[Sanitary-bacteriological characteristics of the soil sprinkled with liquid manure ("shirin-suu")].
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Animals↗
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[The qualitative change of the bacteria-flora in arable soils by manuring with definite organic substances. 1st information (author's transl)].
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Actinomycetales↗
Detoxifying biotransformation of chloramphenicol by Exiguobacterium sp. CAP4 and its bioaugmentation of chloramphenicol biodegradation in simulated wastewater.
The extensive use of chloramphenicol (CAP) in livestock leads the accumulation of CAP in livestock manures, threatening environmental and human health. Therefore, eliminating or reducing CAP concentration in manures before its re-utilization and application through microbial remediation is necessary. Exiguobacterium sp. CAP4, isolated from the plastisphere in duck manures, was capable of degrading CAP with the biodegradation efficiency of 97.8 % at initial CAP concentration of 5 mg/L within 4 days. A total of twenty-four biotransformation products were determined, including two novel transformation products, TP166 and TP203, enriched the integrity of CAP biodegradation pathways. Furthermore, the biotransformation process was proposed as a detoxifying process through biotransformation products toxicity evaluation. Notably, Exiguobacterium sp. CAP4 successfully colonized in the cow manures after inoculation, and bioaugmented the biodegradation of CAP in virgin cow manures. This study significantly extended our understanding of the CAP biotransformation fate, and provided a promising bacterial strain for bioremediation of CAP containing wastewater in situ.
Chloramphenicol↗
Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.
Culture-independent techniques are playing a major role in exploring unique and novel microbial communities from complex ecosystems, leading to an outstanding impact on our basic understanding of the tree of life. Microbial communities are not extensively studied in layer chicken housing environments, particularly from the point of view of taxa carrying antimicrobial resistance genes, virulence genes and their functional potential. This study aimed to extract metagenomic-assembled genomes (MAGs) from the Illumina short-reads shotgun metagenomics sequenced data that originated from an Alberta poultry barn environment and then to study host tracking of antimicrobial resistance genes (ARGs) and the roles of genes involved in functions related to ammonia production, short-chain fatty acid (SCFA)-related pathways, sulfur metabolism, methane emission, stress and disinfectant-related pathways. A total of 251 high-quality MAGs were extracted, including 249 bacterial and two archaeal genomes from sequencing data of 30 metagenomic sequencing samples comprising 15 air and 15 manure samples collected from 15-layer farms. Interestingly 22 bacterial MAGs were not classified to species levels using GTDB-based classification. ARGs were mainly harbored by the genera Staphylococcus, Alistepes, Romboutsia, and Enterococcus. Bacteroides is a main taxon carrying ARGs in air samples. Ammonia production-related genes were mainly tracked in Staphylococcus, Ruminococcus and Corynebacterium genera. The assimilatory sulfate reduction genes responsible for sulfur metabolism and hydrogenase-related genes responsible for hydrogen cycling were traced from Staphylococcus originated from both air and manure. The current study provides characterizations of MAGs from a poultry housing environment by linking microbial taxa with virulence, resistance, and metabolic functions. The findings emphasize the role of microbiota in shaping gas emissions and AMR, with implications for poultry health and worker's safety and the ultimate aim of sustainable poultry production.
Animals↗
Field concentrations and persistence of polybrominated biphenyls in soils and solubility of PBB in natural waters.
Soil samples were collected from 28 fields which had received manure from Michigan's most highly contaminated dairy herds. The number of fields in each concentration range of PBB in soil were: 2, not detectable; 15, 0.0 to 8.0 ppb; 6, 14-102 ppb, and 5, 153 to 371 ppb. Plant tissue sampled from the 10 most highly contaminated fields contained no detectable PBB. No evidence of significant degradation of PBB was noted after 1 year incubation in soil. When 14C hexabromobiphenyl and heptabromobiphenyl isomers were incubated in soil less than 0.2% of the 14C was volatilized. Also gas chromatographic analysis of soil extracts showed no difference in recovery of the six major PBB isomers between sterilized and nonsterilized soil. Analysis of these extracts by thin layer chromatography and autoradiography showed no 14C-PBB intermediates. Photodegradation products of the major hexa- and heptabromobiphenyl isomers showed more but still minor (approximately 3%) biodegradation in soil. Much of the photodegradation products appeared bound to soil, since these products could not be extracted from soil. Photodegradation does not appear to be a significant fate of PBB in manures spread on fields since no change was noted in the relative concentrations of isomers in soil samples from our field survey. Studies with distilled, tap, river, and soil waters showed that PBB solubility was markedly influenced by water composition.
