compost quality and bioprotection potential against Fusarium wilt of date palm

The Fusarium wilt of date palm caused by Fusarium oxysporum f.sp. albedinis (Foa) is the most damaging disease in Morocco. It has destroyed more than 12 million trees in the country. Until now, there is no efficient approach to manage this disease. However, biocontrol of soil-borne phytopathogens with compost is currently an established horticultural approach. This study aimed to evaluate the effect of compost extracts in the biocontrol of Foa and their mechanism of action and to investigate parameters involved in compost maturity. Maturity (phytotoxicity test), sanitary quality (pathogen indicators) and in vitro suppressive effect of four composts were investigated. Date palm by-products compost produced with forced aeration composting system is not phytotoxic presenting a germination index of 83.78%. In contrast, two commercial composts were phytotoxic. The maturity was negatively correlated with salinity, C/N ratio and total soluble phenols. Concentrations of pathogen indicators were below suggested limits in all composts. The biocontrol test showed that the date palm wastes compost was more effective; from the sixth day of incubation, the unsterilized extract of this compost at 10% showed the highest antagonistic effect against the pathogen with an inhibition rate of 100%. The inhibition rate using microfiltrated extract didn't exceed 30%. All autoclaved extracts lost their antagonistic effect against the indicator fungus. Thus, the suppressive effect is mainly due to the indigenous microorganisms. Findings indicate the relevance of maturity in the evaluation of compost quality and the efficiency of date palm wastes compost in the suppression of Foa.

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

Verticillium Wilt of Olive and its Control: What Did We Learn during the Last Decade?

Verticillium (Verticillium dahliae Kleb.) wilt is one of the most devastating diseases affecting olive (Olea europaea L. subsp. europaea var. europaea) cultivation. Its effective control strongly relies on integrated management strategies. Olive cultivation systems are experiencing important changes (e.g., high-density orchards, etc.) aiming at improving productivity. The impact of these changes on soil biology and the incidence/severity of olive pests and diseases has not yet been sufficiently evaluated. A comprehensive understanding of the biology of the pathogen and its populations, the epidemiological factors contributing to exacerbating the disease, the underlying mechanisms of tolerance/resistance, and the involvement of the olive-associated microbiota in the tree's health is needed. This knowledge will be instrumental to developing more effective control measures to confront the disease in regions where the pathogen is present, or to exclude it from V. dahliae-free areas. This review compiles the most recent advances achieved to understand the olive-V. dahliae interaction as well as measures to control the disease. Aspects such as the molecular basis of the host-pathogen interaction, the identification of new biocontrol agents, the implementation of "-omics" approaches to unravel the basis of disease tolerance, and the utilization of remote sensing technology for the early detection of pathogen attacks are highlighted.

Lignocellulosic crop residue composting by cellulolytic nitrogen-fixing bacteria: A novel tool for environmental sustainability

Lignocellulosic crop residue (LCCR) composting is a cost-effective and sustainable approach for addressing environmental pollution associated with open biomass burning and application of chemical fertilizers in agriculture. The value-added bio-product of the composting process contributes to the improvement of the soil properties and plant growth in an environment-friendly way. However, the conventional process employed for composting LCCRs is slow and becomes an impediment for farmers who plant two or three crops a year. This concern has led to the development of different techniques for rapid composting of LCCRs. The use of cellulolytic nitrogen-fixing microorganisms for composting has emerged as a promising method for enhancing LCCR composting and quality of the compost. Therefore, this review addresses the recent progress on the potential use of cellulolytic nitrogen-fixing bacteria (CNFB) for LCCR composting and discusses various applications of nutrient-rich compost for sustainable agriculture to increase crop yields in a nature-friendly way. This knowledge of bacteria with both cellulose-degrading and nitrogen-fixing activities is significant with respect to rapid composting, soil fertility, plant growth and sustainable management of the lignocellulosic agricultural waste and it provides a means for the development of new technology for sustainability.

Compost Amendments Based on Vinegar Residue Promote Tomato Growth and Suppress Bacterial Wilt Caused by Ralstonia Solanacearum

Tomato bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating soil-borne diseases, and compost is to be considered as a resource-saving and environment-friendly measure to control the disease. Herein, a pot experiment was implemented to explore the effects of vinegar residue matrix amendments on the growth performances of tomato seedlings and to examine the suppression ability against bacterial wilt under vinegar residue substrate (VRS), and peat substrate (Peat) with RS inoculation. The results revealed that VRS effectively suppressed the disease incidence of bacterial wilt, increased the number of bacteria and actinomycetes, decreased fungi populations, promoted soil microbial populations and microbial activities, enhanced the growths of tomato seedlings, and modulated defense mechanism. In addition, VRS efficiently inhibited the oxidative damage in RS inoculated leaves via the regulation of excess reactive oxide species (O₂^•− and H₂O₂) production, lessening of malondialdehyde (MDA) content, and causing less membrane injury; resulting in enhancements of antioxidants enzymes activities accompanying with modulating their encoding gene expression. The transcription levels of NPR1, PIN2, PR1b, ACO1, EDS1, PR1B, MAPK3, PIN2, and RRS1 were also modulated with the pathogens inoculated in tomato leaves both in VRS and Peat treatments, which indicated that systemic-acquired resistance possesses cross-talk between salicylic acid, jasmonic acid, and the ethylene-dependent signaling pathway. Besides, the RS inoculation significantly inhibited the growth of tomato seedlings, and all growth indices of plants grown in VRS were considerably higher than those produced in Peat. Taken together, VRS represents a new strategy to control tomato bacterial wilt through boosting the soil microbial populations and microbial activities. Furthermore, VRS promotes the plant immune response to provide a better growth environment for plants surviving in disease conditions.

Bio-inherent attributes of water hyacinth procured from contaminated water body-effect of its compost on seed germination and radicle growth

Compost is generally used for soil conditioning, growing plants and remediation of pollution. It is imperative to evaluate compost standard and toxicity test is a salient parameter for determining compost quality. Seed germination test is an essential method to discern the phytotoxicity of compost. Ecotoxicity of water hyacinth compost was inspected for the denouement of the compost quintessence and its concentration on seed germination indices. The aim of this paper was to assess seed emergence rate index, germination velocity coefficient and rate of germination of L. esculentum and B. oleracea at discrete concentrations of water hyacinth compost. The highest germination percentage achieved was 95% (L. esculentum) at 100 g/L and 100% (B. oleracea) at 32 g/L of the compost extract. The probability of inadvertent ceasing of germination was found to be < 0.0001 for either of the test species. Consequently, the water hyacinth compost aid plant growth and is recommended for substantially ameliorating languishing ecological idiosyncrasy.