Control Of Soil-borne Pathogens Research Articles

Effect of Formulations of Allyl Isothiocyanate on Survival of Macrophomina phaseolina from Strawberry.

Management of Macrophomina phaseolina, causal agent of charcoal rot in many crops worldwide, including strawberry, has become more challenging since the phase out of methyl bromide (MeBr). The search for a fumigant equally effective as MeBr to control soilborne pathogens has been extensive. Allyl isothiocyanate (AITC), a biofumigant recently registered in the United States, was evaluated at different rates, formulations, fumigant combinations, and application methods in the fall of 2014 and 2015 at two research facilities in Balm and Dover, FL. The efficacy of treatments was determined by evaluating the survival of M. phaseolina inoculum on infested corn-cob litter buried in bags 7.6 and 20.3 cm deep in the center, and 7.6 cm deep in the side, of plastic mulched raised beds. The biofumigant was shown to be more or as effective in reducing populations of M. phaseolina in the soil compared with standard fumigants, such as chloropicrin and 1,3-dichloropropene with chloropicrin. Thus, AITC is a promising biofumigant alternative for managing charcoal rot of strawberry, particularly in organic production systems, and should be evaluated for the management of other soilborne pathogens.

Potential of wild Solanum stramonifolium accesses as rootstock resistant to soilborne pathogens in tomato crops

ABSTRACT Resistant rootstocks is one of the most effective method to control soilborne pathogens in tomato crops. Thus, this study was installed to evaluate the reaction of Solanum stramonifolium accesses to Fusarium oxysporum f. sp. lycopersici (Fol) races 2 and 3 and to Meloidogyne enterolobii (Me). The seedlings were grown in trays and inoculated separately with Fol races 2 and 3 at 50 days after planting by immersing the roots in the spore suspension (1×106 microconidia mL-1). Then, seedlings were transplanted in pots containing sterilized soil and kept in greenhouse conditions. To study the reaction of S. stramonifolium accesses to nematodes, we used 27-day old seedlings that were also planted in pots and inoculated with 6,000 eggs and second-stage juveniles in greenhouse conditions. The experiments were evaluated in the 34th day (Fol) and in the 64th day (Me) after inoculation. The experiment consisted of a randomized block design with five replications, where each plot consisted of one pot with three plants (Fol) and one pot with one plant (Me). We observed that the plants used as controls, susceptible to Fol races 2 and 3 and Me, presented 100% of incidence. All accesses were resistant to Fol race 2 and the accesses CNPH-19, CNPH-22, CNPH-23, CNPH-25, CNPH-120, CNPH-122 and CNPH-349 presented multiple resistance to pathogens, indicating great potential for using as resistant rootstock. The CNPH-24, CNPH-119, CNPH-121 and CNPH-336 accesses also presented resistance to nematode. However, they presented slight browning symptoms of vascular tissues when they were inoculated with Fol race 3. This symptom was also observed in the CNPH-21, CNPH-107 and CNPH-117 accesses. All other accesses were resistance to Fol race 3 and susceptible to Me.

Impacts of anaerobic soil disinfestation and chemical fumigation on soil microbial communities in field tomato production system

Anaerobic soil disinfestation (ASD), a potential alternative to pre-plant chemical fumigation for controlling soilborne pathogens, has been demonstrated in several agricultural production systems. The effect of ASD on the soil microbial community is considered one of the major factors responsible for pathogen suppression. However, rather limited information is available regarding the response of the soil microbial community to ASD throughout the cropping season, particularly in sandy soils. A field experiment was conducted to optimize the ASD technique for tomato production in Florida, utilizing two rates of molasses and composted poultry litter (CPL), and a pre-emergent herbicide application. The pre-plant soil treatments included ASD with 6.9 m3 ha−1 of molasses and 11 Mg ha−1 of CPL (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 of CPL (ASD1.0), and chemical soil fumigation control (CSF). The herbicide treatments included with and without halosulfuron application. Soil microbial community composition was monitored using phospholipid fatty acid (PLFA) analysis during the fall 2015 tomato production season. Halosulfuron application did not result in changes in the soil microbial community during the season. CSF led to significantly lower levels of bulk soil total microbial biomass, Gram negative bacteria, Gram positive bacteria and actinomycetes, compared to the ASD treatments. However, the rhizosphere effect of plants under CSF alleviated the microbial suppression and stimulated the growth of Gram negative bacteria and protozoa to reach similar levels to that of rhizosphere soils under the ASD treatments. Compared to 0 day after transplanting (DAT), Gram positive bacteria in bulk soils under the three pre-plant soil treatments significantly decreased while the fungi:bacteria ratio in bulk soils under CSF significantly increased at 36 DAT, and then remained stable throughout the season. Despite the similar microbial composition in bulk and rhizosphere soils between the two ASD treatments, the dynamic changes of some biomarker groups in bulk soils during 0–99 DAT showed distinct patterns particularly for total microbial biomass, Gram negative bacteria, actinomycetes, and fungi. Compared to 0 DAT, bulk soil microbial community composition shifted after 36 DAT under all soil treatments and remained stable until the end of the season. The changes in soil microbial community composition over time were related to changes in soil nutrient availability.

