Composition Of Bacterial Populations Research Articles

Resistance of various soil geosystem bacteria to enzymatic lysis at different pH

Bacteria appear to be an inevitable element of soil geochemistry because they participate actively in chemical transformations of soil media components. One of the factors determining the composition of bacterial population in soil is resistance of bacteria to enzymes which hydrolyze cell walls. In the following research, resistance of bacteria (Priestia megaterium, Micrococcus luteus and Escherichia coli) to lysozyme in the pH range appropriate for soils is investigated. All the three species are proved to be most sensitive to lysozyme in slightly alkaline conditions (P. megaterium is least resistant at pH 8.0, M. luteus at pH 8.3, E. coli at pH 8.5), and resistance of all the three microorganisms in the range of pH values of 6.0—7.0 changes insignificantly. A possible factor defining the pH optimum for lysozyme activity in relation to these bacteria is the structure of negatively charged components of their cell walls and outer membranes.

High-rate ex situ and in situ treatment system for groundwater denitrification via membrane-based bacterial macro-encapsulation

The main aim of this study was to develop a new biotreatment process for denitrification by using a small bioreactor platform (SBP) for macro-encapsulation of a bacterial consortium equipped with a slow-release organic matter core for ex situ and in situ treatment configurations. The biotreatment system in the continuous ex situ mode achieved a maximal nitrate removal load of 38.9 g nitrate/L/day with a short hydraulic retention time (HRT) of 1.3 h. The in situ configuration showed high performance for >50 days, with 85 % nitrate removal from an initial concentration of 110 mg/L. The capsules continuously removed nitrate at the same rate even when the organic matter level in the internal capsule was low. After 30 days of in situ experiments, the bacterial population composition set inside the SBP capsules presented dominant populations of well-known heterotrophic denitrifying bacteria. Thus, the encapsulated process not only demonstrated a short HRT necessary for high nitrate removal rates in ex and in situ configurations, but also potentially lower operational costs and no secondary environmental contamination caused by excess organic matter.

The cytotoxic effect of graphene oxide nanoparticles on bacterial cells

The results of research on the introduction of nanotechnology in various fields of scientific activities are presented. In medical and veterinary practice, nanoparticles of various forms of carbon are considered promising, because they have a wide arsenal of biomodulatory effects on the body, exhibiting little ecotoxic and organismotoxic effects. Their antibacterial effect is of great importance for the use in medicine. Microorganisms are one of the objects of study of the cytotoxic properties of new medicinal products. The cytotoxic effect of oxidized graphene nanoparticles on the main types of bacterial cells was evaluated by light and atomic force microscopy. Light microscopy allowed to establish that the effect of subinhibitory concentrations of nanoparticles of oxidized graphene, achieved by studying the colonies of microorganisms on the border of their growth inhibition, can lead to tinctorial transversion in Gram-positive microorganisms, in particular Staphylococcus aureus, while in Gram-negative E. coli such a phenomenon is not observed. Using the method of atomic force microscopy, it was found that toxic concentrations of oxidized graphene nanoparticles lead to morphological degradation, the degree of which depends on the exposure time of nanoparticles. Morphological degradation of cells in the main types of bacteria (cocci, bacilli), accompanied by a decrease in cell contours, was observed at 30 min exposure. When the exposure was increased from 30 to 90 min, complete morphological destruction of the bacterial cells and decay of the bacterial population composition were observed. The cytotoxic concentration of oxidized graphene nanoparticles is more than 75 µg·ml-1, as determined by the results of microscopy of test culture samples (Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538).

Response of Milk Performance, Rumen and Hindgut Microbiome to Dietary Supplementation with Aspergillus oryzae Fermentation Extracts in Dairy Cows.

