Identification of novel eubacteria from spent mushroom compost (SMC) waste by DNA sequence typing: ecological considerations of disposal on agricultural land

Effects of spent mushroom substrate on the dissipation of polycyclic aromatic hydrocarbons in agricultural soil

Spent mushroom substrate (SMS) is an agricultural waste with a high potential for polycyclic aromatic hydrocarbons (PAH) removal in aged contaminated soils. In this study, fresh and air-dried Pleurotus ostreatus, Pleurotus eryngii, and Auricularia auricular SMSs were used to remove PAHs in agricultural soil under 60-day incubation. The potential of SMS in PAH dissipation was studied by detecting the dissipation rate and the soil physicochemical index, enzyme activity, PAH-degradation bacterial biomass, and microbial diversity. Results showed that SMS significantly enhanced the dissipation of PAHs and fresh SMS had a better effect than air-dried SMS. The highest dissipation rate of 16 PAHs was 34.5%, which was observed in soil amended with fresh P. eryngii SMS, and the PAH dissipation rates with low and high molecular weights were 41.3% and 19.4%, respectively. By comparison, fresh P. eryngii SMS presented high nutrient contents, which promoted the development of PAH-degrading bacteria and changed the soil bacterial community involved in degradation, thereby promoting the PAH dissipation. The lignin-degrading enzymes in fresh SMS were abundant, and the laccase and manganese peroxidase activities in the treatment of fresh P. eryngii SMS was higher than those in other treatments. Fresh P. eryngii SMS improved the relative abundance of Microbacterium, Rhizobium, and Pseudomonas in soil, which were all related to PAH degradation. Consequently, adding fresh P. eryngii SMS was an effective method for remediating aged PAH-contaminated agricultural soils.

Biodegradation of aged polycyclic aromatic hydrocarbons in agricultural soil by Paracoccus sp. LXC combined with humic acid and spent mushroom substrate

Paracoccus sp. LXC combined with humic acid (HA) and spent mushroom substrate (SMS) obtained from Auricularia auricular and Sarcomyxa edulis was tested for the remediation of agricultural soil contaminated with aged polycyclic aromatic hydrocarbons (PAHs). The biomass and diversity of bacteria and fungi and the soil enzyme activity were analyzed. PAH removal and dissipation kinetics were examined. The highest degradation rate of PAHs was 56.5% when soil was amended with Paracoccus sp. LXC combined with HA and unsterilized SMS from A. auricular. The half-life of PAHs decreased from 2323.3 days in natural attenuation to 66.6-277.2 days in amended treatments. Soil treated with Paracoccus sp. LXC combined with HA and SMS from A. auricular acquired high contents of organic matter and nutrients. HA and SMS aided the growth of PAH-degrading bacteria and promoted the diversity of bacteria but not of fungi. The degradation rate of PAHs was mainly correlated positively with soil laccase activity. Low- and middle-molecular-weight PAHs were significantly removed by Paracoccus sp. LXC, HA and SMS. High-molecular-weight PAHs were removed by SMS but not by Paracoccus sp. LXC. Biodegradation by Paracoccus sp. LXC combined with HA and SMS is a promising choice for remediating aged PAH-contaminated agricultural soils.

First report of the nematicidal activity of Flammulina velutipes, its spent mushroom compost and metabolites

The aim of the present work was to evaluate the nematicidal potential of Flammulina velutipes and its spent mushroom compost. Additionally, the nematicidal activity of enzymes and metabolites was analyzed. Isolated F. velutipes and its SMC had significant nematicidal effect on Panagrellus sp. larvae. The percentages of reduction in relation to the control group were: 69, 57.5 and 70% for SMC and 56, 24.5 and 26.6% for the isolated fungus, for 24, 48 and 72 h, respectively. The active SMC crude extract showed nematicidal action with reduction percentages of 43 and 57% for 24 and 48 h of incubation, respectively. The boiled crude extract also showed nematicidal action, however, the reduction percentages were lower than those of the active extract. This demonstrated that the nematicidal action was due to enzyme activities and other metabolites. The results demonstrated that SMC, the isolated fungus, the crude extract and the boiled crude extract showed a significant percentage of reduction on Panagrellus sp. larvae. SMC evidenced a higher nematicidal activity than the isolated fungus. In addition, nematophagous activity of F. velutipes was observed for the first time.

