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Microorganisms Dec 2021As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the production of animals and crops in a shared environment. The ICLFs in the...
As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the production of animals and crops in a shared environment. The ICLFs in the mid-Atlantic region of the United States practice sustainable manure aging or composting processes to provide an on-farm source of soil amendment for use as natural fertilizer and soil conditioner for crop production. However, crop fertilization by soil incorporation of aged manure or compost may introduce different microbes and alter the soil microbial community. The aim of this study was to characterize the influence of aged or composted manure application on the diversity of soil bacterial community in ICLFs. Soil samples from six ICLFs in Maryland were collected before (pre-crop) and during the season (2020-2021) and used to analyze soil bacterial microbiome by 16S rDNA sequencing. Results showed that both phylum- and genus-level alterations of soil bacterial communities were associated with amendment of aged or composted manure. Particularly, Proteobacteria and Actinobacteria were enriched, while Acidobacteria, Bacteroidetes, Planctomycetes, Firmicutes, and Chloroflexi were reduced after manure product application. Meanwhile, the relative abundance of was decreased, while two zoonotic pathogens, and , were enriched by manure amendments. Overall, animal manure amendment of soil increased the phylogenetic diversity, but reduced the richness and evenness of the soil bacterial communities. Although manure composting management in ICLFs benefits agricultural sustainable production, the amendments altered the soil bacterial communities and were associated with the finding of two major zoonotic bacterial pathogens, which raises the possibility of their potential transfer to fresh horticultural produce crops that may be produced on the manured soils and then subsequently consumed without cooking.
PubMed: 34946188
DOI: 10.3390/microorganisms9122586 -
Journal of Zhejiang University.... Dec 2021Mesocotyl elongation is a key trait influencing seedling emergence and establishment in direct-seeding rice cultivation. The phytohormone gibberellin (GA) has positive...
Mesocotyl elongation is a key trait influencing seedling emergence and establishment in direct-seeding rice cultivation. The phytohormone gibberellin (GA) has positive effects on mesocotyl elongation in rice. However, the physiological and molecular basis underlying the regulation of mesocotyl elongation mediated by GA priming under deep-sowing conditions remains largely unclear. In the present study, we performed a physiological and comprehensive transcriptomic analysis of the function of GA priming in mesocotyl elongation and seedling emergence using a direct-seeding rice cultivar ZH10 at a 5-cm sowing depth. Physiological experiments indicated that GA priming significantly improved rice seedling emergence by increasing the activity of starch-metabolizing enzymes and compatible solute content to supply the energy essential for subsequent development. Transcriptomic analysis revealed 7074 differentially expressed genes (false discovery rate of <0.05, |log(fold change)| of ≥1) after GA priming. Furthermore, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed that genes associated with transcriptional regulation, plant hormone biosynthesis or signaling, and starch and sucrose metabolism were critical for GA-mediated promotion of rice mesocotyl elongation. Further analyses showed that the expression of the transcription factor (TF) genes (v-myb avian myeloblastosis viral oncogene homolog (MYB) alternative splicing 1 (), phytochrome-interacting factors 1 (), teosinte branched 1/cycloidea/proliferating cell factor 5 (), slender 1 (), and mini zinc finger 1 ()), plant hormone biosynthesis or signaling genes (brassinazole-resistant 1 (), ent-kaurenoic acid oxidase-like (), GRETCHEN HAGEN 3.2 (), and small auxin up RNA 36 ()), and starch and sucrose metabolism genes (α-amylases ( and )) was highly correlated with the mesocotyl elongation and deep-sowing tolerance response. These results enhance our understanding of how nutrient metabolism-related substances and genes regulate rice mesocotyl elongation. This may facilitate future studies on related genes and the development of novel rice varieties tolerant to deep sowing.
Topics: Gene Expression Profiling; Gene Expression Regulation, Plant; Gibberellins; Oryza; Plant Growth Regulators; Seedlings; Starch; Sucrose
PubMed: 34904413
DOI: 10.1631/jzus.B2100174 -
General and Comparative Endocrinology Jan 2022During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies...
