Bacterial Diversity

Background and Objective: With changing pattern of culture practices in the coastal region of Bangladesh, the euryhaline giant freshwater prawn Macrobrachium rosenbergii has recently gained popularity among farmers of both semi-intensive and extensive culture systems to improve profitability. Since bacteria are the key player in aquaculture facilities governing health and quality of fish and prawn, comparative bacteriological analyses were undertaken to understand the suitable testing system of bacterial analysis for cultured freshwater prawn. Methodology: Both on-farm and laboratory conditions in low-resource settings were considered to monitor bacterial population in terms of bacterial count, gram staining and presence of enteric bacteria associated with prawn and its surrounding environment. Results: On-farm counting was about one log-unit lower total viable count in water, sediment and prawn samples compared to those of laboratory testing. The differences between on-farm and laboratory analysis probably occurred due to the time lapse during sample transportation. Study also showed that gram negative bacteria were dominant and enteric bacteria were present in both the prawn farms with more or less similar frequencies. Conclusion: It is concluded that the apparent difference in bacteriological condition of the two farms is possibly related to the differences in culture practices, environment and culture conditions and the study has recommended on-farm testing as an ideal bacteriological analysis method.

Acanthamoeba spp. are free-living, amphizoic amoebae widely distributed in soil, water and air, with the ability to cause opportunistic infections in both humans and animals. In livestock, ocular acanthamoebiasis can lead to conjunctivitis, keratitis and potential vision loss, resulting in economic losses due to decreased productivity and animal welfare concerns. This study reports the occurrence of Acanthamoeba spp. from ocular discharge samples of buffaloes showing signs of ocular discomfort, such as lacrimation. The water bathing practices were found to be the main cause of eye infections in the present study. Water bodies are heavily loaded with a variety of contaminants, including microbes, bacteria, fungi, pathogenic protozoa and organic substances. High levels of different nutrients in water bodies are responsible for enhancing bacterial growth, such as E. coli. This, in turn, favours the growth of amphizoic amoeba, occasionally present in water bodies. The presence of amphizoic amoebae in water bodies poses a risk for buffalo to contract amoebic infections.

This study highlights the complex relationship among the type of food, the performance of the locusts and midgut proteins as well as the impact of bacterial injection on the midgut proteins of adult. Grasshopper nymphs were supplied by different types of natural vegetation (grass, sorghum, sesban and clover) according to the seasons. The desert locust, Schistocerca gregaria Forskal fed on clover showed highest growth rate and largest mass and, vice versa in grass fed locusts. The insects fed on grass (low protein diet) recorded lowest midgut protein content while those fed on clover (high protein diet) recorded highest midgut protein. The change in diet produced protein profiles differences among the feeding groups of S. gregaria adults. Insects fed on clover had many characteristic bands in protein profile of midgut and vice versa in case of those fed on grass. After Bacillus thuringiensis israelensis (Bti) injection, adults fed on clover showed the least susceptibility to Bti and vice versa in grass. Analysis of midgut proteins by SDS-polyacrylamide gel electrophoresis showed appearance of new bands in the injected adults compared to normal ones. In conclusion, this study emphasizes the close relationship between the type of food and the performance of the insect. It also confirmed the impact of food and Bti injection on midgut proteins.

In order to investigate the bacterial diversity in a number of rivers, reservoirs and lakes in northern and central Portugal during the winter of 2004/5 (atypically dry), we applied molecular methodologies, namely denaturing gradient gel electrophoresis with primers targeting fractions of the bacterial 16S rRNA gene. Environmental parameters such as pH, conductivity, inorganic nutrients, total suspended solids and chlorophyll a were determined in order to characterize the trophic status of the studied water bodies. We found water bodies with oligotrophic to hypereutrophic characteristics. Organisms belonging to the Bacteroidetes and Alphaproteobacteria were found at the highest pH environment. Bacteroidetes were also related to high nutrient concentrations. Verrucomicrobia were associated with the most oligotrophic reservoir and low pH values. Actinobacteria were present in all samples from lakes and reservoirs, indicating its preference for lentic water bodies. Cyanobacteria dominance was related to high pH and conductivity levels. In general the conductivity values recorded in winter 2005 were the highest over recent years and chlorophyll a also reached very high levels. The data emphasize an enhanced risk of eutrophication for the studied water bodies, especially in the subsequent months when the temperature rises.

We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes , respectively. Nevertheless, a phylogenetic analysis ...

