Effect of Two Kinds of Fertilizers on Growth and Rhizosphere Soil Properties of Bayberry with Decline Disease

Decline disease causes severe damage to bayberry. However, the cause of this disease remains unclear. Interestingly, our previous studies found that the disease severity is related with the level of soil fertilizer. This study aims to explore the effect and mechanism of compound fertilizer (CF) and bio-organic fertilizer (OF) in this disease by investigating the vegetative growth, fruit characters, soil property, rhizosphere microflora and metabolites. Results indicated that compared with the disease control, CF and OF exhibited differential effect in plant healthy and soil quality, together with the increase in relative abundance of Burkholderia and Mortierella, and the reduction in that of Rhizomicrobium and Acidibacter, Trichoderma, and Cladophialophora reduced. The relative abundance of Geminibasidium were increased by CF (251.79%) but reduced by OF (13.99%). In general, the composition of bacterial and fungal communities in rhizosphere soil was affected significantly at genus level by exchangeable calcium, available phosphorus, and exchangeable magnesium, while the former two variables had a greater influence in bacterial communities than fungal communities. Analysis of GC-MS metabonomics indicated that compared to the disease control, CF and OF significantly changed the contents of 31 and 45 metabolites, respectively, while both fertilizers changed C5-branched dibasic acid, galactose, and pyrimidine metabolic pathway. Furthermore, a significant correlation was observed at the phylum, order and genus levels between microbial groups and secondary metabolites of bayberry rhizosphere soil. In summary, the results provide a new way for rejuvenation of this diseased bayberry trees.

Plant Growth-Promoting Rhizobacteria HN6 Induced the Change and Reorganization of Fusarium Microflora in the Rhizosphere of Banana Seedlings to Construct a Healthy Banana Microflora

Streptomyces aureoverticillatus HN6 was isolated in our previous study and effectively controlled banana Fusarium wilt. We explored the role of HN6 in constructing a healthy rhizosphere microflora of banana seedlings. The method of antibiotic resistance was used to determine the colonization ability of HN6. The effect of HN6 on the rhizosphere microbial communities was assessed using culture-dependent and high-throughput sequencing. The effect of HN6 on the infection process of the pathogen was evaluated using a pot experiment and confocal laser scanning microscopy. The results showed that HN6 could prevent pathogen infection; it increased the nutrient content and diversity of the bacterial community in the rhizosphere, promoted plant growth, and decreased the mycotoxin fusaric acid content and abundance of pathogens in the banana rhizosphere. Thus, HN6 decreased the relative abundance of Fusarium species, increased the diversity of fungi, and increased the relative abundance of bacteria in the rhizosphere. HN6 induced the change and reorganization of the microbial community dominated by Fusarium in the rhizosphere of banana seedlings, and it evolved into a community dominated that was not conducive to the occurrence of diseases, shaping the rhizosphere microflora and promoting the growth of banana.

Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

This study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the ‘1%’ paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be “cultured” by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

Chemical stress contribution in bacterial biofilm formation

<p>Background: The use of different chemicals for agriculture, industry and mining has caused pollution of agrarian soils which provokes changes in rhizosphere microflora. We have studied 10 bacterial strains isolated from a winter wheat Cd-polluted field in Ukraine by their taxonomic position, biochemical properties and resistance to 3 classes of toxicants: heavy metals (Cu<sup>2+</sup>, Cd<sup>2+</sup>), non-metals (perchlorate-ion), organic xenobiotic (1-chloro-4-nitrobenzene, CNB).  </p> <p>Objectives: To study the effect of toxicants on the biofilm–formation ability of individual strains and a mixed community.</p> <p>Methods: Biofilm characteristics (total microcosm growth, biofilm strength and attachment to the microcosm walls) were studied by combined biofilm assay (n = 4) with four treatments including 100 mg/L Cu<sup>2+</sup>, 25 mg/L Cd<sup>2+</sup>, 300 mg/L ClO<sub>4</sub><sup>-</sup>, and 100 mg/L CNB, with correlations and Principal component analysis (PCA) used to investigate data.</p> <p>Results: We found that microbial community had a greater resistance to the toxicants compare to individual strains. The presence of heavy metals increased the strength of biofilms, and in most cases growth and biofilm strength were positively correlated. However, in the presence of Cd<sup>2+</sup> this correlation was lost. Perchlorate affected bacteria, increasing mucus production and biofilm strength though it also reduced attachment levels. Finally, we also found that CNB could be used as a source of Carbon and energy during biofilm–formation.</p>

Enzyme Activity and Rhizosphere Microflora under Sugarcane Monocropping as Influenced by Integrated Nutrient Management

Sugarcane is one of the lead crops in North Coastal Andhra Pradesh. Farmers in North Coastal Zone are opting for raising more number of ratoons owing to its substantially low cost of production. Ratoon crops however seldom receive proper care and inputs due to considered it as a bonus crop by majority of farmers. Field experiments were conducted consecutively for six years in the same field (2012-13 to 2018-19) at RARS, Anakapalle to study the monocropping effect on soil biology under the influence of different nutrient management practices. Irrespective of the year of ratooning, plots which received 50% recommended dose of chemical fertilizers + 25% nitrogen though vermicompost + 25% nitrogen through green manure incorporation resulted in higher microbial population over chemical fertilizers alone. Activity of dehydrogenase and active carbon pool also showed similar trend in multi-ratooning system of sugarcane. Rhizosphere microbial population at different growth stages revealed that, azospirillum population was observed highest followed by azotobacter while lowest population counts of phosphorus solubilizing bacteria were observed. Highest population counts were recorded in INM plots and population was highest at formative later reduced to harvest. INM with 50% RDFN + 50% through organics (66.80 t ha-1) recorded at par yields with 100% RDF (67.28 t ha-1).

Production and characterization of antimicrobials from isolate Pantoea agglomerans of Medicago sativa plant rhizosphere soil

Due to rise in drug resistance among pathogens, there is always an urge to look for new drug alternatives. So in this study we aimed to identify the unexplored rhizosphere microflora of alfalfa plant for new antimicrobials. With initial screening for isolates from rhizosphere region for antibacterial activity against selected bacterial pathogens, the isolate AL10 had better activity selected for this study. The isolate mass was cultured and secondary metabolites were extracted using ethyl acetate and subjected to FTIR and GC-MS analysis. Based on functional diversity analysis, the isolate subjected to anti-bacterial activity revealed significant activity against Streptococcus pneumonia, Klebsiella, S. aureus with zone of inhibition in the range of18-20 mm. Based on GC-MS analysis report ten compounds were identified and 1-Octadecane and 1-nonadecanol were found to be responsible for bio-activity. FT-IR results showed that N-H stretching functional group was dominantly present in the extract. Molecular identification of the isolate by 16S rRNA sequencing showed the isolate as Pantoea agglomerans. The results showed that the isolate P.agglomerans, gram negative bacteria had wide antibacterial activity due to 1-Octadecane and 1-nonadecanol. Though Alfalfa plant has been described for various biological activities, this is a first report on rhizosphere region of plant reporting for antibacterial potential microbes.