Animals↗
[Residual action of Neguvon, Neocidol, Nuvanol and Dursban on the imaginal and larval stages of the housefly].
It is shown that Dursban, Neocydol and Neguvon preparations, mixed with swine manure at amounts of 500 mg/kg, kill 100 per cent the larvae of the domestic fly up to the 30th, 20th and 10th day, respectively, while the Neguvon and Neocydol preparations in cattle manure, up to the 10th day. Lower concentrations possess a residual effect of a shorter duration. It is also shown that the type of the surfaces and the pH of the mater on which the preparations are placed markedly affect the inctesicide activity and the residual effect of the preparations. The highest activity and the longest residual effect manifest preparations that have been placed on surfaces with a low absorption capacity. The highest effect has been achieved when the preparations are smeared on glass, a lower one, when placed on wood, and the poorest, when laid on mortar.
Animals↗
Genetic Diversity and Population Structure of Zambian Indigenous Cattle.
A study was conducted to determine the genetic diversity of Zambian indigenous cattle using microsatellites. In Zambia, cattle provide draft power, food, manure and generate income. DNA extraction followed the Qiagen protocol, and Arlequin V3.0 was used for data analysis. 72 unrelated animals from three regions, Eastern (Angoni), Southern (Tonga) and Western (Barotse), were sampled. 315 alleles observed were higher in TGLA 263 (106 bp) with 0.861, 0.824 and 0.753, BMS650 (160 bp) with 0.710 and SPS 115 (248 bp) with 0.581, 0.710 and 0.794 for Angoni, Tonga and Barotse, respectively. Effective allele frequency was 4.521 ± 0.351, 4.246 ± 0.299 and 3.888 ± 0.289 for Angoni, Tonga and Barotse, respectively. Global deficit of heterozygotes across populations (Fit) amounted to 4.2%. Overall mean deficit of heterozygotes (Fis = 1%), genetic differentiation among breeds (Fst = 3.2%),, and genetic flow between populations (Nm = 11.3) ranged from RM 067 (40.564) to BLI (3.016). Analysis of molecular variance revealed 2.7% genetic variation among populations and 97.3% within the cattle population, with a mean genetic diversity of 0.753. Structure analysis (PCoA) demonstrated the presence of two subpopulations in which all three populations are represented and these two groups showed evidence of substructuring. In the Bayesian analysis, Tonga and Barotse populations were clustered together, while the Angoni were separated from the rest of the populations in K = 2. There was no evidence of panmixia and linkage equilibrium; the VD (9.153) value is greater than L (5.929), indicating that the population was in equilibrium. This study presents a comprehensive genetic characterisation of indigenous cattle in Zambia, which is important for further studies.
Animals↗
Coupling of spectroscopy and nitrogen-oxygen isotopes unveils the mechanisms of dissolved organic matter and nitrate pollution in lakes within the agro-pastoral transition zone.
Lakes in arid and semi-arid regions are subjected to severe ecological stress, such as organic pollution, eutrophication, and salinization, due to climate change and human activities. This study investigates Chagannur Lake, a typical arid-region lake that is representative and ecologically sensitive in Northern China's agro-pastoral ecotone, to uncover its pollution characteristics and mechanisms. We employed fluorescence spectroscopy and stable isotope analysis to trace dissolved organic matter (DOM) and nitrate sources. The DOM composition was dominated by microbial metabolic byproducts and protein-like substances, suggesting that microbial processes are key to organic matter transformation. Source apportionment revealed that pollutants primarily originated from livestock and poultry manure (37.6 %), agricultural fertilizers (35.6 %), and soil erosion (24.7 %), with agricultural fertilizers contributing most significantly in the Gogstai River (63.3 %). A structural equation model (SEM) coupling spectral and mass spectrometric data revealed that microbial transformation significantly impairs the lake's self-purification capacity, thereby promoting pollutant accumulation (path coefficient = 0.91,*p < 0.05). Moreover, microbial processes link endogenous and exogenous pollution, a mechanism effectively traced by isotopic and fluorescence indices (path coefficient = 0.55, ⁎⁎p < 0.01). These findings enhance the understanding of pollution sources and transformation mechanisms in arid-region lakes and offer foundational theoretical support for policymakers engaged in pollution control strategies.
