Search results for: bacterial abundance

Authors: Suganya Chandrababu, Dhundy Bastola

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Like in the gut, the subgingival microbiota plays a crucial role in oral hygiene, health, and cariogenic diseases. Human activities like diet, antibiotics, and periodontal treatments alter the bacterial communities, metabolism, and functions in the oral cavity, leading to a dysbiotic state and changes in the plaques of orthodontic patients. Fixed periodontal appliances hinder oral hygiene and cause changes in the dental plaques influencing the subgingival microbiota. However, the microbial species’ diversity and complexity pose a great challenge in understanding the taxa’s community distribution patterns and their role in oral health. In this research, we analyze the subgingival microbial samples from individuals with fixed dental appliances (metal/clear) using an in silico approach. We employ exploratory hypothesis-driven multivariate and regression analysis to shed light on the microbial community and its functional fluctuations due to dental appliances used and identify risks associated with complex disease phenotypes. Our findings confirm the changes in oral microbiota composition due to the presence and type of fixed orthodontal devices. We identified seven main periodontic pathogens, including Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Firmicutes, whose abundances were significantly altered due to the presence and type of fixed appliances used. In the case of metal braces, the abundances of Bacteroidetes, Proteobacteria, Fusobacteria, Candidatus saccharibacteria, and Spirochaetes significantly increased, while the abundance of Firmicutes and Actinobacteria decreased. However, in individuals With clear braces, the abundance of Bacteroidetes and Candidatus saccharibacteria increased. The highest abundance value (P-value=0.004 < 0.05) was observed with Bacteroidetes in individuals with the metal appliance, which is associated with gingivitis, periodontitis, endodontic infections, and odontogenic abscesses. Overall, the bacterial abundances decrease with clear type and increase with metal type of braces. Regression analysis further validated the multivariate analysis of variance (MANOVA) results, supporting the hypothesis that the presence and type of the fixed oral appliances significantly alter the bacterial abundance and composition.

Keywords: oral microbiota, statistical analysis, fixed or-thodontal appliances, bacterial abundance, multivariate analysis, regression analysis

Procedia PDF Downloads 192

Authors: S. Alqarni, J. C. McCann, A. Palladino, J. J. Loor

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Seven fistulated Holstein cows were used from 3 weeks prepartum to 4 weeks postpartum to determine the relative abundance of 7 different species of ruminal microorganisms. The prepartum diet was based on corn silage. In the postpartum, diet included ground corn, grain by-products, and alfalfa haylage. Ruminal digesta were collected at five times: -14, -7, 10, 20, and 28 days around parturition. Total DNA from ruminal digesta was isolated and real-time quantitative PCR was used to determine the relative abundance of bacterial species. Eubacterium ruminantium and Selenomonas ruminantium were not affected by time (P>0.05). Megasphaera elsdenii and Prevotella bryantii increased significantly postpartum (P<0.001). Conversely, Butyrivibrio proteoclasticus decreased gradually from -14 through 28 days (P<0.001). Fibrobacter succinogenes was affected by time being lowest at day 10 (P=0.02) while Anaerovibrio lipolytica recorded the lowest abundance at -7 d followed by an increase by 20 days postpartum (P<0.001). Overall, these results indicate that changes in diet after parturition affect the abundance of ruminal bacteria, particularly M. elsdenii (a lactate-utilizing bacteria) and P. bryantii (a starch-degrading bacteria) which increased markedly after parturition likely as a consequence of a higher concentrate intake.

Keywords: rumen bacteria, transition cows, rumen metabolism, peripartal period

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Authors: Yaling Gou, Sucai Yang, Pengwei Qiao

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Integrated chemical-biological treatment is an attractive alternative to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soil; wherein indigenous bacteria is the key factor for the biodegradation of residual PAHs concentrations after the application of chemical oxidation. However, the systematical study on the impact of persulfate (PS) oxidation on indigenous bacteria as well as PAHs removal is still scarce. In this study, the influences of different PS dosages (1%, 3%, 6%, and 10% [w/w]), as well as various activation methods (native iron, H2O2, alkaline, ferrous iron, and heat) on PAHs removal and indigenous bacteria in highly contaminated aged soil were investigated. Apparent degradation of PAHs in the soil treated with PS oxidation was observed, and the removal efficiency of total PAHs in the soil ranged from 38.28% to 79.97%. The removal efficiency of total PAHs in the soil increased with increasing consumption of PS. However, the bacterial abundance in soil was negatively affected following oxidation for all of the treatments added with PS, with bacterial abundance in the soil decreased by 0.89~2.88 orders of magnitude compared to the untreated soil. Moreover, the number of total bacteria in the soil decreased as PS consumption increased. Different PS activation methods and PS dosages exhibited different influences on the bacterial community composition. Bacteria capable of degrading PAHs under anoxic conditions were composed predominantly by Proteobacteria and Firmicutes. The total amount of Proteobacteria and Firmicutes also decreased with increasing consumption of PS. The results of this study provide important insight into the design of PAHs contaminated soil remediation projects.

