Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community

Streptococcus thermophilus JM905-Strain Carbon Source Utilization and Its Fermented Milk Metabolic Profile at Different Fermentation Stages

The metabolic utilization of different carbon sources by Streptococcus thermophilus JM905(S. thermophilus JM905) was determined using a high-throughput microbial phenotyping system, and changes in fermentation characteristics of S. thermophilus JM905 fermented milk were investigated at different fermentation periods, with changes in pH, water-holding capacity, viscosity, nuisance odor, and viable bacteria count being used to define the fermentation characteristics of the strain. Changes in the key metabolites, 2-hydroxybutyric acid, folic acid, L-lactic acid, D-glycerol-D-galactose-heptanol, (R)-leucine, L-aspartic acid, L-proline, D-arginine, L-isoleucine, hydra starch, L-lysine, L-tryptophan, and D-galactose, were clarified. Correspondingly, the fermented milk protein, amino acid, and fermented milk fat quality nutrient contents were determined to be 3.78 ± 0.054 g per 100 g, 3.405 ± 0.0234 g per 100 mL, and 0.161 ± 0.0030 g per 100 g, respectively. This study addressed strain carbon source utilization, changes in fermentation characteristics and metabolites during fermentation, with the aim of investigating the link between fermentation characteristics and metabolite quality components of Streptococcus thermophilus JM905 and its fermented milk with fermentation potential and to provide a useful reference for the screening of superior fermentation strains.

Remediation of Soils Contaminated by Fluoride Using a Fermentation Product of Seaweed (Eucheuma cottonii)

This study investigated the efficacy of fermented seaweed (Eucheuma cottonii) on the remediation of fluoride-contaminated soil. The soil was amended with either 1.25, 3.0, or 5.0% (w/w) fermented seaweed (FSW), parallel with the controls (0%). The amendment improved the physicochemical properties of the soil particularly pH regulated from strong alkaline (9.3) to neutral (7.0) which is essential for germination, crop growth, and yield. The amount of water soluble-fluoride (Ws-F) dropped from 81.7 ± 3.1 mg/kg to 42.7 ± 2.4, 33.7 ± 1.2, 19.6 ± 0.9, and 12 ± 1.3 mg/kg following 0, 1.25, 3, and 5% amendment dosage, respectively. Most of the Ws-F was converted into exchangeable fluoride (Ex-F) and to fluoride-bound to iron and manganese (Fe/Mn-F). Furthermore, the amendment also enhanced microbial mass and diversity in the soil. The FSW contains organic acids which participate in ionic bonding with the multivalent cations in the soil. The formed compound participates in ion exchange with clay or with anionic adsorption to positively charged clay sites at the edges. This interaction is further essential for enhancing the fluoride holding capacity of the soil. The use of seaweed reduced the bioavailability of fluoride in the agricultural soils and had positive effects on promoting soil fertility. However, further studies to observe its effects on crop performance is of significance.

Effects of salinomycin and ethanamizuril on the three microbial communities in vivo and in vitro

The fate of a drug is not only the process of drug metabolism in vivo and in vitro but also the homeostasis of drug-exposed microbial communities may be disturbed. Anticoccidial drugs are widely used to combat the detrimental effects of protozoan parasites in the poultry industry. Salinomycin and ethanamizuril belong to two different classes of anticoccidial drugs. The effect of salinomycin and ethanamizuril on the microbiota of cecal content, manure compost, and soil remains unknown. Our results showed that although both salinomycin and ethanamizuril treatments suppressed some opportunistic pathogens, they failed to repair the great changes in chicken cecal microbial compositions caused by coccidia infection. Subsequently, the metabolite5 profiling of cecal content by LC-MS/MS analyses confirmed the great impact of coccidia infection on chicken cecum and showed that histidine metabolism may be the main action pathway of salinomycin, and aminoacyl tRNA biosynthesis may be the major regulatory mechanism of ethanamizuril. The microbial community of manure compost showed a mild response to ethanamizuril treatment, but ethanamizuril in soil could promote Actinobacteria reproduction, which may inhibit other taxonomic bacteria. When the soil and manure were exposed to salinomycin, the Proteobacteria abundance of microbial communities showed a significant increase, which suggested that salinomycin may improve the ability of the microbiota to utilize carbon sources. This hypothesis was confirmed by a BIOLOG ECO microplate analysis. In the animal model of coccidia infection, the treatment of salinomycin and ethanamizuril may reconstruct a new equilibrium of the intestinal microbiota. In an in vitro environment, the effect of ethanamizuril on composting and soil microbiota seems to be slight. However, salinomycin has a great impact on the microbial communities of manure composting and soil. In particular, the promoting effect of salinomycin on Proteobacteria phylum should be further concerned. In general, salinomycin and ethanamizuril have diverse effects on various microbial communities.

Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Enhancing hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX) remediation through water-dispersible Microbacterium esteraromaticum granules

In the current manuscript, we explored the remediation potential of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by Gram-positive Microbacterium esteraromaticum 12849. The strain detoxified 70.9 and 63.93% RDX in minimal nutrient medium and soil, respectively. Subsequently, the strain 12849 was formulated in form of water-dispersible granules (WDG) using talcum powder and alginic acid as inert ingredients. During the microcosm study, WDG exhibited 8.98% enhanced RDX degradation in contrast to the unformulated Microbacterium esteraromaticum. The LC-MS analysis revealed the presence of two intermediates, namely N-methyl-N, N'-dinitromethanediamine, and methylenedintramine, during the RDX degradation by strain 12849 in soil. Interestingly, no significant difference was observed in the rate of RDX degradation by strain 12849 due to the formulation process. The first-order kinetics was seen in RDX degradation with a degradation coefficient of 0.04 and 0.0339 day^-1 by formulated and unformulated strain, respectively. The current investigation implies M. esteraromaticum as a potential microbe for RDX degradation and opens up the possibility of exploiting it in its effective WDG form for explosive contaminated sites.

Metagenomics analysis of bacterial structure communities within natural biofilm

The bacterial profiles of natural household biofilm have not been widely investigated. The majorities of these bacterial lineages are not cultivable. Thus, this study aims (i) to enumerate some potential bacterial lineages using culture based method within biofilm samples and confirmed using Biolog GEN III and polymerase chain reaction (PCR). (ii) To investigate the bacterial profiles of communities in two biofilm samples using next generation sequencing (NGS). Forty biofilm samples were cultured and colonies of each selected prevailing potential lineages (E. coli, Salmonella entrica, Pseudomonas aeruginosa, Staphylococcus aureus and Listeria monocytogenes) were selected for confirmation. From obtained results, the counts of the tested bacterial lineages in kitchen biofilm samples were greater than those in bathroom samples. Precision of PCR was higher than Biolog GEN III to confirm the bacterial isolates. Using NGS analysis, the results revealed that a total of 110,554 operational taxonomic units (OTUs) were obtained for two biofilm samples, representing kitchen and bathroom biofilm samples. The numbers of phyla in the kitchen biofilm sample (35 OTUs) was higher than that in bathroom sample (18 OTUs). A total of 435 genera were observed in the bathroom biofilm sample compared to only 256 in the kitchen sample. Evidences have shown that the empirical gadgets for biofilm investigation are becoming convenient and affordable. Many distinct bacterial lineages observed in biofilm are one of the most significant issues that threaten human health and lead to disease outbreaks.

Characterization of mercury-reducing potential bacteria isolated from Keputih non-active sanitary landfill leachate, Surabaya, Indonesia under different saline conditions

The objectives of this research were to identify the capability of bacteria isolated from a non-active sanitary landfill to remove mercury under different saline conditions and to understand the removal kinetics. The mercury concentrations used in the minimum inhibitory concentration (MIC) test were 0, 5, 10, 15 and 20 mg/L. The capability of one selected bacterium from the MIC test to remove mercury under different saline conditions (0, 10, 20, and 30‰) was also tested. Five indigenous bacteria were isolated from the Keputih non-active sanitary landfill, Surabaya, Indonesia. The MICs of mercury for FA-1, FA-2, FA-3, FA-4, and FA-5 were 5, 10, 5, 5, and 5 mg/L, respectively. Based on biochemical characterization, FA-2 was identified as Pseudomonas aeruginosa. The isolate of P. aeruginosa was capable of removing Hg under different saline conditions. The optimum saline condition for P. aeruginosa to remove Hg was 10‰, with a removal percentage of 99.7 ± 0.18% following pseudo-second-order kinetics (R² = 0.9939) with k₂ = 2.0059 mg substrate/g adsorbent/hr. Hence, isolated P. aeruginosa showed potential for the bioremediation of mercury-contaminated areas.