Lakes↗
Unraveling anaerobic indole degradation in an acclimated sludge consortium: Candidate pathways and microbial division of labor inferred from metagenomic and metatranscriptomic analyses.
Indole is a widespread nitrogen-containing heterocyclic compound in manure, sludge, and wastewater systems, yet the enzymes and microbial populations involved in its anaerobic transformation remain poorly resolved. Here, we established a long-term acclimated anaerobic sludge consortium and combined degradation assays, metabolite profiling, metatranscriptomics, and genome-resolved metagenomics to investigate the functional basis of anaerobic indole degradation. After 120 days of acclimation, the consortium stably degraded 100 mg/L indole, whereas skatole was not effectively removed under the same strategy, indicating substrate-specific adaptation of the microbial community. Metabolite profiling detected oxindole, dioxindole, isatin, and anthranilic acid, supporting a putative transformation route involving pyrrole-ring oxidation and ring cleavage toward anthranilate-like intermediates. Metatranscriptomic analysis identified 16,660 differentially expressed genes after indole addition, with strong transcriptional responses involving oxidoreductases, hydrolases, cofactor-dependent redox metabolism, aromatic-CoA-related metabolism, and methane metabolism-associated pathways. Transcriptional responses highlighted the xanthine dehydrogenase-like molybdenum-enzyme system and isatin hydrolase as candidate contributors to upstream indole transformation, whereas those of abmG-like, bcrC, and oah genes were consistent with possible anthranilic acid activation and downstream CoA-type processing. MAG-resolved analysis further suggested that these candidate functions may be distributed among populations affiliated with Bacteroidota, Chloroflexota, Desulfobacterota, and Methanobacterium. Together, these findings establish a stable anaerobic indole-degrading consortium and provide a testable functional framework for syntrophic interactions linking upstream indole transformation, aromatic-CoA metabolism, and methanogenesis-associated carbon flow.
Anaerobic degradation↗
Deodorization of pig feces by actinomycetes.
Peg feces, a malodorous substance causing environmental pollution, were completely deodorized within 2 days by Streptomyces. The optimum conditions for deodorization were as follows: pH, 8.6 to 10; temperature, 35 to 40 degrees C; moisture content, 42 to 63%; and minimum amount of inoculum, 2 g of seed culture per 10 g of fresh feces. Many kinds of microorganisms were isolated from the deodorized feces, of which only actinomycetes were found to have the ability to deodorize. Two strains with strong deodorizing activity were identified as Streptomyces griseus and Streptomyces antibioticus. The low-molecular-weight fatty acids, which are the specific malodorous agents of pig feces, scarcely could be found in feces deodorized by the isolated strains. Chemical analysis showed that the deodorized feces are useful as manure.
Animals↗
A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate.
BACKGROUND: Phytate is the primary phosphorus storage molecule of plants and plays a major role in animal nutrition. To enhance phosphate availability and absorption in livestock, and to reduce eutrophication by liquid manure, bacterial phytases are often added to animal feed. The dephosphorylated form of phytate, the polyol myo-inositol (myo-Ins) with multiple functions in eukaryotes, is metabolized by approximately 30% of all bacterial species. RESULTS: Here, we employed a culturomics approach to identify possible metabolic interactions between phytase-producing and myo-Ins degrading bacteria in intestinal samples from pigs. Selective cultivation revealed an unexpectedly high abundance of myo-Ins degrading bacteria, suggesting substantial phytate dephosphorylation in the pig gut. Phytase activity assays performed on gut isolates showed a high degree of variability, suggesting the presence of a diverse set of phytases yet to be characterized. Furthermore, using supernatants of phytase-positive gut strains cultivated in the presence of phytate, we observed cross-feeding of myo-Ins from phytase producers to phytase-negative strains, including the pathogen Salmonella enterica serovar Typhimurium. CONCLUSIONS: The data demonstrate that a wide range of commensal bacteria can potentially benefit from phytase activity by utilizing myo-Ins, released through phytate hydrolysis, as a growth substrate. Video Abstract.
Animals↗
Genome-guided isolation and characterization of a novel bacteriophage infecting Escherichia coli reveal a putative new genus.