Keywords: activation method, chemical oxidation, indigenous bacteria, polycyclic aromatic hydrocarbon

Procedia PDF Downloads 115

Authors: Tamirat Solomon, Tadesse Faltamo, Belete Limani

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This study was conducted on the mountain Damota of Wolaita to assess the abundance and spatial distribution of two locally important indigenous medicinal plants on the mountain landscape. A total of 130 plots measuring 20x20m were established along eight systematically laid transect lines. In each plot, the abundance and distribution of Hagenia abyssinica (tree) and Pentas schiperiana Vatke (shrub) were evaluated. The abundance and distribution of H. abyssinica were evaluated by measuring height and DBH for mature trees and counting seedlings and saplings, whereas the P. schiperiana Vatke was assessed for its abundance and distribution by counting in each plot. In the entire study plots, a total of 485 H. abyssinica and 760 P. schiperiana vatake were recorded. It was observed that the distribution of the species increased while the altitude increased and the highest abundance of the species was recorded at an altitude range between 2332 and 2661m.a.s.l. However, at the altitudes below 2320 m.a.s.l., the species distributions and abundance was decreased, indicating either the ecological preference of the species or the extraction of the local community surrounding the mountain influenced the species. On average, only 28 seedlings/ha of H. abyssinica and 146/ha of P. schiperiana vatke were recorded in the study areas showing the tendency of decline in the abundance and distribution of both species. Finally, we recommend management intervention for the socially important species which are under threat on the mountain landscape.

Keywords: indigenous medicinal plants, H.abyssinic, P. schiperiana, distribution, abundance, socio-economic importance

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Authors: Thalía Moreno-García Malo, Santiago Torres-Ríos, María G. González-Cruz, María M. Hernández-Arroyo, Sergio R. Trejo-Estrada

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Agave atrovirens is the main source of agave sap, the raw material for the production of pulque, an artisanal fermented beverage, traditional since prehispanic times in the highlands of central Mexico. Agave sap is rich in glucose, sucrose and fructooligosaccharides, and strongly differs from agave syrup from A. tequilana, which is mostly a high molecular weight fructan. Agave sap is converted into pulque by a highly diverse microbial community which includes bacteria, yeast and even filamentous fungi. The bacterial diversity has been recently studied. But the composition of consortia derived from directed enrichments differs sharply from the whole fermentative consortium. Using classical microbiology methods, and selective liquid and solid media formulations, either bacterial or fungal consortia were developed and analyzed. Bacterial consortia able to catabolize specific prebiotic saccharides were selected and preserved for future developments. Different media formulations, selective for bacterial genera such as Bifidobacterium, Lactobacillus, Pediococcus, Lactococcus and Enterococcus were also used. For yeast, specific media, osmotic pressure and unique carbon sources were used as selective agents. Results show that most groups are represented in the enrichment cultures; although very few are recoverable from the whole consortium in artisanal pulque. Diversity and abundance vary among consortia. Potential bacterial probiotics obtained from agave sap and agave juices show tolerance to hydrochloric acid, as well as strong antimicrobial activity.

Keywords: Agave, pulque, microbial consortia, prebiotic activity

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Authors: Meenakshi Srivastava, A. K. Mishra

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This study characterizes the metabolic versatility of denitrifying bacterial communities residing in the paddy soil using the GC-MS based Phospholipid Fatty Acid (PLFA) analyses simultaneously with nosZ gene based PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and real time Q-PCR analysis. We have analyzed the abundance of nitrous oxide reductase (nosZ) genes, which was subsequently related to soil PLFA profile and DGGE based denitrifier community structure. Soil denitrifying bacterial community comprised majority or dominance of Ochrobactrum sp. following Cupriavidus and uncultured bacteria strains in paddy soil of selected sites. Initially, we have analyzed the abundance of the nitrous oxide reductase gene (nosZ), which was found to be related with PLFA based lipid profile. Chandauli of Eastern UP, India represented greater amount of lipid content (C18-C20) and denitrifier’s diversity. This study suggests the positive co-relation between soil PLFA profiles, DGGE, and Q-PCR data. Thus, a close networking among metabolic abilities and taxonomic composition of soil microbial communities existed, and subsequently, such work at greater extent could be helpful in managing nutrient dynamics as well as microbial dynamics of paddy soil ecosystem.

Keywords: denaturing gradient gel electrophoresis, DGGE, nitrifying and denitrifying bacteria, PLFA, Q-PCR

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Authors: Ahmad Idi

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The biosynthesis and properties of polyhydroxyalkanoate (PHA) are determined by the bacterial strain and the culture condition. Hence this study elucidates the structure and properties of PHA produced by a newly isolated strain of photosynthetic bacterium, Rhodobacter sphaeroides ADZ101 grown under the optimized culture condition. The properties of the accumulated PHA were determined via FTIR, NMR, TGA, and GCMS analyses. The results showed that acetate and ammonia chloride had the highest PHA accumulation with a ratio of 32.5 mM at neutral pH. The structural analyses showed that the polymer comprises both short and medium-chain length monomers ranging from C5, C13, C14, and C18, as well as the presence of novel PHA monomers. The thermal analysis revealed that the maximum temperature of decomposition occurred at 395°C and 454°C, indicating two major decomposition reactions. Thus this bacterial strain, optimized culture condition, and the abundance of novel monomers enhanced the thermostability of the accumulated PHA.