Kachia military firing range since 1965 in situ characterization of microbes present in explosives contaminated soils was investigated. Bacteria gram stain morphological and biochemical characterization of the different microbial isolates. Bacterial DNA extracted from soil samples was achieved using the 16SrRNA is amplified using Polymerase Chain Reaction with the following microbes (Lysini bacillus, Escherichia coli, Enterobacter spp, Bacillus subtilis, Klebsiella pneumomia, Achromobacter spp and Arcobacter spp) was confirmed and results compared with the sequence obtained from the nucleotide database of National Centre for Biotechnology Information (NCBI). Fungal species isolates are: Rhizopus spp, Aspergillus niger, Penicillium spp, Trametes versicolourand Phanorochate chrysoporium may adapted to metabolise the explosives and heavy metals contaminant xenobiotic by biodegradation. Percentage isolates occurrence: 75% Enterobacterspp (highest) and 33% Escherichia coli (lowest); 67% ...

An alkaline Lonar Lake is a nature's gift to human being. It is an unique Basaltic rock meteorite impact crater present on the earth. The surrounding ecosystem of Lonar crater is responsible for the occurrence of rare and unique life forms. The pH of Lonar lake crater ranges between 10-12 due to the combination of geological, geographical and climatic conditions. Surrounding the lake region there is a presence of various temples which are in deteriorated conditions and away from the attention. Such temples are the dwelling places of bats and monkeys present at Lake region. Bats are mainly dependent upon Lonar lake and its surrounding for its food and water purpose. So such bats which are dependent upon alkaline water of Lonar lake strongly having the chances of production of such enzymes (Amylase, Protease, Lipase, etc.) which are stable at high alkaline pH and so such study about the production and characterization of enzymes from bat guano of Lonar lake is having its great importance regarding to industries such as cloth, paper, detergent, etc

are the most offensive factors showing values of 0.868, 0.933, 0.770, 0.503, 5.063, 0.717, 30mg/L respectively. Remarkably, surface runoffs from municipal drains channelled to stations 1 and 2 contribute significantly to the turbidity with 4.333 and 4.233mg/L respectively, whereupon urbanization and industrialization are seemingly the culprits.

Microbial communities associated to insect species are involved in essential biological functions such as host nutrition, reproduction and survivability. Main factors have been described as modulators of gut bacterial community, such as diet, habit, developmental stage and taxonomy of the host. The present work focuses on the complex changes that gut microbial communities go through when wild insects are introduced to artificial rearing conditions. Specifically, we analyzed the effect of the laboratory colonization on the richness and diversity of the gut bacteriome hosted by the fruit fly pest Anastrepha fraterculus sp. 1. Bacterial profiles were studied by amplicon sequencing of the 16S rRNA V3-V4 hypervariable region in gut samples of males and females, in teneral (1-day-old, unfed) and post-teneral (15-day-old, fed) flies. A total of 3,147,665 sequence reads were obtained and 32 bacterial operational taxonomic units (OTUs) were identified. Proteobacteria was the most abundant phylum (93.3% of the total reads) and, Wolbachia and Enterobacter were the most represented taxa at the genus level (29.9% and 27.7%, respectively, of the total read counts). Wild and laboratory flies showed highly significant differences in the relative abundances of bacteria. The analysis of the core bacteriome showed the presence of five OTUs in all samples grouped by origin, while nine and five OTUs were exclusively detected in laboratory and wild flies, respectively. Irrespective of fly origin or sex, a dominant presence of Wolbachia was observed in teneral flies, whereas Enterobacter was highly abundant in post-teneral individuals. We evidenced significant differences in bacterial richness and diversity among generations under laboratory colonization (F0, F1, F3 and F6) and compared to laboratory and wild flies, displaying also differential patterns between teneral and post-teneral flies. Laboratory and wild A. fraterculus sp. 1 harbor different gut bacterial communities. Laboratory colonization has an important effect on the microbiota, most likely associated to the combined effects of insect physiology and environmental conditions (e.g., diet and colony management).

This study highlights the potential of Lactobacillus isolates (from curd & kefir) as probiotics against bowel infections. The isolates showed optimal growth at 0.5% salt concentration and pH 5, with varying levels of tolerance to different salt concentrations and pH levels. Notably, S12 and S33 exhibited high colony counts at 0.5% salt concentration, indicating their potential as salt-tolerant isolates. Lactobacillus species can strengthen the gut barrier, produce antimicrobial substances, and modulate the immune system, contributing to their potential health benefits. These findings suggest that these isolates could be used to develop novel probiotics or antimicrobial therapies to prevent or treat bowel infections, and further research is needed to explore their mechanisms of action and potential applications.

The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principalcomponent analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.

