Quantification of Saccharopolyspora rectivirgula in composting plants: assessment of the relevance of S. rectivirgula

Exposure to bioaerosols in composting plants can lead to negative health effects on compost workers. Health complaints vary between cough, irritation of the eyes and the skin, sinusitis, or dyspnea among others. It is fact that compost materials harbor high concentrations of microorganisms, which were aerosolized during handling compost. Within the present study, total cell numbers between 3.4 × 10(4) and 1.6 × 10(8) cell counts per m(3) air were determined after 4',6-Diamidin-2-phenylindol DAPI staining in 124 samples from German composting plants. Special attention should be paid to some specific microorganisms, which are able to cause health complaints. Saccharopolyspora rectivirgula, known to be one of the major causes of extrinsic allergic alveolitis (EAA, also called hypersensitivity pneumonitis, HP), was often found in environments of agricultural production, where the classical form of EAA ('farmer's lung disease') is common, but also in composting plants. In Germany, cases are known where workers had to terminate their work due to this disease. However, up to now, the relevance of S. rectivirgula at composting plants is unexplained. This study showed that high concentrations of airborne S. rectivirgula were found in composting plants similar to that found in agricultural production. Altogether, in 86.7% of the 124 analyzed samples, S. rectivirgula was detected using quantitative real-time polymerase chain reaction (PCR). Estimated concentrations ranged between 1.24 × 10(2) cell counts of S. rectivirgula per cubic meter air next to the rotted residues and 1.5 × 10(7) cell counts next to a converter. Furthermore, our methodical proceedings were verified. To analyze DNA extraction limits through the amount of cells within one sample, the DNA concentration was compared with total cell counts (TCCs). Altogether, when TCC was <1.4 × 10(5) cells per DNA extraction assay, no DNA was measurable; when TCC reached 3.5 × 10(6) cells, DNA was always detectable by fluorometric method. To overcome limitation of DNA measurement using fluorometric method, samples without measurable DNA were inserted in a PCR assay with universal primers. Results showed that a gain of 37% was possible, when samples were additionally analyzed by universal PCR. Hence, cell counts >2.0 × 10(6) cells were necessary to measure DNA concentrations in 90% of the analyzed samples, whereas cell counts <3.0 × 10(5) are sufficient to detect PCR products. Therefore, sampling of bioaerosols should be done in consideration of the expected cell count per cubic meter air. Note, to get measurable DNA using a fluorometer, >3.5 × 10(6) cells must be sampled for one DNA extraction assay. With this study, the real-time PCR approach for the detection of S. rectivirgula at workplaces in compost plants was revised, and the results revealed that this method is suitable for occupational exposure measurements.

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

BACKGROUND

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars.However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process.

RESULTS

In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed.

CONCLUSION

The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

Influence of compost addition on lead and arsenic bioavailability in reclaimed orchard soil assessed using Porcellio scaber bioaccumulation test

Long-term application of lead arsenate in orchards has led to a significant accumulation of Pb and As in the topsoil. Reclamation of old orchards for agricultural purposes entails the exposure of humans to Pb and As, which can be reduced by adequate remediation actions. In this study, we assessed the remediation efficiency of compost addition, commonly used as a sustainable agricultural practice, in decreasing the human exposure Pb and As by direct ingestion. The remediation was evaluated based on Pb and As bioavailability, assessed by means of a selective non-exhaustive chemical extraction (modified Morgan extraction, MME), with a physiologically based extraction test (PBET) for the assessment of Pb and As bioavailability in ingested soils and with a novel in vivo bioaccumulation test with isopods (Porcellio scaber). All the tests showed that compost addition consistently reduced Pb, but increased As potential bioavailability. The bioaccumulation test with P. scaber was sensitive to changes in Pb and As bioavailability in test soils. However, the results indicate that the bioavailability of As could be under- or overestimated using solely chemical extraction tests. Indirect assessment of trace metal bioavailability with bioaccumulation in isopods can be used as complementary source of data to the existing in vitro chemical extraction test approach for the estimation of human exposure to trace elements in polluted and remediated soil. This is the first report on the use of As accumulation in P. scaber as a tool for the assessment of As bioavailability in contaminated orchard soil.