Keywords: bioplastic polyhydroxyalkanoates Rhodobacter sphaeroides ADZ101 thermostable PHA

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Authors: Luz Hurtado, Rodrigo Rojas, Jaime Romero, Christopher Concha

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The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture which is a Chilean native species of high gastronomic demand and market value. The microbiota was analyzed in terms of diversity and structure using massive Illumina sequencing. The analysis of alpha diversity was performed in samples of G. chilensis larvae of 6, 18 and 32 dph (days post-hatching) and it was observed that there were significant differences (P = 0.05) between the days of culture for the Chao1 index, being the larvae of 18 dph the one with the highest index followed by the larvae of 6 dph, The lowest value for this index was presented in larvae of 32 dph. There were no significant differences in larvae between the days of culture for the Shannon (P=0.0857) and Simpson (P=0.0714) indices. In general, the larvae of G. chilensis have high rates of diversity. When analyzing the beta diversity, a differentiation between the bacterial communities is observed depending on the day of the culture of the larvae. Considering the PCoA elaborated from the unweighted UniFrac statistic, the explained variance was 46.2% (PC1 29.2% and PC2 17.0%) and in the case of the PCoA elaborated with the weighted UniFrac statistic; the explained variance was 65.5% (PC1 41.8% and PC2 23.7%) these differences were significant based on the Permanova statistical analysis (P= 0.002 and 0.037 respectively). When analyzing the taxonomic composition of the microbiota of the larvae in the different days of culture it was observed that at the phyla level the most abundant in the larvae of 6 dph were Proteobacteria (57%) Verrucomicrobia (24%) and Firmicutes (14%), for the larvae of 18 dph the predominant phyla were Proteobacteria (90%), Dependientiae (5%), Actinobacteria (2%) and Plactomyces (2%), for the larvae of 32 dph the phyla that presented the highest relative abundance were Proteobacteria (57%), Firmicutes (29%), Verrucomicrobia (5%) and Actinobacteria (5%), when comparing the larvae between the days it was observed that the phylum Proteobacteria was the most abundant in the samples of larvae of 6, 18 and 32 dph being the larvae of 18 dph those that present the highest relative abundance, the larvae of 6 dph were those that presented the highest relative abundance for the phylum Verrucomicrobia and in the larvae of 32 dph was observed greater abundance of the phylum Firmicutes compared to the other days of larval culture. At the level of genera, those with the highest relative abundance in larvae of 6 dph were Rubritalea (30%), Psychrobacter (28%), staphylococcus (17%) and Ralstonia (10%), for the larvae of 18 dph the genera with the highest abundance were Psychrobacter (47%), Litoreibacter (13%), Nautella (9%) and Cohesibacter (8%), for the larvae of 32 dph the most abundant genera were Alloiococcus (25%), Dialister (14%), Neptunomonas (13%) and Piscirickettsia (11%). When observing the taxonomic composition of the larvae between the days of larval culture, it is observed that there are differences between them.

Keywords: microbiota, diversity, G. Chilensis, larvae

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Authors: Md Ruhul Amin

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This study was conducted in the experimental field of the Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh during November 2017 to May 2018 with a view to understanding the seasonal abundance of the major sucking pests namely thrips, aphid and red spider mite on rose. The findings showed that the thrips started to build up their population from the middle of January with abundance 1.0 leaf⁻¹, increased continuously, reached to the peak level (2.6 leaf⁻¹) in the middle of February and then declined. Aphid started to build up their population from the second week of November with abundance 6.0 leaf⁻¹, increased continuously, reached to the peak level (8.4 leaf⁻¹) in the last week of December and then declined. Mite started to build up their population from the first week of December with abundance 0.8 leaf⁻¹, increased continuously, reached to the peak level (8.2 leaf⁻¹) in the second week of March and then declined. Thrips and mite prevailed until the last week of April, and aphid showed their abundance till last week of May. The daily mean temperature, relative humidity, and rainfall had an insignificant negative correlation with thrips and significant negative correlation with aphid abundance. The daily mean temperature had significant positive, relative humidity had an insignificant positive, and rainfall had an insignificant negative correlation with mite abundance. The multiple linear regression analysis showed that the weather parameters together contributed 38.1, 41.0 and 8.9% abundance on thrips, aphid and mite on rose, respectively and the equations were insignificant.

Keywords: aphid, mite, thrips, weather factors

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Authors: Suchithra V., Shreedhanya, Kavya Menon, Vidya Niranjan

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Skin metagenomics has a wide range of applications with direct relevance to the health of the organism. It gives us insight to the diverse community of microorganisms (the microbiome) harbored on the skin. In the recent years, it has become increasingly apparent that the interaction between skin microbiome and the human body plays a prominent role in immune system development, cancer development, disease pathology, and many other biological implications. Next Generation Sequencing has led to faster and better understanding of environmental organisms and their mutual interactions. This project is studying the human skin microbiome of different individuals having varied skin conditions. Bacterial 16S rRNA data of skin microbiome is downloaded from SRA toolkit provided by NCBI to perform metagenomics analysis. Twelve samples are selected with two controls, and 3 different categories, i.e., sex (male/female), skin type (moist/intermittently moist/sebaceous) and occlusion (occluded/intermittently occluded/exposed). Quality of the data is increased using Cutadapt, and its analysis is done using FastQC. USearch, a tool used to analyze an NGS data, provides a suitable platform to obtain taxonomy classification and abundance of bacteria from the metagenome data. The statistical tool used for analyzing the USearch result is METAGENassist. The results revealed that the top three abundant organisms found were: Prevotella, Corynebacterium, and Anaerococcus. Prevotella is known to be an infectious bacterium found on wound, tooth cavity, etc. Corynebacterium and Anaerococcus are opportunist bacteria responsible for skin odor. This result infers that Prevotella thrives easily in sebaceous skin conditions. Therefore it is better to undergo intermittently occluded treatment such as applying ointments, creams, etc. to treat wound for sebaceous skin type. Exposing the wound should be avoided as it leads to an increase in Prevotella abundance. Moist skin type individuals can opt for occluded or intermittently occluded treatment as they have shown to decrease the abundance of bacteria during treatment.