Application of catastrophe theory in comprehensive ecological security assessment of plastic greenhouse soil contaminated by phthalate esters

Large amount of phthalate esters (PAEs) used as plasticizers in polyvinyl chloride (PVC) products has caused ubiquitous contamination to the environment and potential ecology security risk all around the world, especially in places plastic films were indispensably utilized due to the widely proposing of facility agriculture in China. A case of PAEs contamination in four suburb areas of Nanjing was analyzed and discussed in this study. A new frame work has been put forward based on multi-criteria evaluation model and mathematical method of catastrophe theory, using farming work, laboratory determination and relevant environmental standards to measure the ecology security risk of PAEs in study areas. The factors were selected based on the availability of the data and the local conditions. The assessment model involves the contamination status of PAEs in soil and vegetables, the contamination effects of PAEs to human and soil organisms and the contamination source of PAEs from plastic films and other products in the four study facility agriculture areas. An evaluation system of the model was composed of thirteen mesosphere indicators and twenty-five underlying indicators including total PAEs concentration in soils, single PAE concentration in soils, total PAEs concentrations in roots, leafy, solanaceous and stem vegetables, PAE human risks, soil microbial counts, microorganism diversity indices, atmospheric deposition of PAEs, whether sewage wastewater irrigation, planting mode of the facility agriculture areas and climate condition of study areas. The modified evaluation system was used in the assessment of ecology security of the same place based on the data of 2012, and the results suggested that the ecology security indicators were reliable and were agree well with the practical situation of the study areas. The results could provide guidance for the application of health risk assessment of soil environment for the strong objectivity of catastrophe theory compared with other evaluation methods.

Analysis on Metabolic Functions of Stored Rice Microbial Communities by BIOLOG ECO Microplates

Microbial contamination has been a pervasive issue during the rice storage and triggers extensive researches. The metabolism of microorganisms was proved as an indicator to mirror the degree of microbial contamination. It is necessary to develop a scientific method to analyze the metabolism of rice microbial communities, thereby monitoring the microbial contamination. In this study, the metabolism of rice microbial communities in different storing-year were investigated by BIOLOG ECO microplates. The three rice samples were respectively stored for 1-3 years. The related indicators of BIOLOG ECO microplates were determined, including average well-color development (AWCD) of carbon sources and three metabolic functional diversity indices. The results showed that there were significant differences in the AWCD of all carbon sources among the three rice microbial communities (p < 0.05), and the functional diversity indices except Simpson index showed significant differences (p < 0.05). Additionally, the three rice microbial communities differed significantly in the metabolic utilization of carboxylic acids and miscellaneous (p < 0.05), and there were, however, no significant differences in the other four types of carbon sources. Furthermore, principal component analysis revealed that the microbial communities of stored rice had obviously different metabolic functions in different storage period. Therefore, the study indicated that the BIOLOG ECO microplate was applicable to evaluate the metabolic functions of rice microbial communities, and carboxylic acids and miscellaneous were two crucial parameters of carbon sources to identify the metabolic differences of microbial communities, a case in which it reflected the conditions of rice microbial contamination.

Differences in carbon source usage by dental plaque in children with and without early childhood caries

Early childhood caries (ECC) is a considerable pediatric and public health problem worldwide. Preceding studies have focused primarily on bacterial diversity at the taxonomic level. Although these studies have provided significant information regarding the connection between dental caries and oral microbiomes, further comprehension of this microbial community’s ecological relevance is limited. This study identified the carbon source metabolic differences in dental plaque between children with and without ECC. We compared the microbial community functional diversity in 18 caries-free subjects with 18 severe ECC patients based on sole carbon source usage using a Biolog assay. The anaerobic microbial community in the ECC patients displayed greater metabolic activity than that of the control group. Specific carbon source metabolism differed significantly between the two groups. Subjects from the two groups were well distinguished by cluster and principal component analyses based on discriminative carbon sources. Our results implied that the microbial functional diversity between the ECC patients and healthy subjects differed significantly. In addition, the Biolog assay furthered our understanding of oral microbiomes as a composite of functional abilities, thus enabling us to identify the ecologically relevant functional differences among oral microbial communities.