We have isolated and characterized a novel bacteriophage termed Jab, with lytic activity against multidrug-resistant clinical isolates of Escherichia coli. Phage Jab was identified from liquid manure by means of metagenome sequencing of a phage community enrichment using an E. coli clinical isolate ECH07 as host. The initial enrichment was composed of four phages, of which phage Jab represented only a minute fraction (less than 1%). Jab isolation strategy comprised a targeted approach using iterative replication rounds while equipping ECH07 with resistance against the numerically dominant phages coupled with a subsequent host switch to E. coli BL21. Whole-genome sequence analysis revealed only a remote evolutionary distance to known phages within the subfamily Vequintavirinae. The dsDNA genome of phage Jab comprises 142,100 bp (GC content 40.09%) and encodes 264 proteins and five transfer RNAs (tRNAs). No lysogeny-associated proteins were detected, suggesting an obligate lytic lifestyle. In silico genome analysis revealed the presence of at least four putative depolymerases. The closest homology of phage Jab is with members of the new genus Septuagintavirus with around 34% nucleotide identity. VIRIDIC and network analyses strongly suggest that phage Jab belongs to a putative novel genus. The host range of phage Jab is likely restricted to E. coli, displaying a moderately narrow host range (i.e., productive lysis in 8 out of 27 isolates tested). Notably, transmission electron microscopy (TEM) revealed the occurrence of conspicuous unique spherical structures attached at the end of the tail fibers when propagated on BL21 but not when propagated on ECH07. Although their function remains enigmatic, the possible role of those structures as a bacterial (vesicle-based) defense mechanism warrants further investigation.
Escherichia coli↗
[Effectiveness of paraformaldehyde foam in continuous disinfection of poultry bedding and dried liquid waste of pigs].
In laboratory experiments 24-hour cultures of poultry strains E. coli, Staphylococcus, Pseudomonas on paper carriers without an agar coat and with it, after 6-hour exposure in dilutions from 10(-4) to 0, were devitalized by paraformaldehyde foam. The Bacillus strain was devitalized only after 24-hour exposure. After adding paraformaldehyde foam in an amount of 0.6% of the weight into litter under a multiplier flock of layers four months before expedition, and after adding paraformaldehyde foam in an amount of 5% and 10% of the weight into the litter for chick broilers, microbial contamination of the litter did not decrease in comparison with the control. 24-hour old cultures of tested microbial strains on carriers were not devitalized after 24-hour exposure in a mixture to litter and paraformaldehyde foam not even after adjusting the volume ratio of mixing to 1 : 9. The disinfecting effect on microbes growing in End's agar and in blood agar with crystal violet was manifested only after adding dried liquid manure of pigs with paraformaldehyde foam at a volume ratio of 50% to 50% after exposure times of 1, 3 and 6.0 weeks. Despite the excellent results obtained with paraformaldehyde foam in disinfecting test-microbes on carriers in laboratory experiments, practical application at a very low volume weight for continuous disinfection of poultry litter is technically unrealistic.
Animals↗
Problems of housefly (Musca domestica) control due to multiresistance to insesticides.
The development of chemical control of Musca domestica on Danish farms 1945--72 is outlined. It has been strongly influenced by successive development of resistance and failure of control by one insecticide after another. The chlorinated hydrocarbons used as residual sprays failed 1947--51. Organophosphorus compounds (OPC) were widely used from 1953, first as strips impregnated with parathion and residual sprays with diazinon. Resistance to OPC was first found in 1955, diazinon was given up in 1957--59 and parathion strips failed in the early '60's. Trichlorfon paint-on baits were widelyused 1958--64 and serious resistance did not appear until 1967, induced by selective pressure of fenthion and dimethoate used as residual sprays. High resistance to the contact effect of trichlorfon now occurs everywhere in Denmark. However, trichlorfon baits are still able to kill many flies. Residual sprays with fenthion, ronnel and fenitrothion were used to some extent 1960--70, but increased resistance reducing the residual effect developed in 2--3 years. Dimethoate was used on the majority of farms 1965--72. It was very effective the first years and resistance increased slowly until 1971--72, when high to extreme dimethoate-resistance became general on Danish farms. This was associated with high resistance to other OPC for fly control, e.g. fenthion, fenitrothion, bromophos, and tetrachlorvinphos, and to carbamates, with the result that no generally effective residual sprays were available. In 1971--72 frequent treatments with synergized pyrethroids have been tried. However, the method is often expensive, and serious resistance problems have appeared on a few farms. In this situation preventive, sanitary measures to eliminate or reduce fly breeding in manure are becoming decisive again, but difficult to practise due to lack of farm labour. The extreme Danish situation is compared with those in other areas, and probable reasons for differences in resistance and control problems are discussed, as well as possibilities for strategies to reduce resistance development.