Keywords: bacterial 16S rRNA , next generation sequencing, skin metagenomics, skin microbiome, taxonomy

Procedia PDF Downloads 171

Authors: Z. Asadgol, A. Nadali, H. Arfaeinia, M. Khalifeh Gholi, R. Fateh, M. Fahiminia

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The present investigation was conducted to detect the type and concentrations of bacterial and fungal bioaerosols in one room (bedroom) of each selected residential building located in different regions of Qom during February 2015 (n=9) to July 2016 (n=11). Moreover, we evaluated the efficiency of negative air ions (NAIs) in bioaerosol reduction in indoor air in residential buildings. In the first step, the mean concentrations of bacterial and fungal in nine sampling sites evaluated in winter were 744 and 579 colony forming units (CFU)/m³, while these values were 1628.6 and 231 CFU/m³ in the 11 sampling sites evaluated in summer, respectively. The most predominant genera between bacterial and fungal in all sampling sites were detected as Micrococcus spp. and Staphylococcus spp. and also, Aspergillus spp. and Penicillium spp., respectively. The 95% and 45% of sampling sites have bacterial and fungal concentrations over the recommended levels, respectively. In the removal step, we achieved a reduction with a range of 38% to 93% for bacterial genera and 25% to 100% for fungal genera by using NAIs. The results suggested that NAI is a highly effective, simple and efficient technique in reducing the bacterial and fungal concentration in the indoor air of residential buildings.

Keywords: bacterial, fungal, negative air ions (NAIs), indoor air, Iran

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Authors: Yan Li, Qingxiang Meng, Bo Zhou, Zhenming Zhou

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The objective of this study was to compare the effects of ensiled mulberry leaves (EML), and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers fed the following 3 diets: a standard TMR diet, standard diet containing EML and standard diet containing SMFP, and the diets had similar protein and energy levels. Bacterial communities in the fecal content were analyzed using Illumina Miseq sequencing of the V4 region of the 16S rRNA gene amplification. Quantitative real-time PCR was used to detect the selected bacterial species in the feces. Most of the sequences were assigned to phyla Firmicutes (56.67%) and Bacteroidetes(35.90%), followed by Proteobacteria(1.86%), Verrucomicrobia(1.80%) and Tenericutes(1.37%). And the predominant genera included the 5-7N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia(1.11%). As for the treatments, no significant differences were observed in Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17) and Tenericutes (p = 0.75). On the genus level, classified genera with high abundance (more than 0.1%) mainly came from two phyla: Bacteroidetes and Firmicutes. Also no differences were observed in most genera level, 5-7N15 (p = 0.21), CF231 (p = 0.62), Oscillospira (p = 0.9), Paludibacter (p = 0.33) and Akkermansia (p = 0.37), except that rc4-4 were lower in the CON and SMFP groups compared to the EML animals (p = 0.02). Additionally, there were no differences in richness estimate and diversity indices (p > 0.16), and treatments had no significant effect on most selected bacterial species in the fecal (p > 0.06), except that Ruminococcus albus were higher in the EML group (p < 0.01) and Streptococcus bovis were lower in the CON group (p < 0.01). In conclusion, diets supplemented with EML and SMFP have little influence on fecal bacterial community composition in finishing steers.

Keywords: fecal bacteria community composition, sequencing, ensiled mulberry leaves (EML), sun-dried mulberry fruit pomace (SMFP)

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Authors: Sarah Almuhayya, Andrew Mcbain, Gavin Humphreys

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Background. The microbiome of the upper respiratory tract (URT) has received less research attention than other body sites. This study aims to investigate the microbial ecology of the human URT with a focus on the antagonism between the corynebacteria and staphylococci. Methods. Mucosal swabs were collected from the anterior nares and nasal turbinates of 20 healthy adult subjects. Genomic DNA amplification targeting the (V4) of the 16Sr RNA gene was conducted and analyzed using QIIME. Nasal swab isolates were cultured and identified using near full-length sequencing of the 16S rRNA gene. Isolates identified as corynebacteria or staphylococci were typed using (rep-PCR). Antagonism was determined using an agar-based inhibition assay. Results. Four major bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) were identified from all volunteers. The typing of cultured staphylococci and corynebacteria suggested that intra-individual strain diversity was limited. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between staphylococci and corynebacteria. Despite the apparent antagonism between these genera, it was limited when investigated on agar. Of 1000 pairwise interactions, observable zones of inhibition were only reported between a single strain of C.pseudodiphtheriticum and S.aureus. Imaging under EM revealed this effect to be bactericidal with clear lytic effects on staphylococcal cell morphology. Conclusion. Nasal microbiota is complex, but culturable staphylococci and corynebacteria were limited in terms of clone type. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between these genera suggesting an antagonism or competition between these taxonomic groups.