Biotechnology represents a transformative force at the intersection of biology, chemistry, and technology, poised to revolutionize various facets of our lives. At its core, biotechnology harnesses the inherent power of living organisms and biological systems to develop innovative solutions with broad-reaching applications. This introductory abstract provides a glimpse into the dynamic realm of biotechnology, highlighting its diverse domains and the immense potential it holds.In the realm of healthcare, biotechnology has spearheaded groundbreaking advancements, including the development of novel pharmaceuticals, gene therapies, and diagnostic tools. These innovations have revolutionized disease treatment and prevention, offering new hope to patients worldwide. Biotechnology also plays a pivotal role in agriculture, where genetically modified crops have the potential to enhance yields, reduce environmental impact, and mitigate food security challenges in a rapidly changing world.In the energy sector, biotechnology offers sustainable alternatives through biofuels, utilizing microorganisms to convert organic matter into renewable energy sources. This not only reduces our dependence on fossil fuels but also addresses environmental concerns. Environmental conservation is another critical arena where biotechnology excels, with applications ranging from bioremediation to protect ecosystems from pollutants to the development of biodegradable materials to curb plastic waste.The growing field of synthetic biology is pushing the boundaries of biotechnology, enabling the design and construction of biological systems for specific purposes. This interdisciplinary approach allows scientists to engineer organisms to perform tasks previously unimaginable, from producing biobased materials to creating artificial organs for transplantation.

An artesian sulfide-and sulfur-rich spring in southwestern Oklahoma is shown to sustain an extremely rich and diverse microbial community. Laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at Zodletone spring. Anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. The microbial community at Zodletone spring was analyzed by cloning and sequencing 16S rRNA genes. A large fraction (83%) of the microbial mat clones belong to sulfur-and sulfate-reducing lineages within ␦-Proteobacteria, purple sulfur ␥-Proteobacteria, -Proteobacteria, Chloroflexi, and filamentous Cyanobacteria of the order Oscillatoria as well as a novel group within ␥-Proteobacteria. The 16S clone library constructed from hydrocarbon-exposed sediments at the source of the spring had a higher diversity than the mat clone library (Shannon-Weiner index of 3.84 compared to 2.95 for the mat), with a higher percentage of clones belonging to nonphototrophic lineages (e.g., Cytophaga, Spirochaetes, Planctomycetes, Firmicutes, and Verrucomicrobiae). Many of these clones were closely related to clones retrieved from hydrocarbon-contaminated environments and anaerobic hydrocarbondegrading enrichments. In addition, 18 of the source clones did not cluster with any of the previously described microbial divisions. These 18 clones, together with previously published or database-deposited related sequences retrieved from a wide variety of environments, could be clustered into at least four novel candidate divisions. The sulfate-reducing community at Zodletone spring was characterized by cloning and sequencing a 1.9-kb fragment of the dissimilatory sulfite reductase (DSR) gene. DSR clones belonged to the Desulfococcus-Desulfosarcina-Desulfonema group, Desulfobacter group, and Desulfovibrio group as well as to a deeply branched group in the DSR tree with no representatives from cultures. Overall, this work expands the division-level diversity of the bacterial domain and highlights the complexity of microbial communities involved in sulfur cycling in mesophilic microbial mats.

An artesian sulfide- and sulfur-rich spring in southwestern Oklahoma is shown to sustain an extremely rich and diverse microbial community. Laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at Zodletone spring. Anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. The microbial community at Zodletone spring was analyzed by cloning and sequencing 16S rRNA genes. A large fraction (83%) of the microbial mat clones belong to sulfur- and sulfate-reducing lineages within δ- Proteobacteria , purple sulfur γ -Proteobacteria , ε -Proteobacteria , Chloroflexi , and filamentous Cyanobacteria of the order Oscillatoria as well as a novel group within γ -Proteobacteria . The 16S clone library constructed from hydrocarbon-exposed sediments at the source of the spring had a higher diversity than the mat clone library (Shannon-Weiner index of 3.84 compa...

The manufacture use and disposal of explosives as well as the demilitarization of military facilities can result in environmental contamination. The three most widely used explosives are 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

Kachia military firing range since 1965 in situ characterization of microbes present in explosives contaminated soils was investigated. Bacteria gram stain morphological and biochemical characterization of the different microbial isolates. Bacterial DNA extracted from soil samples was achieved using the 16SrRNA is amplified using Polymerase Chain Reaction with the following microbes (Lysini bacillus, Escherichia coli, Enterobacter spp, Bacillus subtilis, Klebsiella pneumomia, Achromobacter spp and Arcobacter spp) was confirmed and results compared with the sequence obtained from the nucleotide database of National Centre for Biotechnology Information (NCBI). Fungal species isolates are: Rhizopus spp, Aspergillus niger, Penicillium spp, Trametes versicolourand Phanorochate chrysoporium may adapted to metabolise the explosives and heavy metals contaminant xenobiotic by biodegradation. Percentage isolates occurrence: 75% Enterobacterspp (highest) and 33% Escherichia coli (lowest); 67% Aspergillus niger (highest); and 17% for Penicillium sppand Trametes versicolor (lowest) respectively. Microbial biodegradation of explosives is considered to be most favourable under co-metabolic conditions. Site study explosives treatment by bioremediation will requires bioaugmentation of isolated microbes for xenobiotic biodegradation. Explosives impacts on biodiversity was illuminated and treatments protocol.

