Isolation and molecular identification of microorganisms isolated from soils contaminated with heavy metals in Mosul city

This research is concerned with organisms isolated from soils contaminated with heavy metals in industrial and residential areas in Mosul, the center of Nineveh Governorate, and the diagnosis of these organisms using molecular biology techniques. Samples were collected from four locations in the city between the industrial area and residential neighborhoods. Soil samples were analyzed, and dilutions were prepared, then the dilutions were grown on potato extract and dextrose (PDA) medium for the development of fungi and Nutrient agar for bacterial development. The dilutions were planted by the casting method by three replications, then the process of purifying the fungal and bacterial colonies was carried out using the traditional methods. To diagnose these pure colonies using PCR technique, colonies of fungi were grown on the medium of PDA, and bacteria were grown on the medium of nutritious broth. As a result, nine fungal species were diagnosed; two of them are new undiagnosed genera that have been registered in the gene bank, four of them contain genetic mutations, and three of them are known and previously diagnosed fungi. As for bacteria, two new strains were isolated and registered in the gene bank among the four diagnosed types. And some of these genera exhibited severe resistance to antibiotics, while others showed moderate resistance, in contrast to the control, which was very sensitive to antibiotics.

Isolation and molecular identification of microorganisms isolated from soils contaminated with heavy metals in Mosul city

This research is concerned with organisms isolated from soils contaminated with heavy metals in industrial and residential areas in the city of Mosul, the center of Nineveh Governorate, and the diagnosis of these organisms using molecular biology technique. Samples were collected from four locations in the city between the industrial area and residential neighborhoods. Soil samples were analyzed and dilutions were prepared, then the dilutions were grown on potato extract and dextrose (PDA) medium for the development of fungi and Nutrient agar for bacterial development. The dilutions were planted by casting method by three replications, then the process of purifying the fungal and bacterial colonies was carried out using the traditional methods. For the purpose of diagnosing these pure colonies using PCR technique, colonies of fungi were grown on the medium of PDA, and bacteria were grown on the medium of nutritious broth. As a result, nine fungal species were diagnosed, two of them are new undiagnosed genera that have been registered in the gene bank, four of them contain genetic mutations, and three of them are known and previously diagnosed fungi. As for bacteria, two new strains were isolated and registered in the gene bank among the four types that were diagnosed. And some of these genera exhibited severe resistance to antibiotics, while others showed moderate resistance, in contrast to the control, which was very sensitive to antibiotics.

Comparative study of methane oxidation within various biofilter media

A considerable fraction of the methane gas generated by landfills can be oxidized by the landfill cover. In this study, the use of disposable sawdust material to utilize and reduce methane gas from the landfill gas (LFG) was demonstrated. Three laboratory scale bioreactors were constructed to reflect the performance of sawdust with respect to the compost and sand (control media). Patterns of methane (CH₄) oxidation were evaluated through the degree of methane oxidation in correlation to the bacterial development in all three media. Later, the use of nutrients during the respiration of the bacteria was interpreted through the analysis of chemical oxygen demand (COD), biochemical oxygen demand (BOD), and biomass growth variations. The overall methane oxidation efficiency in the sawdust medium was 60% with a biomass content of 238 g/m³, whereas the compost medium had 86% methane oxidation efficiency with a 539 g/m³ biomass content. Furthermore, the COS and BOD removal were 2555 mg/L and 332 mg/L from the compost, and 1984 mg/L and 156 mg/L from the sawdust respectively. The overall results of this study indicated that the sawdust material can be used as a biofilter media for methane utilization from the landfill. The oxidation capacity of sawdust could be accelerated by adding necessary nutrients to this media before implementation. Moreover, the oxidation rate variance between compost and sawdust may be eliminated over time due to nutrient exhaustion in the compost media, and/or production of usable carbon with decomposition of the sawdust media.