Keywords: nasal, microbiota, S.aureus, microbioal interaction

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Authors: Yanin Hosakun, Sujitra Wongkasemjit, Thanyalak Chaisuwan

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Carbon dioxide removal from natural gas is an important process because the existence of carbon dioxide in natural gas contributes to pipeline corrosion, reduces the heating value, and takes up volume in the pipeline. In this study, bacterial cellulose was chosen for the CO2/CH4 gas separation membrane due to its unique structure and prominent properties. Additionally, it can simply be obtained by culturing the bacteria so called “Acetobacter xylinum” through fermentation of coconut juice. Bacterial cellulose membranes with and without silver ions were prepared and studied for the separation performance of CO2 and CH4.

Keywords: bacterial cellulose, CO2, CH4 separation, membrane, nata de coco

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Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

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Authors: Rini Jarial, Puranjan Mishra, Lakhveer Singh, Sveta Thakur, A. W. Zularisam, Mimi Sakinah

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The aim of the present study was to assess the biological properties of Camellia sinensis and to identify its functional compounds. The methanolic leaves-extract (MLE) of commercial green tea (Camellia sinensis) was assessed for anti-bacterial activities by measuring inhibition zones against a panel of pathogenic bacterial strains using agar diffusion method. The flavonoid (5.0 to 8.0 mg/ml) and protein content (10 to 15 mg/ml) of the MLE were recorded. MLE at a concentration of 25 μg/ml showed marked anti-bacterial activity against all bacterial strains (11-30 mm zone of inhibition) and was maximum against Staphylococcus aureus (30 mm). The MLE of Camellia sinensis had the best MIC values of 2.25 and 0.56 mg/ml against S. aureus and Enterobacter sp., respectively. The MLE also possessed good anti-lipolytic activity (65%) against a Porcine pancreatic lipase (PPL) and cholesterol oxidase inhibition (79%). The present study provided strong experimental evidences that the MLE of Camellia sinensis is not only a potent source of natural anti-oxidants and anti-bacterial activity but also possesses efficient cholesterol degradation and anti-lipolytic activities that might be beneficial in the body weight management.

Keywords: anti-oxidant, anti-bacterial activity, anti-lipolytic activity, Camellia sinensis, phyto-chemicals

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Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

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Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

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Authors: Nur Atirah Hasmi, Nadia Nisha Musa, Hasnun Nita Ismail, Zulfadli Mahfodz

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The effect of water quality parameters on the abundance of aquatic insects has been studied in Batu Berangkai, Dipang, Kuala Woh and Lata Kinjang Rivers, Perak, northern peninsular Malaysia. The focuses are to compare the abundance of aquatic insects in each sampling areas and to investigate the physical and chemical factors (water temperature, depth of water, canopy, water velocity, pH value, and dissolved oxygen) on the abundance of aquatic insects. The samples and data were collected by using aquatic net and multi-probe parameter. Physical parameters; water velocity, water temperature, depth, canopy cover, and two chemical parameters; pH value and dissolved oxygen have been measured in situ and recorded. A total of 631 individuals classified into 6 orders and 18 families of aquatic insects were identified from four sampling sites. The largest percentage of samples collected is from order Plecoptera 35.8%, followed by Ephemeroptera 32.6%, Trichoptera 17.0%, Hemiptera 8.1%, Coleoptera 4.8%, and the least is Odonata 1.7%. The aquatic insects collected from Dipang River have the highest abundance of 273 individuals from 6 orders and 13 families and the least insects trapped at Lata Kinjang which only have 64 individuals from 5 orders and 6 families. There is significant association between different sampling areas and abundance of aquatic insects (p<0.05). High abundance of aquatic insects was found in higher water temperature, low water velocity, deeper water, low pH, high amount of dissolved oxygen, and the area that is not covered by canopy.

Keywords: aquatic insect, physicochemical parameter, river, water quality

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Authors: A. Elragig, S. Townley, H. Dreiwi

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In this paper we introduce a bacteria-leukocyte model with bacteria chemotaxsis. We assume that bacteria develop a tactic defense mechanism as a response to Leukocyte phagocytosis. We explore the effect of this tactic motion on Turing space in two parameter spaces. A fine tuning of bacterial chemotaxis shows a significant effect on developing a non-uniform steady state.

Keywords: chemotaxis-diffusion driven instability, bacterial chemotaxis, mathematical biology, ecology

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Authors: Baharuddin Patandjengi, A. Pabborong, T. Kuswinanti

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Bacterial ring rot caused by a gram-positive Coryneform bacterium Corynebacterium michiganensis subsp. sepedonicus is an important disease on potato crops in the world. The disease still belongs to an A1 quarantine pathogen in Indonesia, although it was found in West Java since 2013. The objective of this study was to know the presence of bacterial ring rot in four potato district areas in South Sulawesi. Infected samples were collected from potato fields and storage warehouses in Enrekang, Gowa, Jeneponto and Bantaeng districts. Potato tuber samples were cut and observed their vasiculer vessels and the bacterial ooze was used for isolation on Nutrient Agar and Nutrient Broth–Yeast extract medium. Bacterial isolates were then morphologically and physiologically characterized. A patogenicity test on eggplant and molecular characterization using PCR with specific primer for Cms (50F and Cms 50 R) was revealed for further identification. The results showed that Cms has become widespread in four districts of South Sulawesi. The bacterial ringrot disease incidence in these districts was reached above 30 %. All of 14 bacterial isolates that identified before using standard methods of EPPO, showed DNA band in size of 224 bp in PCR test, which indicated positively belong to C. michiganensis subsp. sepedonicus.