Kachia military firing range since 1965 in situ characterization of microbes present in explosives contaminated soils was investigated. Bacteria gram stain morphological and biochemical characterization of the different microbial isolates. Bacterial DNA extracted from soil samples was achieved using the 16SrRNA is amplified using Polymerase Chain Reaction with the following microbes (Lysini bacillus, Escherichia coli, Enterobacter spp, Bacillus subtilis, Klebsiella pneumomia, Achromobacter spp and Arcobacter spp) was confirmed and results compared with the sequence obtained from the nucleotide database of National Centre for Biotechnology Information (NCBI). Fungal species isolates are: Rhizopus spp, Aspergillus niger, Penicillium spp, Trametes versicolourand Phanorochate chrysoporium may adapted to metabolise the explosives and heavy metals contaminant xenobiotic by biodegradation. Percentage isolates occurrence: 75% Enterobacterspp (highest) and 33% Escherichia coli (lowest); 67% ...

The manufacture use and disposal of explosives as well as the demilitarization of military facilities can result in environmental contamination. The three most widely used explosives are 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

Background: Cockroaches are among the most common pests in public dwellings and health facilities. Their presence can raise safety concerns, especially as they maybe carriers of pathogenic organisms. Methods: This study was carried out to isolate and identify the bacterial flora from German cockroaches (Blattella germanica). Cockroaches collected by hand catches from two public hospital environments in Tebessa city (northeast Algeria) were screened for microbial load from their external surfaces and alimentary tract using standard bacterial protocols. Results: A total of 174 bacterial isolates were isolated from 39 German cockroach specimens. The most common and abundant bacterial species belonged to the Pseudomonas group (23.5%) and Serratia (13.2%). Pathogens like Staphylococcus aureus were also isolated, as well as opportunistic pathogens like Klebsiella species and food spoilage bacteria such as Enterobacter and Citrobacter species were isolated from both external surface and digestive tract of the insect. Generalized linear models (GLM) were performed to analyze the variation of abundances and occurrences of bacterial isolates harboured by B. germanica. The GLMs revealed that the main factors affecting variation of bacterial diversity and abundance were sex and hospital (P , 0.001). The findings of this study suggest that German cockroach acts as reservoir and potential vector of some bacterial pathogens.

Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.

Background: Nebulizers are used to provide treatment to respiratory patients. Concerns over nosocomial infection risks from contaminated nebulizers raise the critical need to identify all microbial populations in nebulizers used by patients. However, conventional culture-dependent techniques are inadequate with the ability to identify specific microbial populations only. Therefore, the aims of this study were to acquire complete profiles of microbiomes in nebulizers used by in-patients with culture-independent high-throughput sequencing and identify sources of microbial contaminants for the development of effective practices to reduce microbial contamination in nebulizer devices. Methods: This study was conducted at the University of Tennessee Medical Center in Knoxville, TN. Nebulizers were collected between May 2018 and October 2018 from inpatients admitted to the floors for pneumonia or chronic obstructive pulmonary disease exacerbations. Nebulizers were sampled for 16S rRNA gene-based amplicon sequencing to profile nebulizer microbiomes and perform phylogenetic analysis. A Bayesian community-wide culture-independent microbial source tracking technique was used to quantify the contribution of human-associated microbiota as potential sources of nebulizer contamination. Results: Culture-independent sequencing detected diverse microbial populations in nebulizers, represented by 18 abundant genera. Stenotrophomonas was identified as the most abundant genus, accounting for 12.4% of the nebulizer microbiome, followed by Rhizobium, Staphylococcus, Streptococcus, and Ralstonia. Phylogenetic analysis revealed the presence of multiple phylotypes with close relationship to potential pathogens. Contributing up to 15% to nebulizer microbiomes, human-associated microbiota was not identified as the primary sources of nebulizer contamination. Conclusion: Culture-independent sequencing was demonstrated to be capable of acquiring comprehensive profiles of microbiomes in nebulizers used by in-patients. Phylogenetic analysis identified differences in pathogenicity between closely related phylotypes. Microbiome profile-enabled community-wide cultureindependent microbial source tracking suggested greater importance of environmental sources than human sources as contributors to nebulizer microbiomes, providing important insight for the development of effective strategies for the monitoring and control of nebulizer devices to mitigate infection risks in the hospital.