Fungal additives had beneficial effects on milk performance in dairy cows. Previous studies investigating the effects of fungal additives mainly focused on the rumen, such influences on the hindgut remain limited. This study aimed to investigate the effects of Aspergillus oryzae fermentation extracts (AOE) on the milk performance and microbiome in the rumen and hindgut using 16S rRNA gene sequencing. Twenty lactating multiparous Holstein cows were randomly assigned to control and treatment (5g AOE per cow per day). The results showed that AOE increased the milk yield, milk protein and lactose concentration, but did not affect the milk fat concentration. Feeding AOE did not affect the ruminal VFA pattern, pH, NH3-N, and microbial cell protein production, but decreased lipopolysaccharide concentration and tended to decrease lactate concentration. The addition of AOE increased the fecal pH and the proportions of propionate, isovalerate and valerate, and decreased the acetate to propionate ratio. PCoA analysis showed that AOE did not affect the overall ruminal bacterial population composition. Only three genera changed slightly in relative abundance. In the feces, PCoA analysis showed that AOE changed the bacterial population composition. Feeding AOE increased the relative abundances of Ruminococcaceae UCG-010 and unclassified Clostridiales vadinBB60 group, and decreased Christensenellaceae R-7 group, unclassified Muribaculaceae, Prevotellaceae UCG-001 and Romboutsia. Spearman correlation showed unclassified Clostridiales vadinBB60 group was positively correlated with propionate proportion. Overall, we present that AOE not only functioned in rumen, but also in hindgut. The hindgut microbiome changes might play an important role in the milk performance improvement of dairy cows.

Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation.

Shotgun metagenomics studies have improved our understanding of microbial population dynamics and have revealed significant contributions of microbes to gut homeostasis. They also allow in silico inference of the metagenome. While they link the microbiome with metabolic abnormalities associated with disease phenotypes, they do not capture microbial gene expression patterns that occur in response to the multitude of stimuli that constantly ambush the gut environment. Metatranscriptomics closes that gap, but its implementation is more expensive and tedious. We assessed the metabolic perturbations associated with gut inflammation using shotgun metagenomics and metatranscriptomics. Shotgun metagenomics detected changes in abundance of bacterial taxa known to be SCFA producers, which favors gut homeostasis. Bacteria in the phylum Firmicutes were found at decreased abundance, while those in phyla Bacteroidetes and Proteobacteria were found at increased abundance. Surprisingly, inferring the coding capacity of the microbiome from shotgun metagenomics data did not result in any statistically significant difference, suggesting functional redundancy in the microbiome or poor resolution of shotgun metagenomics data to profile bacterial pathways, especially when sequencing is not very deep. Obviously, the ability of metatranscriptomics libraries to detect transcripts expressed at basal (or simply low) levels is also dependent on sequencing depth. Nevertheless, metatranscriptomics informed about contrasting roles of bacteria during inflammation. Functions involved in nutrient transport, immune suppression and regulation of tissue damage were dramatically upregulated, perhaps contributed by homeostasis-promoting bacteria. Functions ostensibly increasing bacteria pathogenesis were also found upregulated, perhaps as a consequence of increased abundance of Proteobacteria. Bacterial protein synthesis appeared downregulated. In summary, shotgun metagenomics was useful to profile bacterial population composition and taxa relative abundance, but did not inform about differential gene content associated with inflammation. Metatranscriptomics was more robust for capturing bacterial metabolism in real time. Although both approaches are complementary, it is often not possible to apply them in parallel. We hope our data will help researchers to decide which approach is more appropriate for the study of different aspects of the microbiome.

Intestinal microbiota disturbance affects the occurrence of African swine fever

Intestinal microbiota not only participates in the digestion and absorption of nutrients, but also plays an important role in regulating host metabolism and health. The current study aimed to explore the intestinal microbiota characteristics in pigs infected with African swine fever. Below the same term, fresh fecal samples of sick and healthy pigs were collected. Primers were designed and PCR was extracted based on the 16S rDNA gene of bacteria by Illumina NovaSeq sequencing platform. The results showed that the bacterial alpha diversity index of healthy pigs was significantly higher than that of sick pigs (p < 0.05). On the phylum taxa, dominant bacteria more than 98.5% in the two groups are composed of Firmicutes, Spirobacteria, and Bacteroides, of which the abundance of Firmicutes and Bacteroidetes decreased and Spiricobacteria increased extremely significant in sick pigs (p < 0.01). On the genus taxa, the relative abundance of Oscillospira, Streptococcus and Roseburia decreased significantly (p < 0.05). Most notably, Treponema performed excellently in distinguishing pigs infected with African swine fever with the abundance increased extremely significantly (p < 0.01). In conclusion, African swine fever could alter the abundance of dominant bacteria in pigs, and Treponema may be one of the important inducers for swine pathogenicity. Highlights The bacterial population composition in sick pigs and healthy pigs was basically similar, but the relative abundance of dominant bacteria was significantly difference. ASF could alter the abundance of dominant bacteria in pigs, and Treponema may be one of the important inducers for swine pathogenicity. These results will provide further evidence for the ASF infection in local pig farms and provide reference for their microecological control, which has important practical significance and social value for effective control of ASF, stability of pig production and guarantee of market supply.