Keywords: bacterial ring rot, clavibacter michiganensis pv. sepedonicus, PCR, potato

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Authors: Lena Payati, Maria Kazou, Effie Tsakalidou

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Table olives are one of the most popular fermented vegetables worldwide, which along with olive oil, have a crucial role in the world economy. They are highly appreciated by the consumers for their characteristic taste and pleasant aromas, while several health and nutritional benefits have been reported as well. Until recently, microbial biogeography, i.e., the study of microbial diversity over time and space, has been mainly associated with wine. However, nowadays, the term 'terroir' has been extended to other crops and food products so as to link the geographical origin and environmental conditions to quality aspects of fermented foods. Taking the above into consideration, the present study focuses on the microbial fingerprinting of the most important olive varieties of Greece with the state-of-the-art amplicon-based metagenomics analysis. Towards this, in 2019, 61 samples from 38 different olive varieties were collected at the final stage of ripening from 13 well spread geographical regions in Greece. For the metagenomics analysis, total DNA was extracted from the olive samples, and the 16S rRNA gene and ITS DNA region were sequenced and analyzed using bioinformatics tools for the identification of bacterial and yeasts/fungal diversity, respectively. Furthermore, principal component analysis (PCA) was also performed for data clustering based on the average microbial composition of all samples from each region of origin. According to the composition, results obtained, when samples were analyzed separately, the majority of both bacteria (such as Pantoea, Enterobacter, Roserbergiella, and Pseudomonas) and yeasts/fungi (such as Aureobasidium, Debaromyces, Candida, and Cladosporium) genera identified were found in all 61 samples. Even though interesting differences were observed at the relative abundance level of the identified genera, the bacterial genus Pantoea and the yeast/fungi genus Aureobasidium were the dominant ones in 35 and 40 samples, respectively. Of note, olive samples collected from the same region had similar fingerprint (genera identified and relative abundance level) regardless of the variety, indicating a potential association between the relative abundance of certain taxa and the geographical region. When samples were grouped by region of origin, distinct bacterial profiles per region were observed, which was also evident from the PCA analysis. This was not the case for the yeast/fungi profiles since 10 out of the 13 regions were grouped together mainly due to the dominance of the genus Aureobasidium. A second cluster was formed for the islands Crete and Rhodes, both of which are located in the Southeast Aegean Sea. These two regions clustered together mainly due to the identification of the genus Toxicocladosporium in relatively high abundances. Finally, the Agrinio region was separated from the others as it showed a completely different microbial fingerprinting. However, due to the limited number of olive samples from some regions, a subsequent PCA analysis with more samples from these regions is expected to yield in a more clear clustering. The present study is part of a bigger project, the first of its kind in Greece, with the ultimate goal to analyze a larger set of olive samples of different varieties and from different regions in Greece in order to have a reliable olives’ microbial biogeography.

Keywords: amplicon-based metagenomics analysis, bacteria, microbial biogeography, olive microbiota, yeasts/fungi

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Authors: Philip Semaha, Zhongfang Lei, Ziwen Zhao, Sen Liu, Zhenya Zhang, Kazuya Shimizu

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The increasing generation of saline wastewater through various industrial activities is becoming a global concern for activated sludge (AS) based biological treatment which is widely applied in wastewater treatment plants (WWTPs). As for the AS process, an increase in wastewater salinity has negative impact on its overall performance. The advent of conventional aerobic granular sludge (AGS) or bacterial AGS biotechnology has gained much attention because of its superior performance. The development of algal-bacterial AGS could enhance better nutrients removal, potentially reduce aeration cost through symbiotic algae-bacterial activity, and thus, can also reduce overall treatment cost. Nonetheless, the potential of salt stress to decrease biomass growth, microbial activity and nutrient removal exist. Up to the present, little information is available on saline wastewater treatment by algal-bacterial AGS. To the authors’ best knowledge, a comparison of the two AGS systems has not been done to evaluate nutrients removal capacity in the context of salinity increase. This study sought to figure out the impact of salinity on the algal-bacterial AGS system in comparison to bacterial AGS one, contributing to the application of AGS technology in the real world of saline wastewater treatment. In this study, the salt concentrations tested were 0 g/L, 1 g/L, 5 g/L, 10 g/L and 15 g/L of NaCl with 24-hr artificial illuminance of approximately 97.2 µmol m¯²s¯¹, and mature bacterial and algal-bacterial AGS were used for the operation of two identical sequencing batch reactors (SBRs) with a working volume of 0.9 L each, respectively. The results showed that salinity increase caused no apparent change in the color of bacterial AGS; while for algal-bacterial AGS, its color was progressively changed from green to dark green. A consequent increase in granule diameter and fluffiness was observed in the bacterial AGS reactor with the increase of salinity in comparison to a decrease in algal-bacterial AGS diameter. However, nitrite accumulation peaked from 1.0 mg/L and 0.4 mg/L at 1 g/L NaCl in the bacterial and algal-bacterial AGS systems, respectively to 9.8 mg/L in both systems when NaCl concentration varied from 5 g/L to 15 g/L. Almost no ammonia nitrogen was detected in the effluent except at 10 g/L NaCl concentration, where it averaged 4.2 mg/L and 2.4 mg/L, respectively, in the bacterial and algal-bacterial AGS systems. Nutrients removal in the algal-bacterial system was relatively higher than the bacterial AGS in terms of nitrogen and phosphorus removals. Nonetheless, the nutrient removal rate was almost 50% or lower. Results show that algal-bacterial AGS is more adaptable to salinity increase and could be more suitable for saline wastewater treatment. Optimization of operation conditions for algal-bacterial AGS system would be important to ensure its stably high efficiency in practice.