Animals↗
Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality.
The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.
Animals↗
Isolation of animal viruses from farm livestock waste, soil and water.
Ten porcine enteroviruses, 2 porcine adenoviruses and 1 coronavirus were isolated directly from 32 samples of slurry collected from a pig fattening house. Concentration of the same samples by adsorption with the polyelectrolyte PE-60 yielded 24 porcine enteroviruses and 3 porcine adenoviruses. A porcine enterovirus was isolated, following PE-60 concentration, from 1 to 6 slurry samples from a sow farrowing house. No virus was isolated from 12 samples of slurry from dairy cows nor from 6 slurry samples from a calf-rearing unit. A porcine enterovirus was isolated from soil samples, after concentration with PE-60, collected 1, 2 and 8 days after pig slurry was spread on hay stubble. Two porcine enteroviruses were isolated by membrane filtration from 26 samples of surface run-off from land on which pig slurry was routinely spread, and 2 bovine enteroviruses were isolated from cattle feedlot run-off after adsorption to layers of talc and celite followed by hydroextraction. A porcine enterovirus was also isolated from 1 of 33 samples of surface water collected on farms on which pig slurry was routinely spread on the land, but no virus was isolated from 36 samples of ground water from the same farms. The surface water and ground water samples were concentrated by talc-celite adsorption and hydroextraction.
Adenoviridae↗
The inactivation of viruses in cattle and pig slurry by aeration or treatment with calcium hydroxide.
Porcine enterovirus type 2 or porcine adenovirus type 3 were seeded into samples of pig slurry, and a bovine enterovirus was seeded into cattle slurry, and samples of the slurry were aerated in the laboratory for 21 days. The viruses were inactivated more rapidly in the aerated slurry than in control slurry which was not aerated. The difference in inactivation rate was greatest for the porcine adenovirus and least for the bovine enterovirus. Inactivation of the porcine enterovirus in aerated distilled water and in aerated, autoclaved pig slurry proceeded at a similar rate as in the same materials which were not aerated. Ten samples of aerated slurry were collected from an aeration tank which received weekly additions of raw pig slurry which was sampled at the same times. Each sample yielded a porcine enterovirus after concentration with the polyelectrolyte PE-60, but in three comparative titrations the viral infectivity titre in concentrates of the raw slurry was at least 1000 times greater than in the aerated slurry. Porcine enterovirus type 2 and porcine adenovirus type 3, which were seeded into pig slurry, and a bovine enterovirus seeded into cattle slurry, were inactivated by treatment of the slurry with calcium hydroxide at pH 11.5. The inactivation rate was highest for the bovine enterovirus and lowest for the porcine adenovirus.
Adenoviridae↗
Bacteriological quality of runoff water from pastureland.
Runoff from a cow-calf pasture in eastern Nebraska was monitored for total coliforms (TC), fecal coliforms (FC), and fecal streptococci (FS) during 1976, 1977, and 1978. Bacteriological counts in runoff from both grazed and ungrazed areas generally exceeded recommended water quality standards. The FC group was the best indicator group of the impact of grazing. Rainfall runoff from the grazed area contained 5 to 10 times more FC than runoff from the fenced, ungrazed area. There was little difference in TC counts between the two areas, but FS counts were higher in runoff from the ungrazed area and reflected the contributions from wildlife. Recommended bacteriological water quality standards, developed for point source inputs, may be inappropriate for characterizing nonpoint source pollution from pasture runoff. The FC/FS ratio in pasture runoff was useful in identifying the relative contributions of cattle and wildlife. Ratios below 0.05 were indicative of wildlife sources and ratios above 0.1 were characteristic of grazing cattle. Occasions when the FC/FS ratio of diluted cattle waste exceeded one resulted from differential aftergrowth and die-off between FC and FS. The FC/FS ratio and percentage of Streptococcus bovis in pasture runoff are useful indicators for evaluating the effectiveness of livestock management practices for minimizing bacterial contamination of surface water. The importance of choice of medium for the enumeration of FS in runoff derived from cattle wastes is discussed.
Enterococcus faecalis↗