Bacteria from the surface microlayer (bacterioneuston) and underlying waters (bacterioplankton) were isolated upon exposure to UV-B radiation, and their individual UV sensitivity in terms of CFU numbers, activity (leucine and thymidine incorporation), sole-carbon source use profiles, repair potential (lightdependent and independent), and photoadaptation potential, under different physiological conditions, was compared. Colony counts were 11.5-16.2% more reduced by UV-B exposure in bacterioplankton isolates (P < 0.05). Inhibition of leucine incorporation in bacterioneuston isolates was 10.9-11.5% higher than in bacterioplankton (P < 0.05). These effects were accompanied by a shift in sole-carbon source use profiles, assessed with Biolog ® EcoPlates, with a reduction in consumption of amines and amino acids and increased use of polymers, particularly in bacterioneuston isolates. Recovery under starvation was generally enhanced compared with nourished conditions, especially in bacterioneuston isolates. Overall, only insignificant increases in the induction of antibiotic resistant mutant phenotypes (Rif R and Nal R ) were observed. In general, a potential for photoadaptation could not be detected among the tested isolates. These results indicate that UV effects on bacteria are influenced by their physiological condition and are accompanied by a shift in metabolic profiles, more significant in bacterioneuston isolates, suggesting the presence of bacterial strains adapted to high UV levels in the SML.

Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria ...

Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serr...

The effects of three selected agrochemicals on bacterial diversity in cultivated soil have been studied. The selected agrochemicals are Cerox (an insecticide), Ceresate and Paraquat (both herbicides). The effect on bacterial population was studied by looking at the total heterotrophic bacteria presence and the effect of the agrochemicals on some selected soil microbes. The soil type used was loamy with pH of 6.0-7.0. The soil was placed in opaque pots and bambara bean (Vigna subterranean) seeds cultivated in them. The agrochemicals were applied two weeks after germination of seeds at concentrations based on manufacturer's recommendation. Plant growth was assessed by weekly measurement of plant height, foliage appearance and number of nodules formed after one month. The results indicated that the diversity index (Di) among the bacteria populations in untreated soil and that of Cerox-treated soils were high with mean diversity index above 0.95. Mean Di for Ceresate-treated soil was 0.88, and that for Paraquattreated soil was 0.85 indicating low bacterial populations in these treatment-type soils. The study also showed that application of the agrochemicals caused reduction in the number of total heterotrophic bacteria population sizes in the soil. Ceresate caused 82.50% reduction in bacteria number from a mean of 40 × 10 5 cfu g -1 of soil sample to 70 × 10 4 cfu g -1 . Paraquat-treated soil showed 92.86% reduction, from a mean of 56 × 10 5 cfu g -1 to 40 × 10 4 cfu g -1 . Application of Cerox to the soil did not have any remarkable reduction in bacterial population number. Total viable cell count studies using Congo red yeast-extract mannitol agar indicated reduction in the number of Rhizobium spp. after application of the agrochemicals. Mean number of Rhizobium population numbers per gram of soil was 180 × 10 4 for the untreated soil. Cerox-treated soil recorded mean number of 138 × 10 4 rhizobial cfu g -1 of soil, a 23.33% reduction. Ceresate-and Paraquat-treated soils recorded 20 × 10 4 and 12 × 10 4 cfu g -1 of soil, respectively, representing 88.89% and 93.33% reduction in Rhizobium population numbers. Correspondingly, the mean number of nodules per plant was 44 for the growth in untreated soil, 30 for the plant in the Cerox-treated soil, 8 for the plant in Paraquat-treated soil and 3 for the plant in Ceresate-treated soil. The study has confi rmed detrimental effect of insecticide on bacterial populations in the soil. Total heterotrophic counts, rhizobial counts as well as the number of nodules of all samples taken from the chemically treated soils were all low as compared to values obtained for the untreated soil. However, the effect of the insecticide was minimal in all cases as compared to the effects of the herbicides on the soil fauna. Indiscriminate use of agrochemicals on farms can therefore affect soil fl ora and subsequently food production.

Recent canola acreage and production in western Canada have reached record high levels. Field experiments were conducted from 2014 to 2016 on land previously seeded to continuous canola for 6 yr at three Canadian Prairie sites. We determined that more intensive seed inputs, fertilizer, fungicide, tillage, or chaff removal could increase continuous canola yields compared with a "standard practice" (SP) treatment or match yields compared with canola in rotation. Recommended or 50% higher fertility levels alone or in combination with a higher seeding rate, tillage, chaff removal, or additional fungicide were applied to the same plots in three successive years to determine effects after 1, 2, and 3 yr of treatment imposition. In continuous canola, blackleg incidence and severity were both reduced by fungicide treatment. In rotations where canola was preceded by wheat, blackleg incidence and severity were much lower than in continuous canola. None of the treatments improved continuous canola yields compared with SP after a single year of treatment imposition. In subsequent years, canola yield increases compared with SP usually occurred as a result of additional fertilizer, seed, or fungicide. In the final year, canola yield loss due to continuous canola was largely rescued by additional seed and fertilizer. Without additional inputs, and when preceded by a different crop, canola yields averaged 11% greater than the average of all continuous canola treatments. High fertility regimes generally reduced oil content and increased protein content relative to standard fertility in continuous canola or relative to canola preceded by wheat.

Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sa...

In recent years interest in bacteriophages in aquatic environments has increased. Electron microscopy studies have revealed high numbers of phage particles (10 4 to 10 7 particles per ml) in the marine environment. However, the ecological role of these bacteriophages is still unknown, and the role of the phages in the control of bacterioplankton by lysis and the potential for gene transfer are disputed. Even the basic questions of the genetic relationships of the phages and the diversity of phage-host systems in aquatic environments have not been answered. We investigated the diversity of 22 phage-host systems after 85 phages were collected at one station near a German island, Helgoland, located in the North Sea. The relationships among the phages were determined by electron microscopy, DNA-DNA hybridization, and host range studies. On the basis of morphology, 11 phages were assigned to the virus family Myoviridae , 7 phages were assigned to the family Siphoviridae , and 4 phages we...

Copepods can be associated with different kinds and different numbers of bacteria. This was already shown in the past with culture-dependent microbial methods or microscopy and more recently by using molecular tools. In our present study, we investigated the bacterial community of four frequently occurring copepod species, Acartia sp., Temora longicornis, Centropages sp. and Calanus helgolandicus from Helgoland Roads (North Sea) over a period of 2 years using DGGE (denaturing gradient gel electrophoresis) and subsequent sequencing of 16S-rDNA fragments. To complement the PCR-DGGE analyses, clone libraries of copepod samples from June 2007 to 208 were generated. Based on the DGGE banding patterns of the two years survey, we found no significant differences between the communities of distinct copepod species, nor did we find any seasonality. Overall, we identified 67 phylotypes ([97 % similarity) falling into the bacterial phyla of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The most abundant phylotypes were affiliated to the Alphaproteobacteria. In comparison with PCR-DGGE and clone libraries, phylotypes of the Gammaproteobacteria dominated the clone libraries, whereas Alphaproteobacteria were most abundant in the PCR-DGGE analyses.

Since 1873, the waters at Helgoland Roads (sampling station "Kabeltonne") have been sampled daily to determine temperature and salinity. In 1962, microbiological parameters were determined for the first time to establish microbiological long-term studies on marine bacteria, starting with the colony-forming units (CFU). In the following years, several other microbiological parameters were integrated for different periods of time (e.g. activity parameters like ATP and ectoenzymatic activity, marine yeasts, oil-degrading bacteria, flagellates and molecular methods like PCR followed by denaturing gradient gel electrophoresis). To date, the total count of bacteria, flagellates and viruses have been acquired using fluorescent DNA dyes and epifluorescence microscopy. Here we present both a historical overview of the methods used and examples of results obtained over the past 40 years. Furthermore, we try to evaluate challenging new methods for marine microbial ecology, appropriate for long-term studies of marine bacteria.

The oil palm industry in Malaysia generates huge amount of oil palm biomass every year. The abundant waste of oil palm lignocellulosic biomass is the most favourable renewable source for production of bio-based products. However, the key problem hindering the effective utilisation of oil palm biomass resource is lignin which resulted in low susceptibility of lignocellulose to undergo enzymatic hydrolysis. A biological pre-treatment method using bacteria was chosen in this study to remove lignin. Ligninolytic bacteria have wider tolerance of temperature, pH and oxygen limitations compared to fungi. It is also easier to handle for large-scale growth production and genetic manipulation. Assessment of bacterial community profile in oil palm plantation soils was conducted by using 16S rRNA gene clone library approach and biodiversity index analysis of operational taxonomic units (OTUs). 16S rRNA gene clone library analysis retrieved 351 clones from three selected samples of oil palm plan...

A culture-independent survey of the bacterial diversity in rhizosphere soils of diseased (scab) and diseasefree apple trees was conducted to assess the role of bacteria in disease suppression. Community DNA was extracted from soil samples and amplified by PCR using primers specific for bacterial 16S rRNA gene sequences. Clone libraries were constructed with the PCR products and analysed based on amplified rDNA restriction analysis (ARDRA) patterns. The phylotypes and their frequency distribution in both libraries indicated that the phylotype did not represent a single group. Rarefaction curve, and Shannon and Simpson diversity indices exhibited insignificant diversity differences between the samples in terms of bacterial community composition, whereas more chitinase and β-1,3 glucanase activities were recorded in samples from disease-free trees than from diseased trees. Based on the operational taxonomic units identified in ARDRA, 80 representative clones were selected from the libraries and partially sequenced. Sequence similarity searches with the resulting sequences identified the dominance of uncultured bacteria to the extent of 70% and 72.5% in disease free and diseased rhizospheres, respectively. The foregoing studies conclude a possible role for enhanced microbial activity in terms of enzyme production in tree (apple) health, although no distinct partitioning of composition or significant diversity of bacterial communities inhabiting diseased and disease-free rhizosphere soils was observed at any given time.