During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies parental behaviors and related physiological changes across many vertebrates, including birds and mammals. While circulating prolactin levels often fluctuate across breeding, less is known about how relevant target tissues vary in their prolactin responsiveness via prolactin receptor (PRLR) expression. Recent studies have also investigated prolactin (PRL) gene expression outside of the pituitary (i.e., extra-pituitary PRL), but how PRL gene expression varies during parental care in non-pituitary tissue (e.g., hypothalamus, gonads) remains largely unknown. Further, it is unclear if and how tissue-specific PRL and PRLR vary between the sexes during biparental care. To address this, we measured PRL and PRLR gene expression in tissues relevant to parental care, the endocrine reproductive hypothalamic-pituitary- gonadal (HPG) axis and the crop (a tissue with a similar function as the mammalian mammary gland), across various reproductive stages in both sexes of a biparental bird, the rock dove (Columba livia). We also assessed how these genes responded to changes in offspring presence by adding chicks mid-incubation, simulating an early hatch when prolactin levels were still moderately low. We found that pituitary PRL expression showed similar increases as plasma prolactin levels, and detected extra-pituitary PRL in the hypothalamus, gonads and crop. Hypothalamic and gonadal PRLR expression also changed as birds began incubation. Crop PRLR expression correlated with plasma prolactin, peaking when chicks hatched. In response to replacing eggs with a novel chick mid-incubation, hypothalamic and gonadal PRL and PRLR gene expression differed significantly compared to mid-incubation controls, even when plasma prolactin levels did not differ. We also found sex differences in PRL and PRLR that suggest gene expression may allow males to compensate for lower levels in prolactin by upregulating PRLR in all tissues. Overall, this study advances our understanding of how tissue-specific changes in responsiveness to parental hormones may differ across key reproductive transitions, in response to offspring cues, and between the sexes.
Topics: Animals; Columbidae; Crop, Avian; Female; Gene Expression; Hypothalamo-Hypophyseal System; Male; Pituitary Gland; Pituitary-Adrenal System; Prolactin; Receptors, Prolactin
PubMed: 34756919
DOI: 10.1016/j.ygcen.2021.113940 -
Molecular Plant Pathology Jan 2022Several MYB transcription factors are known to play important roles in plant resistance to environmental stressors. However, the mechanism governing the involvement of...
Several MYB transcription factors are known to play important roles in plant resistance to environmental stressors. However, the mechanism governing the involvement of MYBs in regulating tobacco mosaic virus (TMV) resistance in plants is still unclear. In this study, we found that not only is Nicotiana benthamiana MYB4-like involved in defence against TMV, but also that the ethylene pathway participates in MYB4L-mediated resistance. Transcription of NbMYB4L was up-regulated in N. benthamiana infected with TMV. Silencing of NbMYB4L led to intensified TMV replication, whereas overexpression of NbMYB4L induced significant resistance to TMV. Transcription of NbMYB4L was greater in 1-aminocyclopropanecarboxylic acid (ACC, ethylene precursor)-pretreated plants but lower when the ethylene signalling pathway was blocked during TMV infection. Gene expression analysis showed that the transcription of NbMYB4L was largely suppressed in ETHYLENE INSENSITIVE 3-like 1(EIL1)-silenced plants. The results of electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) experiments indicated that NbEIL1 could directly bind to two specific regions of the NbMYB4L promoter. Furthermore, a luciferase assay revealed that NbEIL1 significantly induced the reporter activity of the MYB4L promoter in N. benthamiana. These results point to NbEIL1 functioning as a positive regulator of NbMYB4L transcription in N. benthamiana against TMV. Collectively, our work reveals that EIL1 and MYB4L constitute a coherent feed-forward loop involved in the robust regulation of resistance to TMV in N. benthamiana.
Topics: Ethylenes; Plant Diseases; Nicotiana; Tobacco Mosaic Virus
PubMed: 34633738
DOI: 10.1111/mpp.13139 -
The Science of the Total Environment Feb 2022Anthropogenic pressure such as agricultural pollution globally affects amphibian populations. In this study, a total of 178 different compounds from five agrochemical...
Anthropogenic pressure such as agricultural pollution globally affects amphibian populations. In this study, a total of 178 different compounds from five agrochemical groups (i.e. antimicrobial drugs residues (ADRs), coccidiostats and anthelmintics, heavy metals, mycotoxins and pesticides) were determined monthly, from March until June 2019 in 26 amphibian breeding ponds in Flanders, Belgium. Furthermore, a possible correlation between the number and concentration of selected contaminants that were found and the percentage of arable land within a 200 m radius was studied. Within each group, the highest detected concentrations were obtained for 4-epioxytetracycline (0.422 μg L), levamisole (0.550 μg L), zinc (333.1 μg L), 3-acetyldeoxynivalenol (0.013 μg L), and terbuthylazine (38.7 μg L), respectively, with detection frequencies ranging from 1 (i.e. 3-acetyldeoxynivalenol) to 26 (i.e. zinc) out of 26 ponds. Based on reported acute and chronic ecotoxicological endpoints, detected concentrations of bifenthrin, cadmium, copper, cypermethrin, hexachlorobenzene, mercury, terbuthylazine, and zinc pose a substantial ecological risk to aquatic invertebrates such as Daphnia magna and Ceriodaphnia dubia, which both play a role in the food web and potentially in amphibian disease dynamics. Additionally, the detected concentrations of copper were high enough to exert chronic toxicity in the gray treefrog (Hyla versicolor). The number of detected compounds per pond ranged between 0 and 5 (ADRs), 0 - 2 (coccidiostats and anthelmintics), 1 - 7 (heavy metals), 0 - 4 (mycotoxins), and 0 - 12 (pesticides) across the four months. Furthermore, no significant correlation was demonstrated between the number of detected compounds per pond, as well as the detected concentrations of 4-epioxytetracycline, levamisole, copper, zinc, enniatin B and terbuthylazine, and the percentage of arable land within a 200 m radius. For heavy metals and pesticides, the number of compounds per pond varied significantly between months. Conclusively, amphibian breeding ponds in Flanders were frequently contaminated with agrochemicals, yielding concentrations up to the high μg per liter level, regardless of the percentage surrounding arable land, however showing temporal variation for heavy metals and pesticides. This research also identifies potential hazardous substances which may be added to the European watch list (CD 2018/408/EC) in the future.