Effect of nicotine from tobacco root exudates on chemotaxis, growth, biocontrol efficiency, and colonization by Pseudomonasaeruginosa NXHG29.

Accumulated evidence suggests that root exudates have a major role in mediating plant-microbe interactions in the rhizosphere. Here, we characterized tobaccorootexudates (TREs) by GC-MS and nicotine, scopoletin, and octadecane were identified as three main components of TREs. Qualitative andquantitative chemotaxis assays revealed that Pseudomonas aeruginosa NXHG29 with antagonistic activity displayed positive chemotactic responses towards TREs and their three main components (nicotine, scopoletin, octadecane) and its enhanced chemotaxis were induced by these substances in a concentration-dependent manner. Furthermore, following GC-MS and chemotaxis analysis, nicotine was selected as the target for evaluation of the effect on NXHG29 regarding antagonism, growth, root colonization and biocontrol efficiency. Results of in vitro studies showed that nicotine as a sole carbon source could enhance growth of NXHG29 and significantly increased the antagonism of NXHG29. We also demonstrated that nicotine exerted enhancing effects on the colonization ability of NXHG29 on tobacco roots by combining CLSM observations with investigation of population leveldynamics by selective dilution plating method. Results from greenhouse experiments suggested nicotine exhibited stimulatory effects on the biocontrol efficiency of NXHG29 against bacterial wilt and black shank on tobacco. The stimulatory effect of nicotine was affected by the concentration and timing of nicotine application and further supported by the results of population level of NXHG29 on tobacco roots. This is the first report on the enhancement effect of nicotine from TREs on an antagonistic bacterium for its root colonization, control of soil-borne pathogens, regarding the chemotaxis and in vitro antagonism and growth.

In vitro and in vivo Assay for Assessment of the Biological Control Potential of Streptomyces sp. KT

Rhizoctonia solani is fungal plant pathogen that infects many different host plants. Recently, biological control agents that are friendly to the environment and ecosystems have attracted much attention as an alternative to the use of chemical fungicide which have been used worldwide to control soil borne pathogens including R. solani. In this study, 53 strains of actinomycetes isolated from environmental soils, and antifungal activities of them were assessed by the dual culture assay. Strain KT showed strong inhibitory activities against 8 phytopathogenic fungi. A great suppressive effect on R. solani growth was observed in the inoculation test of plants using cucumber and chin-geng-sai. In addition, infection of Bipolaris oryzae also could be suppressed in the detached leaf assay using oats. As a result of genetic analysis, it was shown that KT was a species closely related to Streptomyces lavenduligriseus NRRL B-3173T. However, as far as we know, there is no report for biological control agents using S. lavenduligriseus. This study suggests that the strain KT may useful as biological control agents to suppress various crop diseases.

Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion.

ABSTRACTBacillus cereus AR156 was originally isolated from the forest soil of Zhenjiang, a city in China. To shed new light on the molecular mechanisms underlying the biological control of soilborne pathogens, the whole genome of this strain was sequenced. Here, we report the draft genome sequence of this strain, consisting of a single circularized contig measuring 5.66 Mb, with an average GC content of 35.5% and 5,367 open reading frames.

