Quantitative Assessment of Factors Affecting the Recovery of Indigenous and Released Thermophilic Bacteria from Compost

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition

BACKGROUND

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome.

RESULTS

Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed.

CONCLUSION

These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

Characters of aerated compost tea from immature compost that limit colonization of bean leaflets by Botrytis cinerea

AIMS

The aim was to produce and characterize an aerated compost tea (ACT) that suppressed growth of the plant pathogen Botrytis cinerea.

METHODS AND RESULTS

Three different open-windrow composts were sampled weekly from the early secondary mesophilic stage until maturity. Each 10kg of compost sample was extracted in 30 l of aerated water for 24, 48 or 72h. Relative to water, all batches of ACT applied to detached bean leaflets reduced lesion development following single-point inoculations of B. cinerea. There was a significant linear, inverse relationship between the internal windrow temperature of compost (≤51°C) used to prepare ACT and the extent of lesion development. Bacterial diversity in ACTs from one windrow was highest using compost sampled at 48°C. The compost weight-to-water volume ratios of 1:3, 1:10 or 1:30, using compost sampled from a fourth windrow at 50°C, also produced ACTs that reduced the growth of B. cinerea on bean leaflets. The '1 : 3' ACT, and to a lesser degree the same ACT filtered to remove micro-organisms, inhibited the germination of B. cinerea conidia.

CONCLUSIONS

ACT produced using the methods reported here suppressed the growth of B. cinerea on bean leaflets, with an abundant and diverse microbial community likely to contribute to pathogen suppression.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the use of immature compost to produce a pathogen-suppressive ACT, suggesting that compost stage is an important production variable.

Analysis of bacterial activity, biomass and diversity during windrow composting

Two contrasting compost windrows were monitored for various physical, chemical and microbiological parameters for a period of 106 days. The different input materials and management practises gave rise to different temperature, moisture, and oxygen consumption profiles as composting proceeded. However, despite the different composting conditions, the specific respiratory activity, as determined by oxygen consumption per bacterial cell, was remarkably similar for both windrows. Further investigations into diversity dynamics were done through DGGE and cloning and sequencing of bacterial 16S rDNA PCR products. Although sequence analysis showed differing bacterial communities across time and between the different windrows, similarities in the progression were noted. The majority of sequences recovered from the first sampling period (day 1) were highly similar to previously isolated organisms. The clone libraries from the last sampling period (day 106) contained organisms that showed lower homology to their closest relatives, often with other uncultured organisms, and in phyla that contain few cultured representatives. These data suggest that specific respiratory activity may be an important driver of bacterial diversity in composting environments.

Microbiological parameters and maturity degree during composting of Posidonia oceanica residues mixed with vegetable wastes in semi-arid pedo-climatic condition

The aim of this study was to characterize the biological stability and maturity degree of compost during a controlled pile-composting trial of mixed vegetable residues (VR) collected from markets of Tunis City with residues of Posidonia oceanica (PoR), collected from Tunis beaches. The accumulation in beaches (as well as their removal) constitutes a serious environmental problem in all Mediterranean countries particularly in Tunisia. Aerobic-thermophilic composting is the most reasonable way to profit highly-valuable content of organic matter in these wastes for agricultural purposes. The physical, chemical, and biological parameters were monitored during composting over 150 d. The most appropriate parameters were selected to establish the maturity degree. The main result of this research was the deduction of the following maturity criterion: (a) C/N ratio < 15; (b) NH4+-N < 400 mg/kg; (c) CO2-C < 2000 mg CO2-C/kg; (d) dehydrogenase activity < 1 mg TPF/g dry matter; (e) germination index (GI) > 80%. These five parameters, considered jointly are indicative of a high maturity degree and thus of a high-quality organic amendment which employed in a rational way, may improve soil fertility and soil quality. The mature compost was relatively rich in N (13.0 g/kg), P (4.74 g/kg) and MgO (15.80 g/kg). Thus composting definitively constitutes the most optimal option to exploit these wastes.