Topics: Amphibians; Animals; Environmental Monitoring; Metals, Heavy; Ponds; Water Pollutants, Chemical
PubMed: 34597541
DOI: 10.1016/j.scitotenv.2021.150661 -
Journal of Microbiology, Immunology,... Jun 2022Avian trichomonosis is a parasitic infection that affects a wide range of avian species, including free-ranging and pet birds worldwide, and Trichomonas gallinae has...
BACKGROUND/PURPOSE
Avian trichomonosis is a parasitic infection that affects a wide range of avian species, including free-ranging and pet birds worldwide, and Trichomonas gallinae has been considered as the only causative agent for decades. The sequence of the 5.8S ribosomal RNA with internal transcribed spacer (ITS) regions was widely used for identifying genotypes and determining inter-specific and intra-specific diversity. Moreover, the sequence of Fe-hydrogenase (FeHyd) was proposed as the second genetic marker for providing improved resolution of strain subtyping discrimination. Though the correlation between genetic variability and strain virulence is controversial, FeHyd analyses seemed to be useful to investigate the host or geographic origin of isolates. This study aimed to investigate the genetic characteristics of avian Trichomonas spp.
METHODS
Forty-seven oral swabs and crop lavage fluids were collected from 9 avian genera, which were diagnosed as Trichomonas-positive by microscopy in animal hospitals in Japan, were analyzed.
RESULTS
Genetic analysis of clonal isolates revealed the prevalence of the single genotype, ITS-OBT-Tg-1, by ITS region analysis, while two different subtypes, A2 and novel A3, were suggested by FeHyd gene analysis among Japanese companion birds. Phylogenetic analyses of available ITS sequences obtained from the Asia region (China, Iran, Iraq, and Saudi Arabia) were also preformed, revealing endemic ITS-OBT-Tg-1, ITS-OBT-Tg-2, ITS-OBT-Ttl-1, genotype III, and Saudi Arabia's unique lineages. Furthermore, ITS-OBT-Tg-2 predominance in these countries indicates different strains origination from Japan.
CONCLUSION
This is the first report of the genetic characterization of T. gallinae in Japan with discovery of novel subtype A3.
Topics: Animals; Bird Diseases; Birds; Humans; Japan; Phylogeny; Trichomonas; Trichomonas Infections
PubMed: 34246556
DOI: 10.1016/j.jmii.2021.05.010 -
Animal : An International Journal of... Jul 2021The provision of suitable bedding for rearing broilers is an ongoing challenge for poultry producers. The aim of the present study was to evaluate the effect of using...
The provision of suitable bedding for rearing broilers is an ongoing challenge for poultry producers. The aim of the present study was to evaluate the effect of using different types of crop residues as alternative bedding materials to wheat straw on growth performance, carcass traits, health, and welfare of broilers; moreover, the effects on the bedding and air quality were analyzed. We randomly assigned 180 1-day-old chickens (Cobb 500) across six bedding groups (three replicates of 10 birds each). Chickens in all groups were reared under similar housing conditions. Chickens of one group were reared on a wheat straw bedding (control), whereas those of the remaining five groups were reared on clover straw, cornstalk chips (CS), sugarcane top chips, chopped palm spines (CPS), and corn ear husks. Cornstalk chip and chopped palm spines were associated with the lowest (P < 0.05) ammonia concentrations compared with the remaining beddings. The mean values of bedding moisture percentage (P < 0.05), caking score, and ammonia concentrations (P < 0.05) were decreased with 6-week-old broilers reared on cornstalk chips. At 6 weeks, wheat straw, clover straw, sugarcane top chips and corn ear husks resulted in higher (P < 0.0001) BW and average daily gain compared with CS and CPS. Broilers reared on clover straw bedding showed the best FCR during 4-6 weeks of age (P < 0.01), and those kept on clover straw and sugarcane top chips exhibited the best (P < 0.01) feed conversion ratio (1.61 and 1.64, respectively) during 0-6 weeks of age. The carcass dressing yield, airborne dust concentration, bedding pH, and bacterial counts did not differ among the different bedding materials. The proportions of the drumsticks, gizzards, and abdominal fat of 6-week-old broilers were affected by bedding type (P < 0.05); but the differences among the bedding treatments were small. The mean incidence of footpad dermatitis and breast blisters was significantly less using clover straw. Broilers reared on chopped palm spine had the highest (P < 0.05) heterophil/lymphocyte ratio when compared with their counterparts. Conclusively, using clover straw or cornstalks as an alternative bedding material may be a beneficial strategy and should be highly recommended for rearing broilers.