Anaerobic soil disinfestation is an alternative to soil fumigation for control of some soilborne pathogens in strawberry production

Alternatives to soil fumigation are needed for soilborne disease control. The aim of this study was to test anaerobic soil disinfestation (ASD) as an alternative to soil fumigation for control of critical soilborne pathogens in Californian strawberry production. Controlled environment experiments were conducted at 25 and 15 °C to test different materials as carbon sources for ASD using soil inoculated with Verticillium dahliae. Field trials were conducted in three locations comparing ASD with 20 Mg ha−1 rice bran (RB) against fumigated and untreated controls, steam, mustard seed meal and fish emulsion. In ASD‐treated soils, temperature and extent of anaerobic conditions were critical for control of V. dahliae, but multiple carbon inputs reduced inoculum by 80–100%. In field trials, ASD with RB provided control of a number of pathogens, and in three of four trials produced marketable fruit yields equivalent to fumigation. Little weed control benefit from ASD was found. ASD with RB also induced changes in the soil microbiome that persisted through the growing season. When equivalent yields were obtained, net returns above harvest and treatment costs with ASD RB were 92–96% of those with bed fumigation based on average prices over the previous 5 years. ASD can be a viable alternative for control of some soilborne pathogens. Growers are adopting ASD in California strawberry production, but research to determine optimal soil temperatures, anaerobicity thresholds and carbon sources for effective control of specific pathogens is needed.

Soil amended with Brassica juncea plant tissue reduces sclerotia formation, viability and aggressiveness of Rhizoctonia solani AG1-IA towards rice

Brassica juncea plant tissue rich in glucosinolates has been used as a soil biofumigant for control of soilborne pathogens. Biocidal effects are attributed to volatile allyl isothiocyanate released upon hydrolysis of glucosinolates. In vitro inhibition of the mycelium growth of Rhizoctonia solani by B. juncea is well documented. The objective of this study was to determine the impacts of B. juncea as a soil amendment on the viability, aggressiveness, and sclerotia formation of R. solani AG1-IA, the causal agent of sheath blight in rice (Oryza sativa). In laboratory experiments, the effects of B. juncea amendment rate (0, 0.2, 0.4, 0.8, 1.6 or 3.2% wt/wt) and duration of exposure (7, 14, or 28 days) on R. solani AG1-IA were evaluated. Mycelium exposed to soils amended with B. juncea at 0.2–3.2% with 7, 14 or 28 days of exposure resulted in significantly reduced sclerotia formation when compared to the mycelium exposed to the non-amended soil. The viability of sclerotia after exposure for 14 and 28 days to soils amended with 1.6 and 3.2% of B. juncea was significantly lower than that of sclerotia exposed to non-amended soil. Sclerotia or mycelium exposed to soil amended with 3.2% of B. juncea for 28 days, resulted in a reduction in aggressiveness as shown by smaller sheath blight lesion development on detached rice leaves than the non-treated controls. Results of this study demonstrate for the first time that B. juncea soil amendment can reduce the viability and aggressiveness of mycelium and sclerotia and further affect the formation of sclerotia of R. solani. The reduction of sclerotia formation by B. juncea introduction may result in the reduction of primary inoculum of sheath blight in the following rice season.

Antagonistic Fungi, Soil Amendment and Soil Solarization as an Integrated Tactics for Controlling Fusarium Root Rot of Lupine ( Lupinus termis )

The efficient control of soil-borne pathogens while avoiding environmental hazards and degradation of natural resources is the paramount challenge in crop protection sciences. Lupinus termis (lupine) is a fabaceous crop grown in Egypt for food, medical and industrial uses. The management of Fusarium root rot pathogens, which are responsible for serious losses on a number of economically important crops, including lupine, is being investigated. This study aimed to control Fusarium lupine root rot, under field conditions with no or low environmental impact; by using different control measures such as: antagonistic fungi, soil amendment and solarization singly or as an integrated disease management strategy. The integration of pest management methods is not only merely worthy, but also the more powerful practical solution for controlling soil-borne pests. Results showed that the solarized treated soil as well as the fungal antagonists, as single treatment methods in controlling Fusarium root rot revealed 80% and 81% healthy plants compared with their control that showed only 41%. Integrating soil solarization with mixed fungal inocula and soil organic amendment have been improving efficacy of controlling of lupine-fusarium-root rot by increasing the percentage number of healthy plants from 81 %, 79 % in treated unsolarized soil to 86 %, 82 % respectively in treated solarized soil. Using tactics such as solarization antagonistic fungi, and organic amendment as an integrated method, proved to be efficient for controlling the Fusarium root rot pathogen in Lupinus termis.

