Quantitative microbial indices in biogas and raw cattle slurries

Feed digestibility, digesta passage and faecal microbial biomass in desert-adapted goats exposed to mild water restriction

In arid and semi-arid environments, extensively managed ruminants regularly experience drinking water shortage, especially in the dry season. The present study therefore investigated the effects of mild drinking water restriction on feed intake, feed digestibility, solid digesta passage and composition of faeces including faecal microbial biomass. A feeding trial was conducted in Oman, during the dry summer months. Nine adult male Batinah goats were subjected to three watering regimes in a 3 × 3 Latin Square design. Treatments were (1) water offered ad libitum (100%, W100); (2) water restricted to 85% ad libitum consumption (W85); and (3) water restricted to 70% ad libitum consumption (W70). Animals were offered Rhodes grass hay and whole barley grains (1:1 ratio) at 1.3 times maintenance energy requirements. Each of the three experimental periods comprised 16 days of adaptation and 8 days of measurements. During the latter, feed offered and refused as well as faeces were sampled and quantified. Gastrointestinal digesta passage was determined using ytterbium-labelled Rhodes grass hay. Ergosterol and amino sugars were used as markers for faecal microbial biomass, that is the sum of fungi and bacteria. Water restriction had no effect on feed intake and digesta passage. However, feed dry matter, organic matter and fibre digestibility increased (p < 0.05) in W70 compared with W85, and the excreted amount of faecal dry matter, organic matter, nitrogen and neutral detergent fibre decreased (p < 0.05) in W70 compared with W85. Even though water restriction did not affect total faecal microbial biomass carbon (C) concentration, that of fungal biomass C increased (p < 0.05) in W70 compared with W85. Therefore, mild water restriction seems unproblematic from a physiological and nutrient utilization perspective as it increases feed digestibility without compromising feed intake.

Microbial diversity dynamics during the self-acidification of dairy slurry

Slurry acidification has been shown to be effective in reducing environmentally damaging gases. However, this involved the use of concentrated acids on farms. Therefore, due to the health and safety concerns, there is an interest in self-acidification of slurry technique. This study was designed to determine the microbial dynamics leading to self-acidification of slurry. A fresh cattle slurry was amended 10% brewing sugar and stored over 30 days. This fermentable carbon source promoted self-acidification of the slurry from pH 7.0 to 4.7 within four days, and was associated with the accumulation of lactic acid and a reduction in methane and relative ammonia emissions. A metagenomics approach through next generation sequencing (NGS) using an Illumina MiSeq platform was used to determine the microbial diversity and dynamics (bacteria and archaea) in the stored amended slurry. 16S ribosomal ribonucleic acid (rRNA) sequence data revealed the presence of the Order of Lactobacillales was associated with the lactic acid production. The operational taxonomic units (OTUs) abundance indicates that the methanogenic community was dominated by hydrogenotrophic methanogens from the member Order of Methanobacteriales, Methanomicrobiales, and Methanosarcinales. The decrease in tolerance by the methanogens in the self-acidified slurry was probably the main reason for the reduced methane emission. These results confirm, at the microbial level, the mechanism of inhibiting methane production via self-acidification during storage period.

Determination of microbial numbers in anaerobically digested biofertilisers

This study aimed to quantity total numbers of bacteria, fungi and archaea in different types of commercial liquid anaerobic digestates, and to identify common patterns in their microbial numbers post-digestion and possible implications of their use as biofertiliser. Relationships between microbial numbers and physical-chemical traits of the digestates were also investigated. Quantification was performed using culturable and molecular (quantitative PCR) approaches. Bacterial and fungal CFUs ranged up to five orders of magnitude (10⁵-10¹⁰; 0-10⁵ g^-1 DW, respectively) between different types of anaerobic digestates. Bacterial, archaeal and fungal gene copy numbers (GCN) varied by two orders of magnitude (10⁸-10¹⁰; 10⁷-10⁹; 10⁴-10⁶ g^-1 DW, respectively) between digestates. All microbial variables analysed showed significant differences between the different types of anaerobic digestate investigated (p < 0.05). Culturable microbial numbers for fungi (6.43 × 10⁴ CFU g^-1 DW) were much lower than for bacteria (2.23 × 10⁹ CFU g^-1 DW). Gene copy numbers were highest for bacteria (16S) (1.09 × 10¹⁰ g^-1 DW), followed by archaea (16S) (5.87 × 10⁸ g^-1 DW), and fungi (18S) (1.77 × 10⁶ g^-1 DW). Liquid anaerobic digestates were predominantly dominated by bacteria, followed by archaeal and fungal populations. At 50% similarity level, the microbial profiles of the eleven anaerobic digestates tested separated into just two groups, indicating a broad relative degree of similarity in terms of microbial numbers. Higher bacterial (16S) GCN was associated with low OM and C/N ratio in digestates.

Relationships between feeding and microbial faeces indices in dairy cows at different milk yield levels

A study was carried out to gain quantitative information on the diet-dependent faecal microbial biomass of dairy cows, especially on the biomass fractions of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. Groups of high-yield, low-yield and non-lactating cows were investigated at four different farms. A mean faecal microbial biomass C (MBC) concentration of 33.5 mg g-1 DM was obtained by the chloroform fumigation extraction method. This is similar to a mean microbial C concentration of 31.8 mg g-1 DM, which is the sum of bacterial C and fungal C, estimated by cell-wall derived muramic acid (MurN) and fungal glucosamine (GlcN), respectively. However, the response of these two approaches to the feeding regime was contradictory, due to feeding effects on the conversion values. The higher neutral detergent fibre (NDF) and acid detergent fibre (ADF) concentrations in the non-lactating group led to higher (P < 0.05) concentrations of cellulose and lignin in their faeces in comparison with the lactating cows. This change in faecal chemical composition in the non-lactating group was accompanied by usually higher ratios of G+/G- phospholipid fatty acids (PLFA), ergosterol/MBC and fungal C/bacterial C. Although bacteria dominate the faecal microbial biomass, fungi contribute a considerable mean percentage of roughly 20% to the faecal microbiome, according to PLFA and amino sugar data, which requires more attention in the future. Near-infra red spectroscopic estimates of organic N and C fractions of cow faeces were able to model microbial biomarkers successfully, which might be useful in the future to predict its N2O emission potential and fertilizer value.

Biogas residue parameterization for soil organic matter modeling

A variety of biogas residues (BGRs) have been used as organic fertilizer in agriculture. The use of these residues affects the storage of soil organic matter (SOM). In most cases, SOM changes can only be determined in long-term observations. Therefore, predictive modeling can be an efficient alternative, provided that the parameters required by the model are known for the considered BGRs. This study was conducted as a first approach to estimating the organic matter (OM) turnover parameters of BGRs for process modeling. We used carbon mineralization data from six BGRs from an incubation experiment, representing a range of substrate inputs, to calculate a turnover coefficient k controlling the velocity of fresh organic matter (FOM) decay and a synthesis coefficient η describing the SOM creation from FOM. An SOM turnover model was applied in inverse mode to identify both parameters. In a second step, we related the parameters k and η to chemical properties of the corresponding BGRs using a linear regression model and applied them to a long-term scenario simulation. According to the results of the incubation experiment, the k values ranged between 0.28 and 0.58 d^-1 depending on the chemical composition of the FOM. The estimated η values ranged between 0.8 and 0.89. The best linear relationship of k was found to occur with pH (R² = 0.863). Parameter η is related to the C_t/N_org ratio (R² = 0.696). Long-term scenario simulations emphasized the necessity of specific k and η values related to the chemical properties for each BGR. However, further research is needed to validate and improve these preliminary results.