Keywords: algal-bacterial aerobic granular sludge, bacterial aerobic granular sludge, Nutrients removal, saline wastewater, sequencing batch reactor

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Authors: Odejayi Adedayo Olugbenga, Aina Adebisi

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Weather variables (rainfall and temperature) affect the diversity and abundance of both fauna and flora species. This study compared the weather variables with spider abundance in two ecological zones of Ogun State, Nigeria namely Ago-iwoye (Rainforest) in the Ijebu axis and Aiyetoro (Derived Savannah) in the Yewa axis. Seven study sites chosen by Simple Random Sampling in each ecosystem were used for the study. In each sampling area, a 60 m x 120 m land area was marked and sampled, spider collection techniques were; hand picking, use of sweep netting, and Pitfall trap. Adult spiders were identified to the species level. Species richness was estimated by a non-parametric species estimator while the diversity of spider species was assessed by Simpson Diversity Index and Species Richness by One-way Analysis of Variance. Results revealed that spiders were more abundant in rainforest zones than in derived savannah ecosystems. However, the pattern of spider abundance in rainforest zone and residential areas were similar. During high temperatures, the activities of spiders tended to increase according to this study. In contrast, results showed that there was a negative correlation between rainfall and spider species abundance in addition to a negative and weak correlation between rainfall and species richness. It was concluded that heavy downpour has lethal effects on both immature and sometimes matured spiders, which could lead to the extinction of some unknown species of spiders. Tree planting should be encouraged, as this shelters the spider.

Keywords: spider, abundance, species richness, species diversity

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Authors: Seyedeh Belin Tavakoly Sany, Rosli Hashim, Majid Rezayi, Aishah Salleh, Omid Safari

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The purpose of this paper is to describe the main characteristics of macroinvertebrate species in response to environmental forcing factors. Overall, 23 species of Mollusca, 4 species of Arthropods, 3 species of Echinodermata and 3 species of Annelida were identified at the 9 sampling stations during four sampling periods. Individual species of Mollusca constituted 36.4% of the total abundance, followed by Arthropods (27.01%), Annelida (34.3%) and Echinodermata (2.4%). The results of Kruskal-Wallis test indicated that a significant difference (p <0.05) in the abundance, richness and diversity of the macro-benthic community in different stations. The correlation analysis revealed that anthropogenic pollution and natural variability caused by these variations in spatial scales.

Keywords: benthic invertebrates, diversity, abundance, West Port

Procedia PDF Downloads 441

Authors: Md. Ruhul Amin, Shakura Namni, Md. Ramiz Uddin Miah, Md. Giashuddin Miah, Mohammad Zakaria, Sang Jae Suh, Yong Jung Kwon

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Insect species abundance and diversity associated with meteorological factors during January to June 2013 at a mango-based agroforestry research field in Bangladesh, and the effects of pests and pollinator species on mango are presented in this study. Among the collected and identified insects, nine species belong to 3 orders were found as pollinator, 11 species in 5 orders as pest, and 13 species in 6 orders as predator. The mango hopper, fruit fly and stone weevil appeared as major pest because of their high levels of abundance and infestation. The hoppers caused 100% inflorescence damage followed by fruit fly (51.7% fruit) and stone weevil (31.0% mature fruit). The major pests exerted significantly higher abundance compared to pollinator, predator and minor pests. Hemipteroid insects were most abundant (60%) followed by Diptera (21%), Hymenoptera (10%), Lepidoptera (5%), and Coleoptera (4%). Insect population increased with increasing trend of temperature and humidity, and revealed peak abundance during April-May. The flower visiting insects differed in their landing duration and showed preference to forage with time of a day. Their foraging activity was found to be peaked between 11.00 am to 01.00 pm. The activity of the pollinators led to higher level of fruit set. This study provides baseline information about the phenological patterns of insect abundance in an agroforestry research field which could be an indication to incorporate some aspects of pest management.

Keywords: agroforestry, abundance, abiotic factors, insects, mango

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Authors: Afiq Mohd Fahmi, Tony Gutierrez, Sebastian Hennige

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Increasing amounts of CO₂ entering the marine environment, also known as ocean acidification, is documented as having harmful impacts on a variety of marine organisms. When considering the future risk of hydrocarbon pollution, which is generally detrimental to marine life as well, this needs to consider how OA-induced changes to microbial communities will compound this since hydrocarbon degradation is influenced by the community-level microbial response. This study aims to evaluate the effects of increased atmospheric CO₂ conditions and oil enrichment on the phytoplankton-associated bacterial communities. Faroe Shetland Channel (FSC) is a subarctic region in the northeast Atlantic where crude oil extraction has recently been expanded. In the event of a major oil spill in this region, it is vital that we understand the response of the bacterial community and its consequence on primary production within this region—some phytoplankton communities found in the ocean harbor hydrocarbon-degrading bacteria that are associated with its psychosphere. Surface water containing phytoplankton and bacteria from FSC were cultured in ambient and elevated atmospheric CO₂ conditions for 4 days of acclimation in microcosms before introducing 1% (v/v) of crude oil into the microcosms to simulate oil spill conditions at sea. It was found that elevated CO₂ conditions do not significantly affect the chl a concentration, and exposure to crude oil detrimentally affected chl a concentration up to 10 days after exposure to crude oil. The diversity and richness of the bacterial community were not significantly affected by both CO₂ treatment and oil enrichment. The increase in the relative abundance of known hydrocarbon degraders such as Oleispira, Marinobacter and Halomonas indicates potential for biodegradation of crude oil, while the resilience of dominant taxa Colwellia, unclassified Gammaproteobacteria, unclassified Rnodobacteria and unclassified Halomonadaceae could be associated with the recovery of microalgal community 13 days after oil exposure. Therefore, the microbial community from the subsurface of FSC has the potential to recover from crude oil pollution even under elevated CO₂ (750 ppm) conditions.

