Patrick Dabert

Dynamics of a pig slurry microbial community during anaerobic storage and management.

ABSTRACT The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration

Abstract. The microbial community of a conventional anaerobic–aerobic sequencing batch reactor was investigated by cloning and sequencing bacterial 16S rDNA. The 92 16S rDNA sequences analysed ranged across 50 different operational taxonomic units (OTU). The majority of these sequences were not closely related to known species. They belonged to 12 different groups, but essentially to the Cytophagales and the Proteobacteria beta, which represented 38% and 17% of the retrieved sequences respectively. No OTU numerically outnumbered the others. However, similarities were observed with previous reports on molecular characterisation of phosphorus-accumulating ecosystems, suggesting an enrichment in microorganisms belonging to the Rhodocyclus group. Thereafter, the ability of this anaerobic–aerobic microbial community to accumulate phosphorus with nitrate as its energy source was investigated. The reactor was shifted from anaerobic–aerobic running conditions to anaerobic–anoxic conditions by injection of nitrate; and its microbial community was monitored by PCR-single strand conformation polymorphism (SSCP). The reactor maintained a good phosphorus accumulation and similar SSCP microbial community patterns for a period of 17 days, suggesting that the same microbial community was able to respire both oxygen and nitrate. However, this situation was unstable, since a breakdown in phosphorus accumulation occurred thereafter.

Livestock waste treatment systems for environmental quality, food safety, and sustainability

The intensification of livestock operations has benefited production efficiency but has introduced major environmental issues, becoming a concern in both developed and developing countries. The aim of this paper is primarily to address the impact of the livestock sector on environmental pollution (ammonia, greenhouse gases and pathogens), evaluate the related health risks and, subsequently, assess the potential role of waste treatment systems in attenuating these environmental and health issues. This paper is a collection of data pertaining to world trends in livestock production, since the mid 1990s and intensive livestock farming practices along with their impact on: water pollution by nitrates and through eutrophication; air pollution, particularly ammonia and greenhouse gases emissions, and soil pollution because of nutrient accumulation. Finally, this paper examines some of the benefits of treating livestock manures, issues related to the adoption of treatment systems by livestock operations and current as well as past technological developments.

Microvirgula aerodenitrificans gen. nov., sp. nov., a new Gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions

A denitrifier micro-organism was isolated from an upflow denitrifying filter inoculated with an activated sludge. The cells were Gram-negative, catalase- and oxidase-positive curved rods and very motile. They were aerobic as well as anoxic heterotrophs that had an atypical respiratory type of metabolism in which oxygen and nitrogen oxides were used simultaneously as terminal electron acceptors. The G&C content was 65 mol%. Our isolate was phenotypically similar to Comamonas testosteroni, according to classical systematic classification systems. However, a phylogenetic analysis based on the 165 rRNA sequence showed that the aerobic denitrifier could not be assigned to any currently recognized genus. For these reasons a new genus and species, Microvirgula aerodenitrificans gen. nov., sp. nov., is proposed, for which SGLY2T is the type strain.

Sulphur fate and anaerobic biodegradation potential during co-digestion of seaweed biomass (Ulva sp.) with pig slurry

Seaweed (Ulva sp.) stranded on beaches were utilized as co-substrate for anaerobic digestion of pig slurry in three-month co-digestion tests in pilot scale anaerobic digesters in the laboratory. The methanogenic potential of Ulva sp. was low compared to that of other potential co-substrates available for use by farmers: 148 N m3CH4/t of volatile solids or 19 N m3CH4/t of crude product. When used as a co-substrate with pig manure (48%/52% w/w), Ulva sp. seaweed did not notably disrupt the process of digestion; however, after pilot stabilisation, biogas produced contained 3.5% H2S, making it unsuitable for energy recovery without treatment. Sequentially addition of the sulphate reduction inhibitor, potassium molybdate, to a final concentration of 3mM, temporarily reduced H2S emissions, but was unable to sustain this reduction over the three-month period. According to these pilot tests, the use of seaweed stranded on beaches as co-substrate in farm-based biogas plants shows some limitations.

Prediction of hydrogen sulphide production during anaerobic digestion of organic substrates

The main objective of this study was to develop a methodology to predict the hydrogen sulphide content of raw biogas produced during anaerobic mono-digestion of a bioenergy feedstock. Detailed chemical and biological analyses were made on 37 different feedstocks originating from urban wastewater treatment plants, farms, agri-food facilities and municipal wastes. Total sulphur content ranged from 1 to 29.6 mg S/kg of total solids, and 66% of the feedstocks analysed contained less than 5 mg S/kg of total solids. The biochemical methanogenic potential and biochemical biogas potential of each feedstock combined with its S content were used to predict appearance of H(2)S in the raw biogas. A model to link H(2)S in biogas with the carbon:sulphur ratio was established. Based on this model, a minimum carbon:sulphur ratio of 40 is required in feedstock to limit the concentration of hydrogen sulphide in raw biogas to less than 2% (volume/volume).

