Endogenous Microbial Community Research Articles

Deleterious Interaction Between Honeybees (Apis mellifera) and its Microsporidian Intracellular Parasite Nosema ceranae Was Mitigated by Administrating Either Endogenous or Allochthonous Gut Microbiota Strains

Honey bees (Apis mellifera) are facing multiple stressors affecting their lifespan, health and productivity. Among them, Nosema ceranae is an intracellular microsporidian parasite, which plays a major impact on honey bees colonies. However, both efficiency and innocuity of current treatment against N. ceranae are observed, thus raising the urgent need to develop alternative prophylactic and curative strategies. Endogenous microbial communities (i.e. host microbiota) are known to play a major role in disease prevention, and more recently both bacterial and yeast strains issued from gut microbiota were observed to improve hosts resistance against intracellular parasites both in mammals and insect models. The use of probiotics in honey bee nutrition is therefore promising to treat or prevent diseases. Therefore, further investigations are needed to properly select microorganisms with probiotic properties. In an in vivo experimental infection by Nosema ceranae, the probiotic effect of two honeybee gut bacterial strains (Parasaccharibacter apium (PC1 sp.) and (Bacillus sp. (PC2 sp.)), and two broad spectra probiotics (Bactocell® and Levucell SB®) has been measured. Both curative and prophylactic administrations were tested: honey bees infected with N. ceranae and non-infected. For the four probiotic candidates, significant increases of survival probabilities (20-30%) were measured after two weeks of treatment with the administration of 103 CFU/mL in sugar syrup, both in curative and prophylactic treatments. The present study shows that endogenous bacterial strains were at least as much efficient and safe than broad spectra probiotics in increasing survival in the context of experimental infection with N. ceranae. Therefore, taking advantage of beneficial host microbiota properties is a promising avenue to develop efficient and sustainable curative strategies against opportunistic diseases in honey bee colonies.

Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw

A new pretreatment method of lignocellulosic biomass was explored by using a wet aerobic process with an alkaline lignin and a mineral salt solution. This treatment significantly improved structural modification of rape straw used as substrate model in this study. Change in cellulose accessibility to cellulase of rape straw rose up to six fold within the first days of this pretreatment without generated significant modification of van Soest lignocellulose fractionation. The biological pretreatment apply to rape straw induced a high microbial activity revealed by quantitative PCR and sequencing techniques, suggesting that bacteria including Xanthomonadales and Sphingobacteriales may be involved in this lignocellulosic biomass transformation. Moreover, results of this work demonstrate that the endogenous microbial community associated with rape straw plays a key role in its alteration.

Focus on kineticcs of removal antibiotics wastewater by nano-zero valent iron in oxidation and photoxidation process

Pharmaceutical wastewater can be difficult to treat with conventional physical/chemical and biological treatment systems. The presence of antibiotics in sewage selects for resistance markers that are able to spread through the microbial community and as a result, antibiotic resistant bacteria can potentially disseminate their resistance genes widely among members of the endogenous microbial community. The sludge products of urban and rural wastewater treatment plants are increasingly used to fertilize agricultural crops, dispersing unknown amounts of resistance genes and antibiotics that withstand standard sewage treatment. Pharmaceutical wastewater effluents are well known for their difficult elimination by traditional biotreatment methods and their important contribution to environmental pollution due to its fluctuating and recalcitrant nature. OTC is one of the nonbiodegradable antibiotics that makes antibiotic-resistant, so it can make be high risk for environment. NZVI can be a good choice for removal of OTC in aqueous solution. Response surface methodology (RSM) was used to optimize the amounts of NZVI and OTC to be used at pH 3 and under 200 W, UV-A irradiation. The responses were removal percent of absorption at 290 and 348 nm, TOC and COD of OTC. In the optimum condition, Linear model was performed 155 ppm of OTC were removed by 1000 ppm NZVI after 6.5 hours and the removal efficiency of absorption at 290 and 348 nm, TOC and COD were 87, 95, 85 and 89 percent, respectively. In the similar process, there is no organic compound after 14 hours. The parameters ORP, DO and pH were investigated for 6:30 hours to study the type of NZVI reaction in process. In the beginning of reaction, oxidation was the dominant reaction after 3 hours, photo catalytic reaction was remarkable. The mechanism of OTC degradation is proposed by HPLC/ESI-MS and four by products were found. Also the rate constants (first order kinetic chain reaction model) were 0.0099, 0.0021, 0.0010, 0.0049 and 0.0074 min-1, respectively.