Implications of polluted soil biostimulation and bioaugmentation with spent mushroom substrate (Agaricus bisporus) on the microbial community and polycyclic aromatic hydrocarbons biodegradation

Different applications of spent Agaricus bisporus substrate (SAS), a widespread agro-industrial waste, were investigated with respect to the remediation of a historically polluted soil with Polycyclic Aromatic Hydrocarbons (PAH). In one treatment, the waste was sterilized (SSAS) prior to its application in order to assess its ability to biostimulate, as an organic amendment, the resident soil microbiota and ensuing contaminant degradation. For the other treatments, two bioaugmentation approaches were investigated; the first involved the use of the waste itself and thus implied the application of A. bisporus and the inherent microbiota of the waste. In the second treatment, SAS was sterilized and inoculated again with the fungus to assess its ability to act as a fungal carrier. All these treatments were compared with natural attenuation in terms of their impact on soil heterotrophic and PAH-degrading bacteria, fungal growth, biodiversity of soil microbiota and ability to affect PAH bioavailability and ensuing degradation and detoxification. Results clearly showed that historically PAH contaminated soil was not amenable to natural attenuation. Conversely, the addition of sterilized spent A. bisporus substrate to the soil stimulated resident soil bacteria with ensuing high removals of 3-ring PAH. Both augmentation treatments were more effective in removing highly condensed PAH, some of which known to possess a significant carcinogenic activity. Regardless of the mode of application, the present results strongly support the adequacy of SAS for environmental remediation purposes and open the way to an attractive recycling option of this waste.

Bdellovibrio bacteriovorus HD100 guards against Pseudomonas tolaasii brown-blotch lesions on the surface of post-harvest Agaricus bisporus supermarket mushrooms

BACKGROUND

Pseudomonas tolaasii is a problematic pathogen of cultured mushrooms, forming dark brown 'blotches' on mushroom surfaces and causing spoilage during crop growth and post-harvest . Treating P. tolaasii infection is difficult, as other, commensal bacterial species such as Pseudomonas putida are necessary for mushroom growth, so treatments must be relatively specific.

RESULTS

We have found that P. tolaasii is susceptible to predation in vitro by the δ-proteobacterium Bdellovibrio bacteriovorus. This effect also occurred in funga, where B. bacteriovorus was administered to post-harvest mushroom caps before and after administration of the P. tolaasii pathogen. A significant, visible improvement in blotch appearance, after incubation, was observed on administration of Bdellovibrio. A significant reduction in viable P. tolaasii cell numbers, recovered from the mushroom tissue, was detected. This was accompanied by a more marked reduction in blotch severity on Bdellovibrio administration. We found that there was in some cases an accompanying overgrowth of presumed-commensal, non-Pseudomonas bacteria on post-harvest mushroom caps after Bdellovibrio-treatment. These bacteria were identified (by 16SrRNA gene sequencing) as Enterobacter species, which were seemingly resistant to predation. We visualised predatory interactions occuring between B. bacteriovorus and P. tolaasii on the post-harvest mushroom cap surface by Scanning Electron Microscopy, seeing predatory invasion of P. tolaasii by B. bacteriovorus in funga. This anti-P. tolaasii effect worked well in post-harvest supermarket mushrooms, thus Bdellovibrio was not affected by any pre-treatment of mushrooms for commercial/consumer purposes.

CONCLUSIONS

The soil-dwelling B. bacteriovorus HD100 preys upon and kills P. tolaasii, on mushroom surfaces, and could therefore be applied to prevent spoilage in post-harvest situations where mushrooms are stored and packaged for sale.

Inactivation of human pathogens during phase II composting of manure-based mushroom growth substrate

Commercial production of white button mushrooms (Agaricus bisporus) requires a specialized growth substrate prepared from composted agricultural by-products. Because horse and poultry manures are widely used in substrate formulations, there is a need to determine the extent to which the composting process is capable of eliminating human pathogens. In this study, partially composted substrate was inoculated with a pathogen cocktail (log 10⁶ to 10⁸ CFU/g) containing Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella. Pathogen and indicator-organism reductions were followed at temperatures that typically occurred during a standard 6-day phase II pasteurization and conditioning procedure. Controlled-temperature water bath studies at 48.8, 54.4, and 60°C demonstrated complete destruction of the three pathogens after 36.0, 8.0, and 0.5 h, respectively. Destruction of L. monocytogenes and E. coli O157:H7 at 54.4°C occurred more slowly than E. coli, total coliforms, Enterobacteriaceae, and Salmonella. Microbial reductions that occurred during a standard 6-day phase II pasteurization and conditioning treatment were studied in a small-scale mushroom production research facility. After phase II composting, E. coli, coliforms, and Enterobacteriaceae were below detectable levels, and inoculated pathogens were not detected by direct plating or by enrichment. The results of this study show that a phase II composting process can be an effective control measure for eliminating risks associated with the use of composted animal manures during mushroom production. Growers are encouraged to validate and verify their own composting processes through periodic microbial testing for pathogens and to conduct studies to assure uniform distribution of substrate temperatures during phase II.

Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis

An investigation of bacterial diversity in compost was performed using molecular chronometer in order to reveal its phylogeny. Thirty-three bacterial isolates isolated from compost were analyzed by 16S rRNA gene sequencing which revealed phylogenetic lineage of class Bacilli, γ, β-Proteobacteria, and Actinobacteria. Among these lineages, isolates belonging to class Bacilli consisted of species from genera Staphylococcus, Bacillus, Terribacillus, and Lysinibacillus. From phylum Actinobacteria: Microbacterium barkeri and Kocuria sp. were identified. Other bacterial groups had phylogenetic linkage with genera Comamonas and Acidovorax (class β-Proteobacteria); Serratia, Klebsiella, and Enterobacter (class γ-Proteobacteria). Similar isolates were analyzed through ARDRA. Amplified product of 16S rRNA gene from each isolates was subjected to cleavage by enzymes HpaII, HinfI, and MspI in separate reaction tubes. HpaII generated 2-6 bands ranging from 90-688 bp, HinfI generated 2-5 bands of 71-1,038 bp, and MspI 2-7 bands of 69-793 bp. The restriction patterns from HpaII, HinfI, and MspI were normalized separately and combined by means of pattern recognition software "Diversity Database." HpaII had highest discrimination index (0.72) than HinfI (0.68) and MspI (0.65), and the combination of all three showed discrimination index (0.69). Numerical analysis of ARDRA patterns demonstrated sufficient phylogenetic information for characterizing bacterial diversity. Phylogenetic relationship obtained among isolates through ARDRA was compared with 16S rRNA gene sequence and ARDRA results showed sufficiently similar 16S rRNA gene sequence analysis, but not an overlapping. It has been observed that ARDRA technique facilitates the identification of bacteria in less than 36 h as compared to traditional 16S rRNA gene sequencing.

Isolation and characterization of cellulose-decomposing bacteria inhabiting sawdust and coffee residue composts

Clarifying the identity and enzymatic activities of microorganisms associated with the decomposition of organic materials is expected to contribute to the evaluation and improvement of composting processes. In this study, we examined the cellulolytic and hemicellulolytic abilities of bacteria isolated from sawdust compost (SDC) and coffee residue compost (CRC). Cellulolytic bacteria were isolated using Dubos mineral salt agar containing azurine cross-linked (AZCL) HE-cellulose. Bacterial identification was performed based on the sequence analysis of 16S rRNA genes, and cellulase, xylanase, β-glucanase, mannanase, and protease activities were characterized using insoluble AZCL-linked substrates. Eleven isolates were obtained from SDC and 10 isolates from CRC. DNA analysis indicated that the isolates from SDC and CRC belonged to the genera Streptomyces, Microbispora, and Paenibacillus, and the genera Streptomyces, Microbispora, and Cohnella, respectively. Microbispora was the most dominant genus in both compost types. All isolates, with the exception of two isolates lacking mannanase activity, showed cellulase, xylanase, β-glucanase, and mannanase activities. Based on enzyme activities expressed as the ratio of hydrolysis zone diameter to colony diameter, it was suggested that the species of Microbispora (SDCB8, SDCB9) and Paenibacillus (SDCB10, SDCB11) in SDC and Microbispora (CRCB2, CRCB6) and Cohnella (CRCB9, CRCB10) in CRC contribute to efficient cellulolytic and hemicellulolytic processes during composting.

First Preliminary Report on Isolation and Characterization of Novel Acinetobacter spp. in Casing Soil Used for Cultivation of Button Mushroom, Agaricus bisporus (Lange) Imbach

Despite evaluation of large number of agroindustrial wastes for their use as casing material for Agaricus bisporus (Lange) Imbach cultivation, scant attention has been given to the importance of biological properties of casing materials. In the present study, an attempt was made to characterize the bacterial flora in casing layer, namely, Farm Yard Manure (FYM) and Spent Mushroom Substrate/spent compost (SMS/SC) (FYM+SC, 3 : 1) and FYM and Vermi Compost (VC) (FYM+VC, 3 : 1), employing partial 16S rDNA sequencing. Available data showed a significant variety of organisms that included Acinetobacter and Pseudomonas of the γ-proteobacteria, that were the most frequently encountered genera. This is the first preliminary report on the microbial diversity of casing soils and demonstrates the presence of Acinetobacter spp. that has not been previously described in casing material.