Overview of organic amendments for management of plant-parasitic nematodes, with case studies from Florida

Organic amendments have been widely used for management of plant-parasitic nematodes. Relatively rapid declines in nematode population levels may occur when decomposing materials release toxic compounds, while longer-term effects might include increases in nematode antagonists. Improved crop nutrition and plant growth following amendment use may lead to tolerance of plant-parasitic nematodes. Results depend on a great variety of factors such as material used, processing/composting of material, application rate, test arena, crop rotation and agronomic practices, soil type, climate, and other environmental factors. Reasons for variable performance and interpretation of results from amendment studies are discussed. Case studies of amendments for nematode management are reviewed from Florida, where composts and crop residues are the most frequently used amendments. Plant growth was often improved by amendment application, free-living nematodes (especially bacterivores) were often stimulated, but suppression of plant-parasitic nematodes was inconsistent. Amendments were generally not as effective as soil fumigation with methyl bromide for managing root-knot nematodes (Meloidogyne spp.), and often population levels or galling of root-knot nematodes in amended plots did not differ from those in non-amended control plots. While amendments may improve plant growth and stimulate soil food webs, additional study and testing are needed before they could be used reliably for management of plant-parasitic nematodes under Florida conditions.

Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate

AIMS

  This work aimed to characterize microbial tolerance to 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid that has emerged as a novel biomass pretreatment for lignocellulosic biomass.

METHODS AND RESULTS

  Enrichment experiments performed using inocula treated with [C2mim][OAc] under solid and liquid cultivation yielded fungal populations dominated by Aspergilli. Ionic liquid-tolerant Aspergillus isolates from these enrichments were capable of growing in a radial plate growth assay in the presence of 10% [C2mim][OAc]. When a [C2mim][OAc]-tolerant Aspergillus fumigatus strain was grown in the presence of switchgrass, endoglucanases and xylanases were secreted that retained residual enzymatic activity in the presence of 20% [C2mim][OAc].

CONCLUSIONS

  The results of the study suggest that tolerance to ionic liquids is a general property of the Aspergilli.

SIGNIFICANCE AND IMPACT OF THE STUDY

  Tolerance to an industrially important ionic liquid was discovered in a fungal genera that is widely used in biotechnology, including biomass deconstruction.

Temperature effect on water extractability of cadmium, copper, lead and zinc from composted organic solid wastes of south-west Nigeria

The effect of temperature changes (10 to 80 degrees C) on water-extractable metal (Zn, Cu, Cd and Pb) concentrations of composted wastes of Nigerian origin was investigated in batch extraction experiments. Metal concentrations were measured using a calibrated atomic absorption spectrophometer after acid digestions. Results showed that the water-extractable metal fractions (I) did not exceed 10% of total metal concentrations of the bulk composts, which corresponded to 0.30 to 6.63% for Zn, 0.09 to 7.51% for Pb, 1.83 to 9.29% for Cu and 0.67 to 9.23% for Cd. Water extractable metal fraction showed positive correlations (r = 0.137 to 0.917*; p* < 0.01) for Cu, Cd and Pb in most cases but negative for Zn (-0.067 to -0.445). Simulations revealed that a steady temperature rise from 0.1 to 1.5 degrees C might increase I by 0.13 to 168% for all the metals, although stability to gradual temperature rise was demonstrated in some instances. The study revealed that the degree of temperature effect on water extractability of heavy metals from the bulk composts was dependent on metal type, compost formulation and waste type.

Biodegradability evaluation of polymers by ISO 14855-2

Biodegradabilities of polymers and their composites in a controlled compost were described. Polycaprolactone (PCL) and poly(lactic acid) (PLA) were employed as biodegradable polymers. Biodegradabilities of PCL and PLA samples in a controlled compost were measured using a Microbial Oxidative Degradation Analyzer (MODA) according to ISO 14855-2. Sample preparation method for biodegradation test according to ISO/DIS 10210 was also described. Effects of sizes and shapes of samples on biodegradability were studied. Reproducibility of biodegradation test of ISO 14855-2 by MODA was confirmed. Validity of sample preparation method for polymer pellets, polymer film, and polymer products of ISO/DIS 10210 for ISO 14855-2 was confirmed.