Wolbachia load variation in Drosophila is more likely caused by drift than by host genetic factors

Symbiosis is a continuum of long-term interactions ranging from mutualism to parasitism, according to the balance between costs and benefits for the protagonists. The density of endosymbionts is, in both cases, a key factor that determines both the transmission of symbionts and the host extended phenotype, and is thus tightly regulated within hosts. However, the evolutionary and molecular mechanisms underlying bacterial density regulation are currently poorly understood. In this context, the symbiosis between the fruit fly and its intracellular bacteria Wolbachia (wMelPop strain) is particularly interesting to study. Although vertically transmitted, the symbiont is pathogenic, and a positive correlation between virulence and wMelPop density is observed. In addition, the number of repeats of a bacterial genomic region -Octomom- is positively correlated with Wolbachia density, underlying a potential genetic mechanism that controls bacterial density. Interestingly, the number of repeats varies between host individuals, but most likely also within them. Such genetic heterogeneity within the host could promote conflicts between bacteria themselves and with the host, notably by increasing within-host competition between symbiont genotypes through a process analogous to the tragedy of the commons. To characterize the determinisms at play in the regulation of bacterial density, we first introgressed wMelPop in different genetic backgrounds of D. melanogaster, and found different density levels and Octomom copy numbers in each host lineage. To determine whether such variations reflect a host genetic determinism on density regulation through Octomom copy number selection, we replicated the introgressions and performed reciprocal crosses on the two Drosophila populations with the most extreme density levels. In both experiments, we detected an absence of directionality in the patterns of infection, associated with a strong instability of these patterns across generations. Given that bacterial density was highly correlated with Octomom copy numbers in all experiments, these results rather suggest a strong influence of drift and a random increase in the frequency of certain bacterial variants. We then discuss how drift, both on the symbiont population during transmission and on the host population, could limit the efficiency of selection in such a symbiotic system, and the consequences of drift on the regulation of density and composition of bacterial populations.

A New Paradigm in the Relationship between Melatonin and Breast Cancer: Gut Microbiota Identified as a Potential Regulatory Agent.

Simple SummaryThe relationship between melatonin and breast cancer has been widely described. On the other hand, in recent years, an imbalance in the composition of the intestinal bacterial population has been linked as another possible trigger for this disease. Given that changes in the gut microbiota have been observed to stimulate the kinurenine pathway, reducing circulating melatonin levels, in this review, we summarize the relationship between circadian disruption and breast cancer, as well as the connection with dysbiosis as possible causing this pathology due to a series of changes that lead to an increase in circulating estrogen levels.In this review we summarize a possible connection between gut microbiota, melatonin production, and breast cancer. An imbalance in gut bacterial population composition (dysbiosis), or changes in the production of melatonin (circadian disruption) alters estrogen levels. On the one hand, this may be due to the bacterial composition of estrobolome, since bacteria with β-glucuronidase activity favour estrogens in a deconjugated state, which may ultimately lead to pathologies, including breast cancer. On the other hand, it has been shown that these changes in intestinal microbiota stimulate the kynurenine pathway, moving tryptophan away from the melatonergic pathway, thereby reducing circulating melatonin levels. Due to the fact that melatonin has antiestrogenic properties, it affects active and inactive estrogen levels. These changes increase the risk of developing breast cancer. Additionally, melatonin stimulates the differentiation of preadipocytes into adipocytes, which have low estrogen levels due to the fact that adipocytes do not express aromatase. Consequently, melatonin also reduces the risk of breast cancer. However, more studies are needed to determine the relationship between microbiota, melatonin, and breast cancer, in addition to clinical trials to confirm the sensitizing effects of melatonin to chemotherapy and radiotherapy, and its ability to ameliorate or prevent the side effects of these therapies.