Control of Soil-borne Pathogens by Soil Fumigation with Paraformaldehyde (Fogidesfarm) as Alternative to Methyl Bromide

Control of Soil-borne Pathogens by Soil Fumigation with Paraformaldehyde (Fogidesfarm) as Alternative to Methyl Bromide

Optimizing anaerobic soil disinfestation for fresh market tomato production: Nematode and weed control, yield, and fruit quality

Anaerobic soil disinfestation (ASD) has potential as an alternative to chemical-fumigation for controlling soilborne pathogens and pests. Previously, control of nutsedge was sub-optimal and the quantity of inputs for commercial production was an impediment to adoption. Field studies were conducted in Citra and Immokalee, Florida to assess the effects of ASD with reduced amendments and inclusion of a pre-emergent herbicide on weed and nematode populations, tomato yield, and fruit quality. Pre-plant soil treatments included ASD with 6.9m3ha−1 of molasses and 11Mgha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9m3ha−1 of molasses and 22Mgha−1 of CPL (ASD1.0), and chemical soil fumigation using Pic-Clor 60 (CSF). Subplot treatments were halosulfuron-methyl (Sandea®) herbicide and no herbicide application. ASD0.5 reached high and equivalent accumulation of anaerobic conditions as ASD1.0 during the three-week soil treatment in both locations. Root galling and plant-parasitic nematode population at harvest in ASD treatments were similar in nematode suppression to CSF in both locations, while ASD1.0 resulted in higher non-parasitic nematode populations in soil compared to CSF in Citra. In Citra, ASD treatments did not differ from CSF in total marketable fruit yield; however, ASD0.5 resulted in higher total yield of extra-large fruit than CSF and ASD1.0. In Immokalee, no difference was observed in total marketable yield between ASD0.5 and CSF, whereas ASD1.0 produced 26.3% and 20.4% higher total marketable yield than that of CSF and ASD0.5, respectively. ASD treatments had no impact on fruit quality attributes including color, firmness, pH, total soluble solids, and dry matter content. Herbicide application improved nutsedge control and had no negative impact on the development of anaerobicity in ASD-treated plots, while total marketable yield and fruit quality were not impacted by herbicide treatment in either location. Despite some variations between the two locations, reduced application rates of CPL and molasses produced results similar to the full rates of amendment as well as the fumigation treatment. Overall, combining ASD with an herbicide had no negative impacts on crop production and resulted in improved weed control.

Biopesticides: Use of Rhizosphere Bacteria for Biological Control of Plant Pathogens

The pesticides used to control pests and diseases are also implicated in ecological, environmental and human health hazards. To reduce the deleterious effects of these agrochemicals, certain antagonistic microorganisms have been characterised from rhizosphere of different crop plants that suppress various plant diseases and thus, minimize the use of pesticides. The application of these specific antagonistic microorganisms in biological control of soilborne pathogens has been studied intensively in the last two decades. These beneficial rhizosphere microorganisms inhibit the pathogenic bacteria and fungi by producing antibiotics, bacteriocins, siderophores, hydrolytic enzymes and other secondary metabolites. The efficiency of these biocontrol products can be improved by manipulation of the environment, using mixtures of beneficial organisms, physiological and genetic enhancement of the biocontrol mechanisms, manipulation of formulations and integration of biocontrol with other alternative methods that provide additive effects. These biocontrol agents could be effectively utilised in sustainable agriculture for improving growth of crop plants.