Comamonas nitrativorans sp. nov., a novel denitrifier isolated from a denitrifying reactor treating landfill leachate.

A group of Gram-negative denitrifying bacteria has been isolated from a denitrifying reactor treating landfill leachate. The new isolates produced both oxidase and catalase and showed growth on acetate, butyrate, n-caproate, i-butyrate, i-valerate, propionate, n-valerate, lactate, alanine, benzoate, phenylalanine and ethanol. No growth was observed on sugars. The bacteria could perform anoxic reduction of nitrate, nitrite and nitrous oxide to nitrogen, coupled to the oxidation of the same substrates as those used under aerobic conditions, except for aromatic compounds. They were very efficient denitrifiers, as estimated from the specific rate of N2 gas production. All the strains showed the same 16S rDNA restriction profile and one of them, designated 23310T, was selected for phylogenetic analysis. The organism clustered within the family Comamonadaceae, being related to Comamonas terrigena (95.8% sequence similarity). On the basis of the phylogenetic analysis, physiological characterization and the ability to efficiently reduce nitrate to N2, it is proposed that the bacterium be assigned to a new species, Comamonas nitrativorans. The type strain is 23310T (= DSM 13191T = NCCB 100007T = CCT 7062T).

Nitrification and microbiological evolution during aerobic treatment of municipal solid wastes.

Nitrification is a key step in the nitrogen cycle in various ecosystems. In this study, the nitrogen dynamic and the evolution of groups of microorganisms were studied during aerobic treatment of fine organic fraction of municipal solid wastes. Mineralization of organic nitrogen exhibited two phases and resulted in two ammonia emissions peaks. The nitrogen balance indicated the onset of nitrification only during the maturation stage, which was confirmed by the accumulations of both nitrite and nitrate and the nitrous oxide emissions in this period. A significant development of ammonia-oxidizing bacteria correlated to the onset of nitrification. On the contrary, ammonia-oxidizing archaea were less abundant and declined through treatment. Identification of these ammonia oxidizers indicates that the Nitrosomonas europaea/eutropha-like ammonia oxidizing bacteria were responsible for ammonia oxidation instead of other groups of ammonia oxidizers during aerobic treatment of fine organic fraction of municipal solid wastes.

Characterizing the variability of food waste quality: A need for efficient valorisation through anaerobic digestion

In order to determine the variability of food waste (FW) characteristics and the influence of these variable values on the anaerobic digestion (AD) process, FW characteristics from 70 papers were compiled and analysed statistically. Results indicated that FW characteristics values are effectively very variable and that 24% of these variations may be explained by the geographical origin, the type of collection source and the season of the collection. Considering the whole range of values for physicochemical characteristics (especially volatile solids (VS), chemical oxygen demand (COD) and biomethane potential (BMP)), FW show good potential for AD treatment. However, the high carbohydrates contents (36.4%VS) and the low pH (5.1) might cause inhibitions by the rapid acidification of the digesters. As regards the variation of FW characteristics, FW categories were proposed. Moreover, the adequacy of FW characteristics with AD treatment was discussed. Four FW categories were identified with critical characteristics values for AD performance: (1) the high dry matter (DM) and total ammonia nitrogen (TAN) content of FW collected with green waste, (2) the high cellulose (CEL) content of FW from the organic fraction of municipal solid waste, (3) the low carbon-to-nitrogen (C/N) ratio of FW collected during summer, (4) the high value of TAN and Na of FW from Asia. For these cases, an aerobic pre-treatment or a corrective treatment seems to be advised to avoid instabilities along the digestion. Finally, the results of this review-paper provide a data basis of values for FW characteristics that could be used for AD process design and environmental assessment.

Contribution of molecular microbiology to the study in water pollution removal of microbial community dynamics

Molecular tools based on 16S rRNA geneidentification are revolutioning microbialecology. After a short presentation of theadvantages and drawbacks of these new tools,the paper gives a succinct review of theirpossibilities as they have been applied to themicrobial ecology of water pollution removal.Examples of applications are presented in thefields of anaerobic digestion, nitrogen andphosphorus removal, filamentous bacteria andbioaugmentation. The data provided give someinsights about microbial diversity, populationdynamics, ecosystems stability and specificmicrobial population activity.