Comparative study of methane oxidation within various biofilter media

A considerable fraction of the methane gas generated by landfills can be oxidized by the landfill cover. In this study, the use of disposable sawdust material to utilize and reduce methane gas from the landfill gas (LFG) was demonstrated. Three laboratory scale bioreactors were constructed to reflect the performance of sawdust with respect to the compost and sand (control media). Patterns of methane (CH₄) oxidation were evaluated through the degree of methane oxidation in correlation to the bacterial development in all three media. Later, the use of nutrients during the respiration of the bacteria was interpreted through the analysis of chemical oxygen demand (COD), biochemical oxygen demand (BOD), and biomass growth variations. The overall methane oxidation efficiency in the sawdust medium was 60% with a biomass content of 238 g/m³, whereas the compost medium had 86% methane oxidation efficiency with a 539 g/m³ biomass content. Furthermore, the COS and BOD removal were 2555 mg/L and 332 mg/L from the compost, and 1984 mg/L and 156 mg/L from the sawdust respectively. The overall results of this study indicated that the sawdust material can be used as a biofilter media for methane utilization from the landfill. The oxidation capacity of sawdust could be accelerated by adding necessary nutrients to this media before implementation. Moreover, the oxidation rate variance between compost and sawdust may be eliminated over time due to nutrient exhaustion in the compost media, and/or production of usable carbon with decomposition of the sawdust media.

Pathogenesis, Epidemiology and Variants of Melissococcus plutonius (Ex White), the Causal Agent of European Foulbrood

The bacterium Melissococcus plutonius is the etiologic agent of the European foulbrood (EFB), one of the most harmful bacterial diseases that causes the larvae of bees to have an intestinal infection. Although EFB has been known for more than a century and is practically present in all countries where beekeeping is practiced, the disease has been little studied compared to American foulbrood. Recently, great advances have been made to understand the disease and the interaction between the pathogen and its host. This review summarizes the research and advances to understand the disease. First, the morphological characteristics of M. plutonius, the infection process and bacterial development in the gut of the larva are described. Also, the epidemiological distribution of EFB and factors that favor the development of the disease as well as the classification of M. plutonius according its genomic and phenotype characteristics are reported. Finally, the new molecular tools for the study of M. plutonius, possible virulence factors in its genome, the issue of current EFB control measures and possible alternatives to the use of antibiotics are addressed.

A bacterial prophage small peptide counteracts DnaA activities in B. subtilis

Bacteriophages are able to hijack host essential machineries to benefit their fitness and assemble their own progeny. Phage proteins targeting major bacterial pathways can be powerful tools to understand cell functions and have possible applications in human health and industry. Bacterial genomes also harbor cryptic prophages carrying genes that may contribute to their host fitness and properties. The cryptic prophages are mostly transcriptionally silent and most of the functions they encode are not annotated. In B. subtilis, the 48 kb-long skin element is a prophage carrying the yqaF-yqaN operon, which is tightly regulated by the Xre-like repressor sknR. The small yqaH gene potentially encodes the protein YqaH in absence of SknR. It was previously reported that YqaH interacts with the replication initiator DnaA in yeast two-hybrid assay and its expression in B. subtilis causes defects in the chromosomal cycle. In this study, we report that, in addition to DnaA, YqaH interacts with Spo0A, a master regulator of sporulation. To decipher yqaH mode of action, we used the yeast two-hybrid to isolate single mutations in yqaH that separate interactions with DnaA and Spo0A. We isolated mutations that caused loss-of-interaction (LOI) with DnaA but not Spo0A. However, all mutations disrupting the interaction with Spo0A were also DnaA-LOI functions, suggesting that these functions could not be separated. We found that expression YqaH carrying DnaA-LOI mutations affects both chromosome integrity and DnaA-mediated transcription, leading to growth inhibition as well as preventing bacterial development such as sporulation and biofilm formation. These results show that YqaH acts as an antimicrobial peptide in B. subtilis and pave the way for the structural design of mutants with improved antibacterial action.

Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei

In this study, we show that calcium pectinate beads (CPB) allow the formation of 20 µm spherical microcolonies of the probiotic bacteria Lacticaseibacillus paracasei (formerly designated as Lactobacillus paracasei) ATCC334 with a high cell density, reaching more than 10 log (CFU/g). The bacteria within these microcolonies are well structured and adhere to a three-dimensional network made of calcium-pectinate through the synthesis of extracellular polymeric substances (EPS) and thus display a biofilm-like phenotype, an attractive property for their use as probiotics. During bacterial development in the CPB, a coalescence phenomenon arises between neighboring microcolonies accompanied by their peripheral spatialization within the bead. Moreover, the cells of L. paracasei ATCC334 encased in these pectinate beads exhibit increased resistance to acidic stress (pH 1.5), osmotic stress (4.5 M NaCl), the freeze-drying process and combined stresses, simulating the harsh conditions encountered in the gastrointestinal (GI) tract. In vivo, the oral administration of CPB-formulated L. paracasei ATCC334 in mice demonstrated that biofilm-like microcolonies are successfully released from the CPB matrix in the colonic environment. In addition, these CPB-formulated probiotic bacteria display the ability to reduce the severity of a DSS-induced colitis mouse model, with a decrease in colonic mucosal injuries, less inflammation, and reduced weight loss compared to DSS control mice. To conclude, this work paves the way for a new form of probiotic administration in the form of biofilm-like microcolonies with enhanced functionalities.

Бактерии в гифосфере Phytophthora infestans и Alternaria alternata на картофеле

Фитофтороз и альтернариоз, вызываемые фитопатогенами Phytophthora infestans (Mont.) de Bary и Alternaria alternata (Fr.) Keissl., опаснейшие болезни картофеля и томата. Бактериозы картофеля другая опасная проблема как картофеля и томата, так и других с.-х. культур. Нередко возбудители бактериозов, особенно пектолитические бактерии, присутствуют на пораженных растениях вместе с фитопатогенными псевдогрибами и грибами, в том числе с Ph. infestans и A. alternata. Цель исследования оценить присутствие бактерий в гифосфере Phytophthora infestans и Alternaria alternata, а также влияние бактерий на характеристики Ph. infestans и A. alternata. Лабораторные исследования проводили в лаборатории сектора фитопатологии кафедры защиты растений в 2016-2019 годах. Использовали изоляты Ph. infestans T-9, IO-37, 161, A. alternatа Д12 из коллекций МГУ имени М. В. Ломоносова и РГАУ-МСХА имени К. А. Тимирязева. Заражение дисков клубней картофеля сортов Жуковский ранний, Ред Скарлетт, Сарпо Мира, Луговской, Удача проводили в марте 2016 года на фоне потепления погодных условий, температура в лаборатории достигала 25 С. Наличие бактерий в мицелиях исследуемых штаммов Ph. infestans, выращиваемых на овсяном агаре, проверялили посредством световой и электронной микроскопии, а также путем смывов с мицелиев и высевом на специальные питательные среды King B и YDS. В результате исследований доказано наличие пектолитических бактерий в гифосфере Ph. infestans и A. alternatа. При наличии бактерий доказаны лизис и изменения морфологии Ph. infestans и конкурентная экспрессия по локусам глюкозо-6 фосфат изомеразы (Gpi-1) и малатдегидрогеназы (Mdh-2). Инокуляция клубневых дисков четырех сортов картофеля Жуковский ранний, Ред Скарлетт, Сарпо Мира и Удача суспензиями патогенов на фоне повышенной температуры выявили значительное развитие бактериозов уже на первые сутки инкубации. Только на сорте Луговской развитие данные симптомов было в значительной степени подавлено. Мицелии Ph. infestans, A. alternata и пектолитические бактерии их гифосферы образуют на картофеле единый и достаточно стабильный патокомплекс с достаточно сложными взаимосвязями, которые предстоит изучать. Этот патокомплекс способен создать напряженный комбинированный инфекционный фон на картофеле, который в ряде случаев способен представлять для него существенную опасность.Late blight and early blight caused with phytopathogens Phytophthora infestans (Mont.) de Bary and Alternaria alternata (Fr.) Keissl. are the dangerous diseases of potato and tomato. Bacteria are connected to the other dangerous problems of both potato and tomato, and other crops. Often bacteria especially pectolytic bacteria occur on affected plants with phytopathogeneous pseudofungi and fungi with Ph. infestans и A. alternata as well. Objective of our investigation is an estimation of bacterial occurrence in Ph. infestans and A. alternata hyphosphaere as well as influence of bacteria on the Ph. infestans and A. alternate properties. Laboratory investigations were conducted at phytopathology branch of department of plant protection of RSAUMTAA in 2016-2019. Ph. infestans isolates T-9, IO-37, 161, A. alternatа isolate D12 of MSU and RSAUMTAA were investigated. Tuber disc inoculation of potato cultivars Zhukovskiy ranniy, Red Scarlett, Sarpo Mira, Lugovskoy and Udacha was done in 2016 at the temperature about 25 C. Checking bacterial occurrence was done in Ph. infestans mycelia grown at oatmeal agar by means of light and electronic microscopy as well as with transferring on special selective media King B and YDS. As a result, occurrence of pectolytic bacteria was proved to be in Ph. infestans and A. alternatа hyphosphaere. At bacterial occurrence Ph. infestans lysis and morphological deviations as well as competitive expression at the loci of Glucose 6 Phosphate Isomerase (Gpi-1) and Malate Dehydrogenase (Mdh-2) are proved to be developed. Inoculation of potato tuber discs of five cultivars Zhukovskiy ranniy, Red Scarlett, Sarpo Mira and Udacha with suspensions of pathogens at increased temperature revealed essential bacterial development at increased temperature during already first day of incubation. Manifestation of these symptoms was significantly suppressed only on cultivar Lugovskoy. Ph. infestans and A. alternata mycelia as well as pectolytic bacteria of their hyphosphaere form on potato unique and stable pathocomplex with complicated interconnections which should be studied as quickly as possible. This pathocomplex provides strong combined infective phone on potato which is able to be essentially dangerous for this crop.