Characterization and Low-Cost Remediation of Soils Contaminated by Timbers in Community Gardens

Urban community gardens worldwide provide significant health benefits to those gardening and consuming fresh produce from them. Urban gardens are most often placed in locations and on land in which soil contaminants reflect past practices and often contain elevated levels of metals and organic contaminants. Garden plot dividers made from either railroad ties or chromated copper arsenate (CCA) pressure treated lumber contribute to the soil contamination and provide a continuous source of contaminants. Elevated levels of polycyclic aromatic hydrocarbons (PAHs) derived from railroad ties and arsenic from CCA pressure treated lumber are present in the gardens studied. Using a representative garden, we 1) determined the nature and extent of urban community garden soil contaminated with PAHs and arsenic by garden timbers; 2) designed a remediation plan, based on our sampling results, with our community partner guided by public health criteria, local regulation, affordability, and replicability; 3) determined the safety and advisability of adding city compost to Boston community gardens as a soil amendment; and 4) made recommendations for community gardeners regarding healthful gardening practices. This is the first study of its kind that looks at contaminants other than lead in urban garden soil and that evaluates the effect on select soil contaminants of adding city compost to community garden soil.

Cytological and other aspects of pathogenesis-related gene expression in tomato plants grown on a suppressive compost

BACKGROUND AND AIMS

Recent studies have shown that certain composts may trigger indirect defence mechanisms by sensitizing the plant to create an increased state of resistance, similar to systemic acquired resistance. In this study, the capacity of a disease-suppressive compost to alter the expression pattern of certain pathogenesis-related (PR) genes in the root system of tomato plants (Solanum lycopersicum) provided the opportunity to study their cellular expression pattern and to investigate putative roles of these genes in the mechanisms of plant defence.

METHODS

Employing the reverse transcription-polymerase chain reaction (RT-PCR) and in situ RNA:RNA hybridization techniques, the accumulation and distribution of the transcripts of the differentially expressed PR genes were examined in plants grown on compost and compared with those of control plants grown on peat.

KEY RESULTS

Elevated levels of expression of the pathogenesis-related genes PR-1, PR-5 and P69/PR-7 were detected in the roots of tomato plants grown on the compost. A clearly distinguished spatial induction pattern was observed for these PR genes: PR-1 transcripts were almost exclusively detected in the pericycle cells surrounding the root stele of the main and lateral roots; PR-5 transcripts were present in the phloem of the root and stem tissues; and the accumulation and distribution of PR-7 transcripts was detected in discrete groups of cells that appeared sporadically in both the parenchyma and vascular system of the root, suggesting that the gene is not expressed in a tissue-specific manner. In addition, a novel cDNA clone was isolated (P69G), which probably encodes a new tomato P69 isoform.

CONCLUSIONS

This study provides evidence that a suppressive compost is able to elicit consistent and increased expression of certain PR genes in the roots of tomato plants, even in the absence of any pathogen. The in situ localization studies reveal expression patterns which are in accordance with the presence of protein or with the putative roles of the respective encoded proteins. The expression of the PR genes may be triggered by the microflora of the compost or could be associated with abiotic factors of the compost.

SELCO-Ecopurin pig slurry treatment system

As the practice of intensive animal production increases, there is a need for affordable treatment technologies that can help manage the large amounts of manure generated. Our approach has been to develop an efficient liquid-solid separation module using polymer technology and integrate this separation module into systems of treatment technologies for both the separated liquid and solids. We describe the progress that has been made in management techniques and new technological alternatives for manure treatment and generation of value added by-products based on the SELCO-Ecopurin separation technology and experiences during the last five years in 12 livestock farms in Spain, Italy and the USA. High recovery of solids (>90%) makes the use of advanced purification of the liquid a more economical alternative. The liquid can be further treated to reduce N and P and produce effluents virtually free of these nutrients. Production of methane and energy was affected by solids concentration; the anaerobic process was optimised with polymer application rate of 120 ppm during separation and a solids content of 13%.

