Panama disease caused by Fusarium oxysporum f. sp. cubense infection on banana is devastating banana plantations worldwide. Biological control has been proposed to suppress Panama disease, though the ...stability and survival of bio-control microorganisms in field setting is largely unknown. In order to develop a bio-control strategy for this disease, 16S rRNA gene sequencing was used to assess the microbial community of a disease-suppressive soil. Bacillus was identified as the dominant bacterial group in the suppressive soil. For this reason, B. amyloliquefaciens NJN-6 isolated from the suppressive soil was selected as a potential bio-control agent. A bioorganic fertilizer (BIO), formulated by combining this isolate with compost, was applied in nursery pots to assess the bio-control of Panama disease. Results showed that BIO significantly decreased disease incidence by 68.5%, resulting in a doubled yield. Moreover, bacterial community structure was significantly correlated to disease incidence and yield and Bacillus colonization was negatively correlated with pathogen abundance and disease incidence, but positively correlated to yield. In total, the application of BIO altered the rhizo-bacterial community by establishing beneficial strains that dominated the microbial community and decreased pathogen colonization in the banana rhizosphere, which plays an important role in the management of Panama disease.
Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses ...through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.
•Feasible C/N ratios enhanced composting efficiency.•Composting treatment and phase influenced bacterial community.•Variations of enzymes were related to bacterial community succession.•Functional ...enzymes related to key taxa enhanced composting efficiency.
A consortium of key bacterial taxa plays critical roles in the composting process. In order to elucidate the identity and mechanisms by which specific bacterial species drive high-efficiency composting, the succession of key bacterial consortia and extracellular enzymes produced during the composting process were monitored in composting piles with varying initial C/N ratios. Results showed that C/N ratios of 25 and 35 enhanced composting efficiency through elevated temperatures, higher germination indices, enhanced cellulose and hemicellulose degradation, and higher cellulase and dehydrogenase activities. The activities of cellulase and β-glucosidase, cellulase and protease, and cellulase and β-glucosidase exhibited significant relationships with bacterial community composition within the mesophilic, thermophilic, and mature phases, respectively. Putative key taxa, linked to a higher composting efficiency, such as Nonomuraea, Desemzia, Cellulosimicrobium, Virgibacillus, Clostridium, and Achromobacter, exhibited significantly positive relationships with extracellular enzyme activities, suggesting a significant contribution to these taxa to the development of composting maturity.
Increases in carbon (C) inputs to soil can replenish soil organic C (SOC) through various mechanisms. However, recent studies have suggested that the increased C input can also stimulate the ...decomposition of old SOC via priming. Whether the loss of old SOC by priming can override C replenishment has not been rigorously examined. Here we show, through data-model synthesis, that the magnitude of replenishment is greater than that of priming, resulting in a net increase in SOC by a mean of 32% of the added new C. The magnitude of the net increase in SOC is positively correlated with the nitrogen-to-C ratio of the added substrates. Additionally, model evaluation indicates that a two-pool interactive model is a parsimonious model to represent the SOC decomposition with priming and replenishment. Our findings suggest that increasing C input to soils likely promote SOC accumulation despite the enhanced decomposition of old C via priming.
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•Composting treatment and phase influenced fungal community.•Composting reduced plant and animal pathogens.•Plant and animal pathogens were negative correlated with compost ...maturity.•Specific OTUs were expected to compete for environmental preferences (niches).
Accumulating evidence indicates that the functional rather than taxonomic composition of microbial communities is closely correlated to local environmental factors. While composting is a widely accepted practice, specific knowledge of how fungal functional groups interact during the composting process remains limited. To address this, the impact of the initial C/N ratio of composting material on fungal community was analyzed in order to reveal the succession of functional diversity. Compared with the raw materials, the final composting product significantly reduced the relative abundances of plant and animal pathogens. Abundances of plant and animal pathogens, as well as dung saprotrophs, were negatively correlated with compost maturity, while abundances of wood saprotrophs exhibited positive correlations. Specific OTUs that showing highly abundant in each treatment were expected to compete for environmental preferences (niches) and/or interact with each other in positive (facilitative) ways. OTU2 (wood saprotroph) exhibiting the highest occurrence was negatively related to OTU7 (animal pathogen) and OTU4 (plant pathogen) during the mesophilic phase. Taken together, high-efficiency composting is represented as pattern variations of fungal community with a process of gradual decline of plant and animal pathogens as well as dung saprotrophs.
Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ...ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of ~700-bp 16S rRNA gene sequences with >96% homology to the "Candidatus Scalindua" group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to "Ca. Scalindua," "Candidatus Brocadia," and "Candidatus Kuenenia." This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.
Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop ...sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Worldwide, banana production is severely hindered by Fusarium wilt, a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). With no widely adopted efficient ...method of control or prevention, the emergence of a new Foc variant, tropical race 4 (Foc TR4), has led to the widespread destruction of plantations in Cavendish-producing areas. Recently, banana Fusarium wilt has been controlled by the consecutive application of biofertilizer (BIO) in newly reclaimed fields. In this study we examine the temporal effects of BIO versus compost application in newly converted banana fields on the composition and abundance of the rhizosphere bacterial and fungal communities and the survival of the biocontrol inoculant, Bacillus amyloliquefaciens NJN-6. Our findings show that BIO-amended rhizosphere soils increased the abundance of bacteria while decreasing fungal abundance. This corresponded to higher bacterial richness and diversity in the BIO amendment, while no trends were observed with the fungal community. Rhizosphere soil bacterial and fungal community composition were significantly different between BIO and compost amendment and treatment, not time, exhibited the largest impact. Other potential taxa involved in disease suppression were also identified, such as increased abundances of Sphingobium, Dyadobacter, and Cryptococcus and lower abundances of Fusarium, Ralstonia, and Burkholderia. Overall, decreased abundances of F. oxysporum and a lack of variability in the abundance of the biocontrol agent NJN-6 over three years contributed to disease suppression, in combination with alterations in fungal and bacterial composition and abundance, pointing to the sustainability of BIO as an amendment for disease suppression.
•Fusarium wilt disease was pre-controlled by biofertilizer (BIO) in reclaimed field.•Higher bacterial richness and diversity were identified in BIO treated soils.•Bacterial and fungal community composition was altered by BIO treatment.•BIO application significantly reduced the abundance of Fusarium oxysporum.•The inoculum Bacillus amyloliquefaciens NJN-6 exhibited little temporal variation.
The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the ...predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO
emissions and potentially mitigates nitrous oxide emissions.
The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO
production.
Overuse or mistimed application of nitrogen fertilizer can cause nitrate contamination in groundwater and surrounding surface waters. Previous greenhouse studies have explored the use of graphene ...nanomaterials, including graphite nano additive (GNA), to reduce nitrate leaching in an agricultural soil while growing lettuce crops. To investigate the mechanism of GNA addition in suppressing nitrate leaching, we conducted soil column experiments using native agricultural soils under saturated or unsaturated flow conditions to simulate varied irrigation. We investigated the effects of temperature (4 °C compared with 20 °C) on microbial activity and dose effect of GNA was also explored (165 mg/kg soil and 1650 mg/kg soil) for biotic soil column experiments whereas a single temperature condition (20 °C) and GNA dose (165 mg/kg soil) was employed for abiotic (autoclaved) soil column experiments. Results showed GNA addition had minimal effects on nitrate leaching in saturated flow soil columns due to short hydraulic residence times (∼3.5 h). In comparison, longer residence times (∼3 d) in unsaturated soil columns reduced nitrate leaching by 25–31% relative to control soil columns without GNA addition. Furthermore, nitrate retention in the soil column was found to be suppressed at 4 °C compared with 20 °C, suggesting a bio-mediated mechanism for GNA addition to reduce nitrate leaching. In addition, the soil dissolved organic matter was found to be associated with nitrate leaching, where less nitrate leaching occurring when higher dissolved organic carbon (DOC) was measured in leachate water. Following studies of adding soil-derived organic carbon (SOC) resulted in greater nitrogen retention in the unsaturated soil columns only when GNA was present. Overall, the results suggest that GNA-amended soil reduces nitrate loss through increased N immobilization in the microbial biomass or loss of N in gaseous phase through enhanced nitrification and denitrification process.
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•Graphene nanomaterials (GNA) added with fertilizers to soil reduced nitrate leaching by up to 31%.•Higher temperatures and GNA addition reduced nitrate leaching, indicating an important biological mediated mechanism.•Solubilization of soil organic matter plays a crucial role in preventing nitrate leaching.•GNA-amended soil enhance nitrogen retention through microbial processes, reducing nitrate loss significantly.
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