Efficacy of fumigant treatments and inoculum placement on control of Macrophomina phaseolina in strawberry beds

Soil disinfestation is one of the main concerns of strawberry growers. The phased-out of methyl bromide (MeBr) and the lack of equally effective fumigants has increased the difficulty in controlling soilborne pathogens such as Macrophomina phaseolina, causal agent of charcoal rot. Soil fumigant treatments were tested in Dover, Florida during the 2012–13, 2013–14 and 2014–15 seasons. The treatments included MeBr as a standard and common alternatives such as chloropicrin (PIC), 1,3-dichloropropene (1,3D), dimethyl disulfide (DMDS), potassium N-methyldithiocarbamate (Kpam) and sodium methyldithiocarbamate (Vapam). The efficacy of different fumigation rates and application methods was also investigated. Treatment effects were evaluated using sclerotia of M. phaseolina buried in bags 7.6 and 20.3 cm deep in the center of the bed, or 7.6 cm deep on the side of the bed (7.6 s). Additionally, strawberry crowns infected with M. phaseolina were buried 7.6 cm deep in the center of the bed during the 2012–13 and 2013–14 growing seasons. At the end of the 2013–14 and 2014–15 growing seasons, plant mortality and charcoal rot incidence (%) were also determined. Except for 1,3-dichloropropene:chloropicrin 39/60, most treatments were effective in reducing the colony forming units (CFUs) of M. phaseolina in buried bags or crowns buried at the center of the bed and reduced percent of charcoal rot incidence each season. Most treatments applied by shank produced similar reductions in inoculum levels at the center and sides of the bed, whereas drip treatments effectively reduced inoculum in bags buried at both depths in the center of the bed, but not at the side of the bed. Thus, one of the main problems of the current fumigants is poor distribution in the soil beds and strawberry growers should consider application methods that will achieve a more uniform distribution of the fumigants.

A Meta-Analysis of the Impact of Anaerobic Soil Disinfestation on Pest Suppression and Yield of Horticultural Crops.

Anaerobic soil disinfestation (ASD) is a proven but relatively new strategy to control soil borne pests of horticultural crops through anaerobic decomposition of organic soil amendments. The ASD technique has primarily been used to control soil borne pathogens; however, this technique has also shown potential to control plant parasitic nematodes and weeds. ASD can utilize a broad range of carbon (C) amendments and optimization may improve efficacy across environments. In this context, a meta-analysis using a random-effects model was conducted to determine effect sizes of the ASD effect on soil borne pathogens (533 studies), plant parasitic nematodes (91 studies), and weeds (88 studies) compared with unamended controls. Yield response to ASD was evaluated (123 studies) compared to unamended and fumigated controls. We also examined moderator variables for environmental conditions and amendments to explore the impact of these moderators on ASD effectiveness on pests and yield. Across all pathogen types with the exception of Sclerotinia spp., ASD studies show suppression of bacterial, oomycete and fungal pathogens (59 to 94%). Pathogen suppression was effective under all environmental conditions (50 to 94%) and amendment types (53 to 97%), except when amendments were applied at rates less than 0.3 kg m-2. The ASD effect ranged from 15 to 56% for nematode suppression and 32 to 81% for weed suppression, but these differences were not significant. Significant nematode moderators included study type, soil type, sampling depth, incubation period, and use of mixed amendments. Weed suppression due to ASD showed significant heterogeneity for all environmental conditions, confirming that these studies do not share a common effect size. Total crop yield was not reduced by ASD when compared to a fumigant control and yield was significantly higher (30%) compared to an unamended control, suggesting ASD as a feasible option to maintain yield without chemical soil fumigants. We conclude ASD is effective against soil borne pathogens and while not conclusive due to a limited number of studies, we expect the same for nematodes and weeds given observed effect sizes. Findings should assist researchers in exploring ASD efficacy in particular environmental conditions and allow for development of standard treatment protocols.