Evaluation of the ability of alkalophilic bacteria to form a biofilm on the surface of Portland cement-based mortars

This paper investigates bacteria colonisation through biofilm formation, based on the premise that biofilm helps bacteria to have a better development. The aim is to homogenize bacterial growth on recycled concrete aggregates (RCA) to obtain a homogeneous precipitation of calcium carbonate (CaCO3). In previous studies, Bacillus halodurans C-125 was selected to perform biocarbonation on RCA to generate a coat of CaCO3 and diminish water absorption. Contrary to expectations, its poor development led to an heterogeneous CaCO3 precipitation, resulting in an inefficient treatment. Within the framework of this criterion the genetic information of B. halodurans C-125 was compared with a homologous specie “Bacillus subtilis str. 168” to know if it possessed the genes to encode Tas A and Tap A proteins. These proteins consolidate a robust biofilm in Bacillus subtilis str. 168, which promotes bacterial development and adhesion to a surface. Remarkably, B. halodurans C-125 lacks the genes to produce Tas A and Tap A. B. halodurans C-125 was also compared with a group of bacteria isolated from RCA to produce biofilm on MSgg media. Curiously, B. halodurans C-125 did not form a robust biofilm while the bacteria isolated from RCA did. Because of the capacity of the isolated bacteria to form biofilm, they were inoculated on a mortar disk with nutrient and MSgg broth. The results showed traces of bacterial development and precipitation of CaCO3 in form of calcite.

EFEKTIVITAS TEPUNG DAUN SAMBILOTO (Andrographis paniculata nees) SEBAGAI ANTIBAKTERI TERHADAP PERFORMANS BROILER YANG TERINFEKSI Escherichia coli

Rapid broiler development is one of the reason farmers’ choice in raising broiler. The effect broiler become weak because of diseases even come from bacteria or viruses. One of the diseases which are leaded by bacteria which attack broiler oftenly is colibacillosis. The aim of this experiment was to examine the addition of sambiloto leaf meal on feed to the inhibition of bacterial development inside the body of infected Escherichia coli broiler toincrease broilers performance. This experiment used 100 day old chicks (DOC) of Cobb strain which were kept for five weeks. The experiment used completely randomized design with five treatments and four replications consisting of 5 broilers in each replication. The treatments were P0 = control (healthy broiler), P1 = P0 infected with Escherichia coli, P2 = P1 + 0,2% sambiloto leaf meal, P3 = P1 + 0,4% sambiloto leaf meal, P4 = P1 + 0,6% sambiloto leaf meal. The data were analyzed with analysis of variance. The variables observed were feed consumption, body weight gain, final body weight, feed conversion ratio, mortality, and total colony bacteria in broiler excreta. The result showed that sambiloto leaf meals 0.6% have a significant effect in decreasing bacteria. Keywords: Antibacterial, Broilers, Eschericia coli, Performance, Sambiloto leaf meal