Keywords: phytoplankton, bacteria, crude oil, ocean acidification

Procedia PDF Downloads 236

Authors: Chiqian Zhang, Kyle D. McIntosh, Nathan Sienkiewicz, Ian Struewing, Erin A. Stelzer, Jennifer L. Graham, Jingrang Lu

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Phytoplankton plays an essential role in freshwater aquatic ecosystems and is the primary group synthesizing organic carbon and providing food sources or energy to ecosystems. Therefore, the identification and quantification of phytoplankton are important for estimating and assessing ecosystem productivity (carbon fixation), water quality, and eutrophication. Microscopy is the current gold standard for identifying and quantifying phytoplankton composition and abundance. However, microscopic analysis of phytoplankton is time-consuming, has a low sample throughput, and requires deep knowledge and rich experience in microbial morphology to implement. To improve this situation, quantitative polymerase chain reaction (qPCR) was considered for phytoplankton identification and quantification. Using qPCR to assess phytoplankton composition and abundance, however, has not been comprehensively evaluated. This study focused on: 1) conducting a comprehensive performance comparison of qPCR and microscopy techniques in identifying and quantifying phytoplankton and 2) examining the use of qPCR as a tool for assessing eutrophication. Twelve large rivers located throughout the United States were evaluated using data collected from 2017 to 2019 to understand the relation between qPCR-based phytoplankton abundance and eutrophication. This study revealed that temporal variation of phytoplankton abundance in the twelve rivers was limited within years (from late spring to late fall) and among different years (2017, 2018, and 2019). Midcontinent rivers had moderately greater phytoplankton abundance than eastern and western rivers, presumably because midcontinent rivers were more eutrophic. The study also showed that qPCR- and microscope-determined phytoplankton abundance had a significant positive linear correlation (adjusted R² 0.772, p-value < 0.001). In addition, phytoplankton abundance assessed via qPCR showed promise as an indicator of the eutrophication status of those rivers, with oligotrophic rivers having low phytoplankton abundance and eutrophic rivers having (relatively) high phytoplankton abundance. This study demonstrated that qPCR could serve as an alternative tool to traditional microscopy for phytoplankton quantification and eutrophication assessment in freshwater rivers.

Keywords: phytoplankton, eutrophication, river, qPCR, microscopy, spatiotemporal variation

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Authors: Zahra Safaeian, Shila Goldasteh, Rouhollah Radjabi

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Flowerflies of Syrphidae family is one of the largest families among the Diptera order that due to predatory habit of some species in larva stage has an important role for controlling aphids of the fields. In the present study, flowerflies fauna in the alfalfa fields of the north of Khouzestan were studied during 2012-2013. The species of the family were collected using appropriate methods including insect collecting sweeping net and Malaise traps. According to the fact that the shape of male genitalia in the male insect is important in identification of these species the male genitalia was separated from the body and microscopical slide was prepared then species identification was done considering the male genitalia, the patterns and figures on the abdomen and using available keys. Based on the finding four species of Sphaerophoria scripta, Sphaerophoria turkmenica, Melanostoma mellinu, Sphaerophoria ruppelli were collected and according to the abundance frequency of the collected species the most abundance was related to Sphaerophoria scripta, then Sphaerophoria turkmenica had the most abundance and the least abundance was related to Sphaerophoria ruppelli.

Keywords: syrphidae, fauna, alfalfa, Iran

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Authors: Geeta Negi, Pankaj, Anjana Srivastava, Anita Sharma

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In the present study, the presence of endosulfan, imidacloprid, carbendazim, in the soil /vegetables/cereals and water samples was observed in agriculture fields of Uttarakhand. In view of biodegradation of these pesticides, nine bacterial isolates were recovered from the soil samples of the fields which tolerated endosulfan, imidacloprid, carbendazim from 100 to 200 µg/ml. Three bacterial consortia used for in vitro bioremediation experiments were three bacterial isolates for carbendazim, imidacloprid and endosulfan, respectively. Maximum degradation (87 and 83%) of α and β endosulfan respectively was observed in soil slurry by consortium. Degradation of Imidacloprid and carbendazim under similar conditions was 88.4 and 77.5% respectively. FT-IR analysis of biodegraded samples of pesticides in liquid media showed stretching of various bonds. GC-MS of biodegraded endosulfan sample in soil slurry showed the presence of non-toxic intermediates. A pot trial with Bacterial treatments lowered down the uptake of pesticides in onion plants.

Keywords: biodegradation, carbendazim, consortium, endosulfan

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Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

Procedia PDF Downloads 87