A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows.

Simple SummaryHigh-yielding dairy cows must receive high-grain diets in order to meet their high energy requirements. However, these diets depress the pH in the rumen, leading to a condition referred to as subacute ruminal acidosis (SARA), and in the large intestine, and may negatively affect the taxonomic composition and the functionality of the populations of microorganisms in the digestive tract. As cows depend on these microorganisms for nutrient utilization and health, disruptions of their composition and functionality can greatly affect the production, health, and welfare of dairy cows. In our study, SARA was induced experimentally by excessive grain feeding. The taxonomic composition of bacterial populations attached to the epithelia of the digestive tract were determined throughout this tract. Our results show that SARA affected the populations of several taxa of bacteria, which suggests that the beneficial effects of these bacteria may be reduced, and that the digestive tract may be at increased risk of invasion by pathogenic microorganisms. The greatest effects of SARA on the taxonomic composition of bacteria on epithelia were in the rumen and large intestine. Their composition on epithelia in the small intestine was also affected, but the affected groups of bacteria differed from those in the rumen and large intestine.The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China.

Raw milk is a nature media of microbiota that access milk from various sources, which constitutes a challenge in dairy production. This study characterizes the relationship between the raw milk quality and the bacteria diversity at different sampling sites in dairy farms, aiming to provide a strong scientific basis for good hygienic practices and optimized procedure in milk production. High-throughput sequencing of 16S rRNA V3-V4 region was used to analyze the components, abundance and diversity of 48 bacterial population sampled from 8 different sites in dairy farm: pre-sterilized cow’s teats (C1), post-sterilized cow’s teats (C2), milking cluster (E), milk in storage tank (M1), transport vehicle (M2), storage equipment (E2), cow’s dung samples (F) and drinking water (W). Firmicutes account for predominantly 32.36% (C1), 44.62% (C2), 44.71% (E), 41.10% (M1), 45.08% (M2), 53.38% (F) of all annotated phyla. Proteobacteria accounts for 81.79% in W group and Actinobacteria 56.43% in E2 group. At the genus level, Acinetobacter was the most abundant genus that causes bovine mastitis, Acinetobacter and Arthrobacter were dominant in C1, C2, and E groups, Kocuria in E2 group and Arcobacter in W group. E, C1, and C2 group have very similar bacterial composition, and M1 and M2 demonstrated similar composition, indicating that the milking cluster was polluted by the environment or contact with cow udders. Bacterial population composition in different sampling sites identified by NGS reveals a correlation between the bacteria communities of raw milk production chain and the quality of raw milk.

Bacterial Community of Neutral Mine Drainage of Elizabeth’s Shaft (Slovinky, Slovakia)

Neutral mine drainage is the less frequent subject of the interest than acid mine drainage but it can have adverse environmental eff ects caused mainly by precipitation of dissolved Fe. Th e aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth’s shaft , Slovinky (Slovakia). Th e pH value of drainage water decreased from 7.1 to 6.5 during the years 2008–2014. Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identifi ed iron–oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008–2014. Using 454 pyrosequencing, there were identifi ed members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chlorofl exi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron–oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth’s shaft drainage water refl ects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.

Application of 16S rDNA Sequencing Technology in the Analysis of Pathogenic Bacteria in Sputum of Severe Pneumonia

The diagnosis of pathogenic bacteria in severe pneumonia is difficult and the prognosis is poor. Its outcome is closely related to bacterial pathogenicity and the timeliness and pertinence of antibiotic treatment. Therefore, early diagnosis is of great significance to the prognosis of patients. Sputum examination and culture is the gold standard for the diagnosis of pathogens of severe pneumonia. However, due to the long time of bacterial culture, the early use of antibiotics, the change of bacteria species, mixed infection and other problems, the results of bacterial culture in sputum are often false negative. With the continuous application of new molecular biology techniques in clinical detection, the classification of bacteria and microorganisms has deepened from the identification of phenotypic characteristics to the classification of gene characteristics. Sequencing analysis with 16S rDNA sequencing technology has the characteristics of high sequencing flux, large amount of data obtained, short cycle, and can more comprehensively reflect the species composition of microbial community, real species distribution and abundance information. In this paper, 16S rDNA sequencing technology was used to analyze the bacterial population composition in the sputum of severe pneumonia, and to explore a new method of etiological diagnosis.