Effect of compost and manure soil amendments on nematodes and on yields of potato and barley: a 7-year study

A 7-year study located in Prince Edward Island, Canada, examined the influence of compost and manure on crop yield and nematode populations. The compost used in this study consisted of cull waste potatoes, sawdust, and beef manure in a 3:3:1 ratio, respectively. No plant-parasitic nematodes were detected in samples collected from windrow compost piles at 5- and 30-cm depths prior to application on field plots. Low population densities of bacterial-feeding nematodes were recovered from compost windrows at the 5-cm depth. Field plots of potato (Solanum tuberosum cv. Kennebec) received compost applied at 16 metric tonnes per hectare, or beef manure applied at 12 metric tonnes per hectare. An adjacent trial with barley (Hordeum vulgare cv. Mic Mac) received only the compost treatment. In both trials the experimental design was a complete randomized block with four replicates. Data averaged over seven growing seasons indicated that population levels of root-lesion nematodes (primarily Pratylenchus penetrans) were higher in root-zone soil in potato plots treated with either compost or manure compared to the untreated control plots. The soil amendments did not affect root-knot nematode (Meloidogyne hapla) population densities in the potato plots, but clover-cyst nematodes (Heterodera trifolii) were more numerous in the root-zone soils of barley treated with compost compared to the untreated plots. Numbers of bacterial-feeding nematodes (primarily Diplogaster lheritieri) were greater in soil in potato plots treated with manure and in soil around barley roots than in untreated plots. Total yields of potato tubers averaged over seven growing seasons increased by 27% in the plots treated with either compost or manure. Grain yields of barley also were increased by 12% when compost was applied. These results indicated that organic amendments increased crop yields, but the impacts on different nematode species varied and usually increased soil population levels.

Foliar Disease in Fresh-Market Tomato Grown in Differing Bed Strategies and Fungicide Spray Programs

A 3-year field study in central Maryland evaluated foliar disease in fresh-market tomato grown using combinations of four bed strategies and three fungicide programs. Bed strategies included uncovered beds with or without a composted dairy manure amendment or beds covered with black polyethylene or hairy vetch mulch. Fungicide programs included no fungicide, weekly fungicide, or fungicide applications scheduled according to the TOMCAST disease predictor. In plots with hairy vetch-covered beds, early blight caused by Alternaria solani, Septoria leaf spot caused by Septoria lycopersici, and defoliation were lower versus uncovered beds each year. Early blight and defoliation were lower in beds covered with vetch versus polyethylene mulch in 2 of 3 years. Disease severity, defoliation, and marketable yield were similar for the weekly and TOMCAST fungicide programs, with 40 to 50% fewer sprays using TOMCAST. Marketable yield was similar among bed strategies except for higher yields in covered versus uncovered and unamended beds in a relatively wet year and lower yields in vetch versus polyethylene beds in a dry year.

Alternate nitrogen amendments for organic fertilizers

The use of compost or manure in agriculture as an organic source of nutrients is common in many tropical, developing countries like Nigeria. One of the drawbacks of such materials is their low nitrogen (N) content (=1% N). Farmers commonly use chemical N fertilizers such as urea, calcium ammonium nitrate (CAN), and NPK formulations to obtain better crop growth and yield. These chemical supplements may have a negative impact on the environment through nitrate leaching into water, leading to eutrophication of surface waters that can affect public health. Gliricidia sepium, a fast-growing, tropical, perennial hedge plant was tested as a source of N in organo-mineral fertilizer formulations. Average nutrient content of Gliricidia is 3.8% N, 0.32% P, 1.8% K, 0.8% Ca, and 0.2% Mg. Using a sand culture and Amaranthus caudatus as a test crop, it was shown that amending commercial composts with 30% Gliricidia prunings would benefit many small-scale farmers and control environmental pollution.