Topics: Animal Feed; Animals; Bedding and Linens; Chickens; Gizzard, Avian; Poultry; Triticum
PubMed: 34116465
DOI: 10.1016/j.animal.2021.100260 -
Science (New York, N.Y.) May 2021We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type...
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
Topics: Adenosine Triphosphatases; Algorithms; Animals; Biological Evolution; Cell Nucleolus; Cell Nucleus; Centromere; Chromosomes; Chromosomes, Human; DNA-Binding Proteins; Eukaryota; Genome; Genome, Human; Genomics; Heterochromatin; Humans; Interphase; Mitosis; Models, Biological; Multiprotein Complexes; Telomere
PubMed: 34045355
DOI: 10.1126/science.abe2218 -
Communications Biology May 2021Birds are characterized by evolutionary specializations of both locomotion (e.g., flapping flight) and digestive system (toothless, crop, and gizzard), while the...
Birds are characterized by evolutionary specializations of both locomotion (e.g., flapping flight) and digestive system (toothless, crop, and gizzard), while the potential selection pressures responsible for these evolutionary specializations remain unclear. Here we used a recently developed molecular phyloecological method to reconstruct the diets of the ancestral archosaur and of the common ancestor of living birds (CALB). Our results suggest a trophic shift from carnivory to herbivory (fruit, seed, and/or nut eater) at the archosaur-to-bird transition. The evolutionary shift of the CALB to herbivory may have essentially made them become a low-level consumer and, consequently, subject to relatively high predation risk from potential predators such as gliding non-avian maniraptorans, from which birds descended. Under the relatively high predation pressure, ancestral birds with gliding capability may have then evolved not only flapping flight as a possible anti-predator strategy against gliding predatory non-avian maniraptorans but also the specialized digestive system as an evolutionary tradeoff of maximizing foraging efficiency and minimizing predation risk. Our results suggest that the powered flight and specialized digestive system of birds may have evolved as a result of their tropic shift-associated predation pressure.
Topics: Animals; Biological Evolution; Birds; Carnivory; Diet; Dinosaurs; Ecology; Ecosystem; Evolution, Molecular; Herbivory; Phylogeny; Predatory Behavior
PubMed: 33986452
DOI: 10.1038/s42003-021-02067-4 -
Frontiers in Microbiology 2021The pandemic sequence type 131 (ST131) carrying plasmid-mediated colistin resistance genes has emerged worldwide causing extraintestinal infections, with lineages...
The pandemic sequence type 131 (ST131) carrying plasmid-mediated colistin resistance genes has emerged worldwide causing extraintestinal infections, with lineages belonging to three major clades (A, B, and C). Clade B is the most prevalent in animals, contaminating associated meat products, and can be transmitted zoonotically. However, the gene has only been associated with C2 subclade so far. In this study, we performed a genomic investigation of an (strain S802) isolated from a kale crop in Brazil, which exhibited a multidrug-resistant (MDR) profile to clinically significant antimicrobials (i.e., polymyxin, broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Whole-genome sequencing analysis revealed that the S802 strain belonged to serotype O25:H4, ST131/CC131, phylogenetic group B2, and virotype D5. Furthermore, S802 carried the clade B-associated allele, genes encoding resistance to clinically important antimicrobials, metals, and biocides, and was phylogenetically related to human, avian, and swine ST131-22 strains. Additionally, IncHI2-IncQ1, IncF [F2:A-:B1], and ColE1-like plasmids were identified harboring , , and , respectively. The emergence of the ST131-22 sublineage carrying , , and in agricultural soil represents a threat to food and environmental safety. Therefore, a One Health approach to genomic surveillance studies is required to effectively detect and limit the spread of antimicrobial-resistant bacteria and their resistance genes.
PubMed: 33897674
DOI: 10.3389/fmicb.2021.659900