The main goal of this research was to evaluate whether the mixture of fresh labile dissolved organic matter (DOM) and accumulated refractory DOM influences bacterial production, respiration, and growth efficiency (BGE) in aquatic ecosystems. Bacterial batch cultures were set up using DOM leached from aquatic macrophytes as the fresh DOM pool and DOM accumulated from a tropical humic lagoon. Two sets of experiments were performed and bacterial growth was followed in cultures composed of each carbon substrate (first experiment) and by carbon substrates combined (second experiment), with and without the addition of nitrogen and phosphorus. In both experiments, bacterial production, respiration, and BGE were always higher in cultures with N and P additions, indicating a consistent inorganic nutrient limitation. Bacterial production, respiration, and BGE were higher in cultures set up with leachate DOM than in cultures set up with humic DOM, indicating that the quality of the organic matter pool influenced the bacterial growth. Bacterial production and respiration were higher in the mixture of substrates (second experiment) than expected by bacterial production and respiration in single substrate cultures (first experiment). We suggest that the differences in the concentration of some compounds between DOM sources, the co-metabolism on carbon compound decomposition, and the higher diversity of molecules possibly support a greater bacterial diversity which might explain the higher bacterial growth observed. Finally, our results indicate that the mixture of fresh labile and accumulated refractory DOM that naturally occurs in aquatic ecosystems could accelerate the bacterial growth and bacterial DOM removal.

The aim of this study was to compare the composition of bacterial and archaeal communities in contaminated sediments (Vidy Bay) with uncontaminated sediments (Ouchy area) of Lake Geneva using 16S rRNA clone libraries. Sediments of both sites were analysed for physicochemical characteristics including porewater composition, organic carbon, and heavy metals. Results show high concentrations of contaminants in sediments from Vidy. Particularly, high contents of fresh organic matter and nutrients led to intense mineralisation, which was dominated by sulphate-reduction and methanogenesis. The bacterial diversity in Vidy sediments was significantly different from the communities in the uncontaminated sediments. Phylogenetic analysis revealed a large proportion of Betaproteobacteria clones in Vidy sediments related to Dechloromonas sp., a group of dechlorinating and contaminant degrading bacteria. Deltaproteobacteria, including clones related to sulphate-reducing bacteria and Fe(III)-reducing bacteria (Geobacter sp.) were also more abundant in the contaminated sediments. The archaeal communities consisted essentially of methanogenic Euryarchaeota, mainly found in the contaminated sediments rich in organic matter. Multiple factor analysis revealed that the microbial community composition and the environmental variables were correlated at the two sites, which suggests that in addition to environmental parameters, pollution may be one of the factors affecting microbial community structure.

Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous &quot;streamer&quot; communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name &quot;Pyropristinus&quot;). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the &quot;Pyropristinus&quot; and Calescamantes populations showed that these organ...

Two adjacent paddies of an experimental rice field, subjected to organic and conventional farming, were characterized aiming the comparative assessment of microbiological variations occurring in the bulk paddy soil over the rice cycle. This study comprehended the simultaneous characterization of general physicochemical soil properties [total carbon and nitrogen, pH (H 2 O and KCl), C:N ratio and water content], biochemical properties [enzymatic activities and Community Level Physiological Profiles (CLPP)], the estimation of cultivable organisms (enumeration of fast growing heterotrophic bacteria, actinomycetes and fungi) and the assessment of bacterial diversity using a culture-independent method (PCR-DGGE fingerprinting). The linkage of the parameters measured was analysed by canonical correspondence analysis (CCA). CCA ordination plots of the CLPP showed a similar pattern of microbial functional activity in both agronomic management systems, except in June. Enzymatic activity, water content and fungi counts were the main factors affecting the observed CLPP time variation. Such a variation was not expressed by the Shannon and evenness indices, which did not evidence significant differences in the bacterial and functional diversity between or within farming type over the analysed period. The cluster and CCA analyses of the DGGE profiles allowed the distinction of the bacterial communities of both paddies, with temporal variations being observed in the organically managed field but not in the conventional paddy. Enzymatic activity, pH and molinate content were the factors which most contributed to the observed variations. Altogether these results underline the functional redundancy of the rice paddy soil and evidence the temporal variations on the metabolic activity of soil, irrespective of farming type.