Soil management in a mountain agroecosystem and clubroot disease

Clubroot, caused by Plasmodiophora brassicae, is a disease limiting the production of Brassica species. Its severity varies according to the density of the pathogen's resting spores and environmental conditions. Although the soil environment (including its physical, chemical and biological characteristics) is determinant in the development of the disease, little is known regarding these characteristics in tropical regions, such as Brazil. The objective of this study was to investigate the relationships between soil attributes, bacterial population composition and clubroot intensity in a tropical mountain agroecosystem. Soil and plant samples were collected from 17 cauliflower‐producing localities in Nova Friburgo, Brazil. The physical and chemical attributes, the bacterial population composition, the number of pathogen resting spores in the soil samples, and the clubroot severity were evaluated. Based on bacterial population composition, two distinct groups of soils were identified, which varied in attributes such as organic matter, potential acidity, pH and disease severity. The organic matter level was associated with differences in soil acidity, bacterial population composition and disease intensity, but there was not a cause and effect relationship between bacterial population composition and clubroot severity. Under the conditions of this agroecosystem, soils with increased organic matter presented higher acidity potential (H + Al), which was strongly correlated to clubroot severity. Thus, high acidity potential could be a key factor leading to clubroot development in mountain regions of Brazil.

Metagenomic analysis of β-lactamase and carbapenemase genes in the wastewater resistome

The emergence and spread of resistance to antibiotics among bacteria is the most serious global threat to public health in recent and coming decades. In this study, we characterized qualitatively and quantitatively β-lactamase and carbapenemase genes in the wastewater resistome of Central Wastewater Treatment Plant in Koziegłowy, Poland. The research concerns determination of the frequency of genes conferring resistance to β-lactam and carbapenem antibiotics in the genomes of culturable bacteria, as well as in the wastewater metagenome at three stages of treatment: raw sewage, aeration tank, and final effluent. In the final effluent we found bacteria with genes that pose the greatest threat to public health, including genes of extended spectrum β-lactamases – blaCTX-M, carbapenemases – blaNDM, blaVIM, blaGES, blaOXA-48, and showed that during the wastewater treatment their frequency increased. Moreover, the wastewater treatment process leads to significant increase in the relative abundance of blaTEM and blaGES genes and tend to increase the relative abundance of blaCTX-M, blaSHV and blaOXA-48 genes in the effluent metagenome. The biodiversity of bacterial populations increased during the wastewater treatment and there was a correlation between the change in the composition of bacterial populations and the variation of relative abundance of β-lactamase and carbapenemase genes. PCR-based quantitative metagenomic analysis combined with analyses based on culture methods provided significant information on the routes of ARBs and ARGs spread through WWTP. The limited effectiveness of wastewater treatment processes in the elimination of antibiotic-resistant bacteria and resistance genes impose the need to develop an effective strategy and implement additional methods of wastewater disinfection, in order to limit the increase and the spread of antibiotic resistance in the environment.

Mathematical modelling to characterise the in vivo dynamics of Salmonella in the naïve and immunised host

Systemic salmonellosis encompasses typhoid and paratyphoid fever, and invasive non-typhoidal salmonellosis, with high mortality and morbidity amongst children and the immunocompromised in low-resource settings. Immunisation efforts remain hampered by the unavailability of safe vaccines with cross-protectivity against causative Salmonella strains. Characterisation of the within-host Salmonella dynamics in the naïve and immunised host can elucidate the mechanisms by which different vaccine types exert their protective effect, and help in vaccine selection and design. Experimental data tracking the changes in bacterial population composition in the different tissues of the host at different timepoints can be coupled with mechanistic mathematical models to estimate the parameters governing the processes of bacterial replication, killing and inter-organ migration. Using a recently described minimisation-divergence estimation approach, we extend a three-compartmental mechanistic model and re-analyse existing datasets to better characterise the bacterial migratory processes between the blood, liver and spleen in the early stages of infection, and the overall Salmonella dynamics in the later phases in the naïve host. We apply the same model to published data from mice immunised with either a live-attenuated or killed whole-cell vaccine to identify their in vivo differential impacts on Salmonella migration, replication and death. Finally, we identify alternative experimental designs to improve the statistical qualities of the mathematical model and allow better inference of parameters governing the unobserved processes of bacterial dynamics.