Methionine auxotroph Escherichia coli growth assay kinetics in antibiotic and antifungal amended selective media

The objective of this work was to determine if Escherichia coli methionine bioassay characteristics were influenced by selective media amended with antibiotics and the antifungal compound cycloheximide. Bacterial cells were grown in minimal media with increasing concentrations of methionine and were incubated at 37 degrees C with vigorous agitation for 6 hours. Addition of antistatic agents to the media did not change the growth kinetic response (P>0.05) to methionine concentration (3.4 to 26.8 microM). This supports the utility of this strain as a methionine bioassay organism for feed and other environmental sources.

Potential for the environmental impact of transgenic crops

In recent years, there has been increasing interest in how changes in agricultural practice associated with the introduction of particular genetically modified (GM) crops might indirectly impact the environment. There is also interest in any effects that might be associated with recombinant and novel combinations of DNA passing into the environment, and the possibility that they may be taken up by microorganisms or other live biological material. From the current state of knowledge, the impact of free DNA of transgenic origin is likely to be negligible compared with the large amount of total free DNA. We can find no compelling scientific arguments to demonstrate that GM crops are innately different from non-GM crops. The kinds of potential impacts of GM crops fall into classes familiar from the cultivation of non-GM crops (e.g., invasiveness, weediness, toxicity, or biodiversity). It is likely, however, that the novelty of some of the products of GM crop improvement will present new challenges and perhaps opportunities to manage particular crops in creative ways.

Microbial characterization during composting of municipal solid waste

This study investigates the prevailing physico-chemical conditions and microbial community; mesophilic bacteria, yeasts and filamentous fungi, bacterial spores, Salmonella and Shigella as well as faecal indicator bacteria: total coliforms, faecal coliforms and faecal Streptococci, present in a compost of municipal solid waste. Investigations were conducted in a semi-industrial pilot plant using a moderate aeration during the composting process. Our results showed that: (i) auto-sterilization induced by relatively high temperatures (60-55 degrees C) caused a significant change in bacterial communities. For instance, Escherichia coli and faecal Streptococci populations decreased, respectively, from 2 x 10(7) to 3.1 x 10(3) and 10(7) to 1.5 x 10(3) cells/g waste dry weight (WDW); yeasts and filamentous fungi decreased from 4.5 x 10(6) to 2.6 x 10(3) cells/g WDW and mesophilic bacteria were reduced from 5.8 x 10(9) to 1.8 x 10(7) bacteria/g WDW. On the other hand, the number of bacterial spores increased at the beginning of the composting process, but after the third week their number decreased notably; (ii) Salmonella disappeared completely from compost by the 25th day as soon as the temperature reached 60 degrees C; and (iii) the bacterial population increased gradually during the cooling phase. While Staphylococci seemed to be the dominant bacteria during the mesophilic phase and at the beginning of the thermophilic phase, bacilli predominated during the remainder of the composting cycle. The appearance of gram-negative rods (opportunistic pathogens) during the cooling phase may represent a serious risk for the sanitary quality of the finished product intended for agronomic reuse. Compost sonication for about 3 min induced the inactivation of delicate bacteria, in particular gram-negatives. By contrast, gram-positive bacteria, especially micrococcus, spores of bacilli, and fungal propagules survived, and reached high concentrations in the compost.

[Thermophilic bacteria resistant to antibiotics in traditional public baths]

Three thermophilic bacteria strains, designated strain BS1, BS2 and BS3, resistant to beta-lactam antibiotics, and leaving at an optimal temperature for growth of about 50 degrees C, were isolated from traditional baths in Meknes-city in Morocco. Physiological and biochemical studies showed that these organisms belong to Gram positive Bacilli. They could not be identified with the Bergey's Manuel of Systematic Bacteriology (1986). The dosage of beta-lactamase during the exponential growth phase has revealed that the strain BS3 produces a maximal amount of this enzyme. Studies aimed at determining the optimal conditions for incubation and growth have been performed in order to optimize the excretion of beta-lactamase by BS3 cells and thus facilitate the purification and and characterization of this enzyme.