Growing for the future: Collective action, land stewardship and soilborne pathogens in California strawberry production

Outlook Growing for the future: Collective action, land stewardship and soilborne pathogens in California strawberry production Margaret Lloyd, UC Cooperative Extension Farm Advisor, Yolo, Solano and Sacramento counties Tom Gordon, Professor, Department of Plant Pathology, UC Davis Sustaining high strawberry yields will require an integrated approach that includes collaborative management of fields to limit the spread of soilborne pathogens. required, one that integrates advances in disease resistance through breeding with closer attention to the factors that influence the survival, activity and spread of pathogen populations in soil. Many of the latter, such as rotating crops and cleaning equipment, frequently involve multiple operators. As a result, there is a need to recognize that patho- gen-free soil is effectively a common-pool resource and that protecting it will require collective action. The end of methyl bromide Since the early 1950s, diseases caused by soilborne pathogens have been managed primarily through the use of preplant soil fumigation. Before that time, Verticillium wilt, caused by Verticillium dahliae, imposed a major limitation on strawberry production. Recognition of the fungicidal prop- erties of chloropicrin and the enhanced efficacy achieved by addition of methyl bromide lifted this http://calag.ucanr.edu • JULY–SEPTEMBER 2016 101 Jack Kelly Clark C alifornia accounts for more than 80% of U.S. strawberry production, a harvest worth $2.5 billion in 2014. Fertile soils and the prevail- ing climate on the Central Coast support per acre yields twice that of Florida, the second largest pro- ducer, and 10 times more than most other states. Yet California strawberry growers face sig- nificant challenges. Among the most important is the declining availability of suitable land. The potential for a given field to produce an acceptable yield depends not only on physical and chemical characteristics of the soil but also, critically, on the presence or absence of soil dwelling pathogens that can infect strawberry roots and cause diseases that limit fruit production. As described below, effec- tive control of soilborne pathogens of strawberries was once readily achieved by means that are no longer available to strawberry growers. It now seems likely that no single measure will suffice to meet the challenge of soilborne patho- gens. Rather, a multi-faceted approach will be

Control of Soil-Borne Pathogens in Ginseng Cultivation through the Use of Cultured Green Manure Crop and Solarization in Greenhouse Facilities

Background: Root diseases caused by Cylindrocarpon destructans and Fusarium solani decrease the yield and quality of ginseng. Cylindrocarpon root rot is a major disease caused by replant failure in ginseng fields. Methods and Results: Solarization of infested greenhouse soil was carried out during the summer season after applying green manure (Sudan grass) and Calcium Cyanamide (CC) on the soil. Mycelium and conidia of C. destructans died at after 15 h, but they did not die at after 15 h. They also died after keeping the soil at for 2 h daily for 9 days, and at for 8 days, but they did not die at for 9 days. Maximum soil temperature was at 5 cm depth, at 10 cm, at 15 cm, at 20 cm, and at 30 cm by incorporating green manure into the soil and using solarization. Solarization using green manure mixed with CC was the most effective in decreasing soil-borne pathogens of 2-year-old ginseng. However, the addition of CC decreased the root weight due to the increase in EC and . Conclusions: Soil disinfection using green manure and solarization in a greenhouse environment was effective in inhibiting root rot, however, it did not completely kill the soil-borne pathogens.

Efficacy of reduced rate fumigant alternatives and methyl bromide against soilborne pathogens and weeds in western forest nurseries

Preplant soil fumigation is commonly used to control soilborne pathogens and weeds in forest seedling nurseries of Oregon and Washington. However, lower chemical inputs are desired to meet state and federal application regulations, to minimize buffer zone size requirements, and to help protect the environment. Therefore, the objectives of this research were to evaluate the efficacy of three reduced rate soil fumigants under totally impermeable film (TIF) in managing soilborne diseases and weeds, and to determine if combined applications of up to four biocontrol agents improved soilborne disease control. Reduced rates of methyl bromide, metam sodium, and 1,3-dichloropropene, all applied in combination with chloropicrin, were effective in decreasing soil populations of Pythium and Fusarium as well as the presence of Pythium in root debris from the previous crop. The roots of Douglas-fir (Pseudotsuga menziesii) seedlings transplanted into each fumigant treatment were also colonized less by Pythium and Fusarium than those transplanted into nonfumigated control plots. However, biocontrol treatments were not effective against either pathogen. Weed biomass and weeding times were also significantly reduced by fumigation. Application costs were similar for all three fumigant treatments, but seedling size was largest from the methyl bromide and metam sodium treatments followed by the 1,3-dichloropropene treatment. Based on the results of this study, reduced rates of methyl bromide, metam sodium, and 1,3-dichloropropene show promise in managing soilborne diseases and weeds in forest nurseries.