Effect of Meloidogyne arenaria and Mulch Type on Okra in Microplot Experiments

The effects of perennial peanut (Arachis glabrata) hay, an aged yard-waste compost (mainly woodchips), and a control treatment without amendment were determined on two population levels of root-knot (Melaidogyne arenaria) nematode over three consecutive years in field microplots. Okra (Hibiscus esculentus, susceptible to the root-knot nematode) and a rye (Secale cereale) cover crop (poor nematode host) were used in the summer and winter seasons, respectively. The organic amendment treatments affected plant growth parameters. In the first year, okra yields were greatest in peanut-amended plots. Yield differences with amendment treatment diminished in the second and third years. Okra plant height, total fruit weight, and fruit number were greater with the lower population level of the root-knot nematode. Residual levels of nutrients in soil were greater where root-knot nematode levels and damage were higher and plant growth was poor. Nutrient levels affected the growth of a subsequent rye cover crop.

Effect of Compost and Maize Cultivars on Plant-parasitic Nematodes

Effects of yard waste compost and maize (Zea mays) cultivar on population densities of plant-parasitic nematodes were examined in four experiments in north Florida. In one experiment, eight maize cultivars were evaluated; the other three experiments involved split-plot designs with compost treatments as main plots and maize cultivars as subplots. The three compost treatments used in these experiments were: 269 mt/ha of a yard-waste compost applied to the soil surface as a mulch, 269 mt/ha of compost incolporated into the soil, and an unamended control. No interactions between compost treatment and cultivar occurred in any experiment. Effects of compost treatment on Mesocriconema spp., Meloidogyne incognita, and Pratylenchus spp. were inconsistent, whereas significant effects of compost on population densities of Paratrichodorus minor were found on four of six sampling occasions. Cultivar affected final population densities (Pf) of M. incognita. In two tests, Pf of M. incognita on a Florida subtropical experimental hybrid (Howard III) were only 36% and 23% of Pf on the standard tropical hybrid (Pioneer Brand X304C). In an integrated approach to management of nematodes in maize, the effects of compost amendment and culfivar choice acted independently. Apparently, cultivar choice is more important than amendment with yard waste compost for management of M. incognita population levels in a maize rotation crop.

Effect of yard waste compost on nematode densities and maize yield

The effects of a yard waste compost on densities of plant-parasitic nematodes and forage yield of maize (Zea mays) were determined over three seasons in two sites in north Florida. In each test, the experimental design was a randomized complete block with five replications and three treatments: 269 mt/ha of a yard waste compost C:N ratio = 35:1 to 46:1) applied to the soil surface as a mulch, 269 mt/ha of compost incorporated into the soil, and an unamended control. Of the nematodes found in these sites, Paratrichodorus minor was affected most by compost treatments, with densities at harvest reduced by a compost treatment on at least one sampling date in all three seasons (P </= 0.05). Meloidogyne incognita was not consistently affected by compost application. Densities of Criconemella spp. and Pratylenchus spp. were reduced by compost treatment much more often in the third season than in the first two seasons of the study (P </= 0.05). Forage yield of maize was increased (P </= 0.05) by both compost treatments in every test, with yield increases ranging from 10% to 212% over yield levels in unamended control plots and varying with season (P </= 0.05). Use of yard waste compost on agricultural sites may provide a beneficial amendment for crop production and a convenient means for disposal of a common waste product from urban areas. Effects of this compost with high C:N ratio on nematodes were long-term, often not appearing until the third season of the study.

Effect of yard waste compost on plant-parasitic nematode densities in vegetable crops

The effects of yard-waste compost on densities of plant-parasitic nematodes were determined on four crops at two sites in north Florida. Separate experiments were conducted with sweet corn (Zea mays), cowpea (Vigna unguiculata), yellow squash (Cucurbita pepo), and okra (Hibiscus esculentus). In each test, the design was a randomized complete block replicated four times and involving three treatments: 269 mt/ha yard-waste compost applied to the soil surface as a mulch, 269 mt/ha compost incorporated into the soil, and an unamended control. Final population densities of Criconemella spp. and Meloidogyne incognita were lower in plots receiving a compost treatment than in unamended control plots in only one of eight tests (P </= 0.05). Final densities of Paratrichodorus minor, Pratylenchus spp., and Xiphinema spp. were unaffected by compost treatment in all tests (P > 0.10). Vegetable yields were either unaffected by treatment or, in some tests, were lowest following the mulch treatment (P </= 0.10). Results indicate that the yard-waste compost used had little effect on densities of plant-parasitic nematodes associated with short-term (ca. 4 months) vegetable crops.

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.