Hazard to man and the environment posed by the use of urban waste compost: a review

This review presents the current state of knowledge on the relationship between the environment and the use of municipal waste compost in terms of health risk assessment. The hazards stem from chemical and microbiological agents whose nature and magnitude depend heavily on the degree of sorting and on the composting methods. Three main routes of exposure can be determined and are quantified in the literature: (i) The ingestion of soil/compost mixtures by children, mostly in cases of pica, can be a threat because of the amount of lead, chromium, cadmium, PCDD/F and fecal streptococci that can be absorbed. (ii) Though concern about contamination through the food chain is weak when compost is used in agriculture, some authors anticipate accumulation of pollutants after several years of disposal, which might lead to future hazards. (iii) Exposure is also associated with atmospheric dispersion of compost organic dust that convey microorganisms and toxicants. Data on hazard posed by organic dust from municipal composts to the farmer or the private user is scarce. To date, microorganisms are only measured at composting plants, thus raising the issue of extrapolation to environmental situations. Lung damage and allergies may occur because of organic dust, Gram negative bacteria, actinomycetes and fungi. Further research is needed on the risk related to inhalation of chemical compounds.

Protease production by Streptomyces thermovulgaris grown on rapemeal-derived media

A range of actinomycete species was tested for their ability to grow on particulate and particle-free rapeseed meal-derived media. Streptomycetes grew on both types of medium and produced a number of extracellular enzymes. Highest activities of protease were produced by Streptomyces thermovulgaris and reflected the high available protein content of rapemeal. Enzyme production and growth were analysed in fermentor-grown batch cultures of S. thermovulgaris using the particle-free rapemeal broth termed medium B. Growth was biphasic and the majority of the protease was produced during the second slower phase. Analysis of the protease as azocaseinase activity revealed a high degree of thermostability in the presence of calcium such that approximately 20% of the activity remained after incubation at 70 degrees C for 24 h. Gel filtration suggested that S. thermovulgaris synthesized more than one kind of protease and this was confirmed by using specific peptide substrates and inhibitors which revealed the presence of distinct serine and metallo-type enzymes.

Improved medium for recovery and enumeration of the farmer's lung organism, Saccharomonospora viridis

A new medium, which we propose to call R8, was developed for the isolation and enumeration of the thermophilic actinomycete, Saccharomonospora viridis. This organism has been implicated in a range of hypersensitivity pneumonitides, including farmer's lung, but is generally isolated in small numbers from contaminated environments. Recovery of S. viridis from moldy hay and mushroom compost on R8 medium was compared with recovery on conventional media. S. viridis was isolated from both substrates but in highest numbers and most consistently on the R8 medium. The selectivity of this medium was best observed when the sedimentation chamber method was used for hay samples. Here S. viridis accounted for up to 80% of the total number of actinomycetes recovered on R8 and could not be recovered on rifampin selective medium under the same conditions. R8 was also found to be an efficient recovery medium for a range of thermophilic actinomycetes from mushroom compost and for another allergenic species, Faenia rectivirgula, from moldy hay. Contamination of isolation plates by thermophilic bacilli was reduced on R8 compared with the activity on half-strength tryptone soy agar, supplemented with 0.2% casein hydrolysate, and this, together with specific improvements in S. viridis growth, accounts for the selective effect. It is possible that the occurrence of S. viridis and its role as a causative agent of hypersensitivity pnuemonitis have been underestimated by the use of suboptimal recovery protocols. It is hoped that use of R8 in conjunction with dilution plate techniques will generate information on the ecology of S. viridis and contribute to health risk assessment studies.