Soil heavy metal contamination resulting from mining activities constitutes a major environmental problem worldwide. The spread of heavy metals is often facilitated by scarce vegetation cover, so there is an urgent need to improve plant survival and establishment in these metalliferous areas. This study is aimed at the isolation and analysis of the phylogenetic relationship of culturable bacteria from the rhizosphere of metallophyte plants growing in the Kettara mine, in Marrakech, in order to select plant growth-promoting rhizobacteria (PGPR), which could be used in assistedphytoremediation. Bacterial isolates were grouped by random amplified polymorphic DNA analysis and identified by 16S rRNA gene sequencing. Strains were further characterized for the production of plant growth-promoting (PGP) substances, such as NH 3 , siderophores, indol-3-acetic acid (IAA), hydrogen cyanide, and extracellular enzymes, for ACC-deaminase activity, their capacity to solubilize phosphate, and for their tolerance to heavy metals and acidic pH. Rhizosphere soils were highly contaminated with Cu and Zn and presented low fertility. Phylogenetic analysis showed that the rhizobacteria were affiliated to three major groups: γ-Proteobacteria (48 %), β-Proteobacteria (17 %), and Bacilli (17 %). The most represented genera were Pseudomonas (38 %), Bacillus (10 %), Streptomyces (10 %), and Tetrathiobacter (10 %). Overall, rhizobacterial strains showed an ability to produce multiple, important PGP traits, which may be helpful when applied as plant growth promoter agents in contaminated soils. PGPR were also able to withstand high levels of metals (up to 2615.2 mg Zn l -1 , 953.29 mg Cu l -1 , and 1124.6 mg Cd l -1 ) and the order of metal toxicity was Cd > Cu > Zn. The rhizobacterial strains isolated in the present study have the potential to be used as efficient bioinoculants in phytoremediation strategies for the recovery of Kettara mine soils.

Background: Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produceassociated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Conclusions: Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa , using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Ar...

Forest regions have good weather conditions for agricultural practices. Crop growth and productivity are affected by the presence of novel bio organisms in these areas. The present study sought to identify the location of the forest rhizosphere soil of some field crops. Screening procedures were used to assess their growth capabilities and evaluate their potential as PGPB. Various features of PGPB, like phosphate and potassium solubilization, nitrogen fixation, indole-3-acetic acid (IAA) production, ammonia (NH3) synthesis, siderophore generation, and hydrogen cyanide (HCN) synthesis, were analyzed morphologically, biochemically, and physiologically during the screening process. One isolate out of the nine only produced good results for every attribute studied that promoted plant development. By sequencing their 16S rRNA, the promising isolates were Original Research Article

The study was conducted on four steam baths in Tripoli at a place where people are located for the purpose of treatment or relaxation and recreation. The samples were collected by means of a cotton swab from the steam room, roof, walls and floor. The total colony counts based on sampling sites was the highest number of bacteria: floor, walls, roof, and less in the steam room. The predominant species were gram-negative rods (49.4%), gram-positive cocci (45.6%) and gram-positive rods (4.9%) respectively. Based on biochemical test and the Api 20E system, the following types were identified (Escherichia coli, Edwardsiella Tarda, Aeromones hydrophila, Vibiro alginolyticus, Plesiomonas shigelloides, Salmonella choleraesuis, Xanthomonas maltophilia, and Shewenella putrefacien followed by positive spherical bacteria and Staphylococcus epidermis, Staphylococcus aureus, Micrococcus luteus, Micrococcus roseus respectively. : The results also showed that the highest total number of bacteria in the baths in this study was higher in S1, U2 and lowest in W3.

Cd-tolerant bacterial strains of fluorescent pseudomonads, mostly belonging to Pseudomonas monteillii, were isolated from termite mound soil (Macrotermes subhyalinus, a litter-forager and fungus-growing termite), in a Sudanese shrubby savanna, Burkina Faso. Such large mounds appeared as sites of great bacterial diversity and could be considered as hot spots of metal-tolerant fluorescent pseudomonads. Microbial isolates were inoculated to Sorghum plants (S. bicolor) in glasshouse experiments with soil amended with CdCl 2 (560 mg Cd kg -1 soil). Microbial functional diversity was assessed at the end of the experiment by measurement of in situ patterns of catabolic potentials. All the bacteria isolates significantly improved the shoot and total biomass of sorghum plants compared to the control. Results concerning root biomass were not significant with some strains. Arbuscular mycorrhiza (AM) was greatly reduced by CdCl 2 amendment, and fluorescent pseudomonad inoculation significantly increased AM colonisation in the contaminated soil. The bacterial inoculation significantly improved Cd uptake by sorghum plants. Measurement of catabolic potentials on 16 substrates showed that the microbial communities were different according to the soil amendment. Soils samples inoculated with pseudomonad strains presented a higher use of ketoglutaric and hydroxybutiric acids, as opposed to fumaric acid in soil samples not inoculated. It is suggested that fluorescent pseudomonads could act indirectly in such metabolic processes by involving a lower rate of degradation of citric acid, in line with the effect of small organic acid on phytoextraction of heavy metals from soil. This is a first contribution to bioremediation of metal-contaminated sites with soil-to-plant transfer, using termite built structures. Further data are required on the efficiency of the bacterial strains isolated and on the processes involved.