English

Soil is an oligotrophic medium for fungal growth. F ungi are important component in soil microbiota. Depending on soil depth and nutrient co nditions, the fungal biomass exceeds that of bacteria in almost every soil except rhizosphere so il which is dominated by bacteria. Filamentous fungi in soil degrade organic matter and help in so il aggregation. Some produce substances similar to humic substances and some are capable of forming ectotrophic associations on the root system of forest trees and help in mobilisation of soil phosp horus and nitrogen into plants. Many fungi are biological control agents for plant pathogens and i nsect pests. In Uttarakhand especially in Dehradun District very scanty information is availa ble regarding soil inhabiting microfungi of Agricultural fields. Therefore some agricultural la nds growing Brassica crop were selected to study the composition, dominance and diversity of microfu ngi and physico-chemical properties of the soil inhabited by these fungi. Five agricultural lands viz. Rajawala (RAJ), Bahada rpur(BAH), Bhauwala (BHAU), Telpura (TLP) and Sudhowala (SUDH) were selected. Each land was s urveyed repeatedly to collect soil samples. Soil samples were collected from different depths v0-5 cm, 5-10 cm, 10-15 cm, 15-20 cm. and 2025 cm and composite samples were made for each agri cultural land. For all soil samples examined, pH varied from 6.42± 1.24 to 7.84±1.56; moisture content varied from8.42±1.68 to 10.84±2.16; organic contents varie d from 1.55 to 3.00 and texture varied from sandy to sandy loam. Micronutrients were very high in all the soil samples. A total of 383 colonies of microfungi belonging to 11 genera and 26 species we re isolated. Anamorphic fungi (Deuteromycota) were dominant and represented by 9 genera and 22 sp ecies followed by Zygomycota represented by 2 genera and 4 species. Fungal populations were alw ays highest in surface soil and decreased along with soil-depth. Maximum fungal species were isolat ed from BAH at the depth of 0-10 cm followed by RAZ, whereas the minimum fungal species were iso lated from BHAU, TPR and SUDH at the depth of 15-20 cm. Of the total 26 species recorded , 8 species were of common occurrence, 9 species of frequent, 8 species of moderate and 1 species of rare occurrence respectively. Shanon- Wiever index of species diversity was highe st (2.734) in BAH followed by RAZ (2.686), TLP (2.583) and SUDH (2.553) while it was lowest for BH AU (2.540). Simpson index of diversity also showed identical trends. Highest similarity (84.2%) was observed between RAJ and BAH and lowest (55.6%) between RAJ and TLP. The present investigation will be helpful in docume ntation and conservation as well as in controlling soil borne pathogens. Further, it certainly opens u p a new horizon for the researchers in this interesting and challenging field of soil microfung al biodiversity.

Bacillus amyloliquefaciens biofilm as a novel biosorbent for the removal of crystal violet from solution

Bacillus amyloliquefaciens biofilm shows promise for use in the control of soil-borne pathogens; however, it has never been used to treat dye-polluted wastewaters. Here, we propose the novel idea of using B. amyloliquefaciens biofilm for the adsorption of crystal violet (CV) from liquids. The relative contents of three main elements (C1s, O1s, and N1s) in the biofilm were 65.55%, 21.21%, and 13.24%, respectively. The results of Fourier transform infrared (FTIR) spectra and X-ray photoelectron spectroscopy revealed that the biofilm contained β-type heteropolysaccharide and proteins. The ruggedness of the biofilm surface due to embedded bacterial cells suggested potential adsorption sites for CV molecules. The maximum capacity for CV adsorption was 582.41mg/g, which is the largest value reported to date for any CV adsorbent. Blueshift occurred in the FTIR spectrum of CV-loaded biofilm as compared to that of virgin biofilm, confirming a physical adsorption process. We found that CV adsorption by biofilm was complex and resulted from intraparticle diffusion as well as surface adsorption. Our data also suggested that the process is exothermal and spontaneous, with micropore diffusion as the rate-limiting step. These findings provide a basis for using B. amyloliquefaciens biofilm as an efficient adsorbent for treating CV-polluted wastewaters.

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417.

BackgroundPlant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.ResultsThe genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.ConclusionsThe genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1632-z) contains supplementary material, which is available to authorized users.