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.

16S rRNA Amplicon Profiling of Cranberry (Vaccinium macrocarpon Ait.) Flower and Berry Surfaces.

Bacterial populations associated with the surfaces of cranberry flowers and early fruits in wetlands bogs in Eastern Massachusetts were examined using pyrosequencing. The composition of bacterial populations was highly dependent on sample site, but the dominant phyla on both flower and berry surfaces were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes.

The effect of introduction of chicken manure on the biodiversity and performance of an anaerobic digester

Background: Ammonium stress is a prime limiting phenomenon that occurs during methane formation from poultry manure. It is caused by elevated ammonium nitrogen concentrations that result from substrate decomposition. The amounts of methane formed depend on the activity of methanogenic microbes. Results: During the research reported in this paper, the response of a mesophilic consortium inhabiting a biogas reactor to rising load of poultry manure was investigated. The taxonomic composition of bacterial population was mostly typical, however syntrophic bacteria were not detected. This absence resulted in limitation of succession of some methanogenic microorganisms, especially obligate hydrogenotrophs. The methanogenic activity of the consortium was totally dependent on the activity of Methanosaeta. Inhibition of methanoganesis was noticed at ammonium nitrogen concentration of 3.68 g/L, total cessation occurred at 5.45 g/L. Significant amounts of acetic acid in the fermentation pulp accompanied the inhibition. Conclusions: The effectiveness of the consortium was totally dependent on the metabolic activity of the acetoclastic Methanoseata genus and lack of SAOB did not allow hydrogenotrophic methanogens to propagate and lead to cessation of biogas production at an elevated ammonium concentration at which acetoclastic methanogens were inhibited.

The Bacterial Population of Neutral Mine Drainage Water of Elizabeth\u2019s Shaft (Slovinky, Slovakia)

Although neutral mine drainage is the less frequent subject of the interest than acid mine drainage, it can have adverse environmental effects caused mainly by precipitation of dissolved Fe. The aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth’s shaft, Slovinky (Slovakia). Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identified iron–oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008–2014. Using 454 pyrosequencing, there were identified members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chloroflexi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron–oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth’s shaft drainage water reflects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.

Antibiotic-free poultry production based on innovative nutritional programs with the involvement of probiotics

EU banned antibiotic growth promoters (AGP) for farm animals and poultry since 2006 in relation to the problem of drug resistance. This requires alternative products for equally efficient prevention and treatment of certain alimentary poultry diseases. One of the most actual trends is the development of innovative nutritional strategies for poultry providing an effective symbiosis between the host and its intestinal microbiota. The study presented was aimed at the comparative evaluation of productivity, nutritive value of meat, and composition of intestinal microbial populations in broiler chicks fed different diets (corn - soybean meal, wheat - sunflower cake, barley - sunflower cake) supplemented with AGP or a probiotic (cellulolytic and lactic microorganisms). In three trials straight-run Cobb 500 broilers reared from 1 to 36 days of age were fed these diets supplemented with bacitracin from 1 to 29 days of age (control) or probiotic preparation from 1 to 36 days of age (70 birds per dietary treatment in each trial). There were no differences in live bodyweight and carcass yield between the treatments in all three trials. In the two trials with sunflower cake, protein content in breast meat was significantly higher by in birds fed probiotic in compare to birds fed AGP (by 10.0 and 6.8%, p<0.05), while fat content in thigh meat was lower by 12.0% (p<0.05) and 14.1% (p<0.01), respectively. Content of amino acids in meat did not differ. Vitamin content in the poultry meat of the experimental groups was significantly higher compared to control (p<0.001). The resulting concentrations of bacitracin in meat in control treatments (no more than 0.02 U/g) did not exceed local legislative limitations. The substitution of the probiotic for AGP beneficially affected the composition of bacterial populations in the duodenum and cecae determined using T-RFLP analysis. It was concluded that the supplementation of diets with probiotic allows to produce antibiotic-free broiler meat without detrimental effects on the productive performance.