Avian influenza, migratory birds and emerging zoonoses: Unusual viral RNA, enteropathogens and Cryptosporidium in poultry litter

The last decade has witnessed the emergence of several new viral infectious agents, most notably avian influenza H5N1, SARS and West Nile Virus. The emergence of these agents is heavily associated with zonotic animal hosts, as well as migratory pathways of infected bird vectors. The environmental survival and persistence of nucleic acid associated with these viral agents may be important for both the detection as well as the occurrence of related diseases. Our hypothesis suggests that nucleic acid from such emerging viruses may enter into a virus-parasite surrogate relationship to aid in viral persistence. We suggest that Cryptosporidium and other gastrointestinal parasites, including Giardia, could be a) a reservoir of genetic material and a environment where assortment between that genetic variation can occur and, b) a source of zoonoses through infection of the ‘target’ animal (including humans). One example which illustrates this may be the uptake dsRNA from rotavirus into cryptosporidial oocysts, as this parasite has previously been shown to contain dsRNA viral-like particles. The importance of such a surrogate relationship is discussed and its implications for human and animal health highlighted.

Cadmium removal from simulated wastewater to biomass byproduct of Lentinus edodes

A kind of agricultural waste, the byproduct of brown-rot fungus Lentinus edodes, was used as an efficient biosorbent for the removal of cadmium from water in this paper. The sorption conditions, such as pH, the dose of biomass and the initial concentration of cadmium were examined. Three kinds of adsorption models were applied to simulate the biosorption data. Uptake of cadmium was higher in weak acid condition than in strong acid condition. Nearly no sorption of cadmium occurred when the pH value was lower than 2.5. Biosorption isothermal data could be well simulated by Freundlich model, and then Langmuir and Temkin model. Langmuir simulation of the biosorption showed that the maximum uptake of cadmium was 5.58mmol/g in weak acid condition, which was much higher than many other biosorbents. The exchanged proton was highly related to the uptake of cadmium in weak acid condition. Fourier transform infrared spectrums and energy-dispersive X-ray microanalyzer were used to reveal ion-exchange mechanism between cadmium and the functional groups or participated inorganic metal ions during biosorption.

Bacterial Diversity in Spent Mushroom Compost Assessed by Amplified rDNA Restriction Analysis and Sequencing of Cultivated Isolates

Spent mushroom compost (SMC) is the residual by-product of commercial Agaricus spp. cultivation, and it is mainly composed of a thermally treated cereal straw/animal manure mixture colonized by the fungal biomass. Research on the valorization of this material is mainly focusing on its use as soil conditioner and plant fertilizer. An investigation of the bacterial diversity in SMC was performed using molecular techniques in order to reveal the origin of SMC microflora and its potential effect on soil microbial communities after incorporation into agricultural soils. The bacterial population was estimated by the plate count method to a mean of 2.7 10(9) colony forming units (cfu) per g of dry weight, while the numbers of Gram-positive and Gram-negative bacteria were 1.9 10(9) and 4.9 10(8) cfu per g dw respectively as estimated by enumeration on semi-selective media. Fifty bacterial isolates were classified into 14 operational taxonomic units (OTUs) following ARDRA-PCR of the 16S rDNA gene. Sequencing of the 16S rDNA amplicon assigned 12 of the 14 OTUs to Gram-positive bacteria, associated with the genera Bacillus, Paenibacillus, Exiguobacterium, Staphylococcus, Desemzia, Carnobacterium, Brevibacterium, Arthrobacter and Microbacterium of the bacterial divisions Firmicutes and Actinobacteria. Two bacterial groups have phylogenetic links with the genera Comamonas and Sphingobacterium, which belong to beta-Proteobacteria and Bacteroidetes respectively. Two potentially novel bacteria are reported, which are associated with the genera Bacillus and Microbacterium. Most of the bacteria identified are of environmental origin, while strains related to species usually isolated from insects, animal and clinical sources were also detected. It appears that bacterial diversity in SMC is greatly affected by the origin of the initial material, its thermal pasteurization treatment and the potential unintended colonization of the mushroom substrate during the cultivation process.