Material and microbial changes during corn stalk silage and their effects on methane fermentation

Silage efficiency is crucial for corn stalk storage in methane production. This study investigated characteristics of dynamic changes in materials and microbes during the silage process of corn stalks from the initial to stable state. We conducted laboratory-scale study of different silage corn stalks, and optimized silage time (0, 2, 5, 10, 20, and 30days) for methane production and the endogenous microbial community. The volatile fatty acid concentration increased to 3.00g/L on Day 10 from 0.42g/L on Day 0, and the pH remained below 4.20 from 5.80. The lactic acid concentration (44%) on Day 10 lowered the pH and inhibited the methane yield, which gradually decreased from 229mL/g TS at the initial state (Day 0, 2) to 207mL/g TS at the stable state (Day 10, 20, 30). Methanosaeta was the predominant archaea in both fresh and silage stalks; however, richness decreased from 14.11% to 4.75%.

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn's Disease.

ABSTRACTCrohn’s disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their nondiseased first-degree relatives (NCDR) in 9 familial clusters living in northern France-Belgium and in healthy individuals from 4 families living in the same area (non-CD unrelated [NCDU]). Principal component, diversity, and abundance analyses were conducted, and CD-associated inter- and intrakingdom microbial correlations were determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms. CD and NCDR groups clustered together in the mycobiome but not in the bacteriome. Microbiotas of familial (CD and NCDR) samples were distinct from those of nonfamilial (NCDU) samples. The abundance of Serratia marcescens and Escherichia coli was elevated in CD patients, while that of beneficial bacteria was decreased. The abundance of the fungus Candida tropicalis was significantly higher in CD than in NCDR (P = 0.003) samples and positively correlated with levels of anti-Saccharomyces cerevisiae antibodies (ASCA). The abundance of C. tropicalis was positively correlated with S. marcescens and E. coli, suggesting that these organisms interact in the gut. The mass and thickness of triple-species (C. tropicalis plus S. marcescens plus E. coli) biofilm were significantly greater than those of single- and double-species biofilms. C. tropicalis biofilms comprised blastospores, while double- and triple-species biofilms were enriched in hyphae. S. marcescens used fimbriae to coaggregate or attach with C. tropicalis/E. coli, while E. coli was closely apposed with C. tropicalis. Specific interkingdom microbial interactions may be key determinants in CD.

Mineralization of the Common Groundwater Pollutant 2,6-Dichlorobenzamide (BAM) and its Metabolite 2,6-Dichlorobenzoic Acid (2,6-DCBA) in Sand Filter Units of Drinking Water Treatment Plants.

The intrinsic capacity to mineralize the groundwater pollutant 2,6-dichlorobenzamide (BAM) and its metabolite 2,6-dichlorobenzoic acid (2,6-DCBA) was evaluated in samples from sand filters (SFs) of drinking water treatment plants (DWTPs). Whereas BAM mineralization occurred rarely and only in SFs exposed to BAM, 2,6-DCBA mineralization was common in SFs, including those treating uncontaminated water. Nevertheless, SFs treating BAM contaminated water showed the highest 2,6-DCBA mineralization rates. For comparison, 2,6-DCBA and BAM mineralization were determined in various topsoil samples. As in SF samples, BAM mineralization was rare, whereas 2,6-DCBA mineralization capacity appeared widespread, with high mineralization rates found especially in forest soils. Multivariate analysis showed that in both SF and soil samples, high 2,6-DCBA mineralization correlated with high organic carbon content. Adding a 2,6-DCBA degradation deficient mutant of the BAM mineralizing Aminobacter sp. MSH1 confirmed that 2,6-DCBA produced from BAM is rapidly mineralized by the endogenous microbial community in SFs showing intrinsic 2,6-DCBA mineralization. This study demonstrates that (i) 2,6-DCBA mineralization is widely established in SFs of DWTPs, allowing the mineralization of 2,6-DCBA produced during BAM degradation and (ii) the first metabolic step in BAM mineralization is rare in microbial communities, rather than its further degradation beyond 2,6-DCBA.

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water.

Anthropogenic activities have resulted in the intensified use of water resources. For example, open pit bitumen extraction by Canada’s oil sands operations uses an estimated volume of three barrels of water for every barrel of oil produced. The waste tailings–oil sands process water (OSPW)–are stored in holding ponds, and present an environmental concern as they are comprised of residual hydrocarbons and metals. Following the hypothesis that endogenous OSPW microbial communities have an enhanced tolerance to heavy metals, we tested the capacity of planktonic and biofilm populations from OSPW to withstand metal ion challenges, using Cupriavidus metallidurans, a known metal-resistant organism, for comparison. The toxicity of the metals toward biofilm and planktonic bacterial populations was determined by measuring the minimum biofilm inhibitory concentrations (MBICs) and planktonic minimum inhibitory concentrations (MICs) using the MBEC ™ assay. We observed that the OSPW community and C. metallidurans had similar tolerances to 22 different metals. While thiophillic elements (Te, Ag, Cd, Ni) were found to be most toxic, the OSPW consortia demonstrated higher tolerance to metals reported in tailings ponds (Al, Fe, Mo, Pb). Metal toxicity correlated with a number of physicochemical characteristics of the metals. Parameters reflecting metal-ligand affinities showed fewer and weaker correlations for the community compared to C. metallidurans, suggesting that the OSPW consortia may have developed tolerance mechanisms toward metals present in their environment.

Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park.

Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was investigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sustained DIR driven by oxidation of acetate, lactate, and H2 . Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abiotic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides. Pyrosequencing of 16S rRNA genes from enrichment cultures showed dominant sequences closely affiliated with Geobacter metallireducens, a mesophilic Fe(III) oxide reducer. Shotgun metagenomic analysis of enrichment cultures confirmed the presence of a dominant G.metallireducens-like population and other less dominant populations from the phylum Ignavibacteriae, which appear to be capable of DIR. Gene (protein) searches revealed the presence of heat-shock proteins that may be involved in increased thermotolerance in the organisms present in the enrichments as well as porin-cytochrome complexes previously shown to be involved in extracellular electron transport. This analysis offers the firstdetailed insight into how DIR may impact the Fe geochemistry and isotope composition of a Fe-rich, circumneutral pH geothermal environment.

The impact of various ozone pretreatment doses on the performance of endogenous microbial communities for the remediation of oil sands process-affected water

The effects of different ozone pretreatment doses on the performance of endogenous microbial populations in degrading naphthenic acids (NAs) for the treatment of oil sands process-affected water (OSPW) were evaluated in this study. Ozone pretreatment enhanced OSPW biodegradability and accelerated the growth of microbial populations in bioreactors. After ozone pretreatment, the maximum chemical oxygen demand (COD) removal through biodegradation occurred at an ozone dose of 50 mg/L. Although OSPW pretreated with a higher ozone concentration removed a higher COD concentration and acid extractable fraction (AEF), organics removal through biodegradation was not further improved. After pretreatment with an ozone dose of 200 mg/L and bioreactor operation for 73 days, the batch bioreactor removed more than 80% of the COD and more than 95% of AEF. High-resolution mass spectrometry analysis showed complete degradation of NAs with specific degrees of cyclization (Z = −2 and −4) after combined treatments of ozonation and biodegradation. At high pretreatment doses of ozone (116 and 200 mg/L), biodegradation completely eliminated the toxicity of OSPW toward Vibrio fischeri (IC20 > 100% v/v).

Finding a Sugary Foothold: How Antibiotics Pave the Way for Enteric Pathogens

Antibiotic therapy predisposes the host to infections with human enteropathogens. In a recent study, Ng et al. (2013) demonstrate that antibiotic-mediated disruption of the microbial food web gives rise to free microbiota-liberated monosaccharides in the gut, which can promote growth of enteropathogenic bacteria.

Microbial communities within field‐collectedCuliseta melanuraandCoquillettidia perturbans

Although mosquitoes are well-known vectors of human and animal diseases, pathogens are only minor components of their total endogenous microbial communities. The midguts of many insects, including mosquitoes, contain diverse microbial communities. In this study, we used denaturing gradient gel electrophoresis to identify the diversity of bacteria in field-collected adult female Culiseta melanura (Diptera: Culicidae) (Coquillett) and Coquillettidia perturbans (Diptera: Culicidae) (Walker). Few significant differences in bacterial fauna between the two mosquito species were found, but the results suggest that host life history may be a determinant of the endogenous bacterial communities in mosquitoes. In the present study, the dominant bacteria are frequently identified as major components of other mosquito species' microbial flora, suggesting the establishment of a stable association between the mosquitoes and the microbes after initial acquisition from the environment.

Ingestion of metal-nanoparticle contaminated food disrupts endogenous microbiota in zebrafish (Danio rerio)

Nanoparticles (NPs) can be ingested by organisms, and NPs with antimicrobial properties may disrupt beneficial endogenous microbial communities and affect organism health. Zebrafish were fed diets containing Cu-NPs or Ag-NPs (500 mg kg−1 food), or an appropriate control for 14 d. Intestinal epithelium integrity was examined by transmission electron microscopy, and microbial community structure within the intestine was assessed by denaturing gradient gel electrophoresis (DGGE) of partial 16S rRNA. No lesions were observed in intestinal epithelia; however, presence of NPs in diets changed intestinal microbial community structure. In particular, some beneficial bacterial strains (e.g., Cetobacterium somerae) were suppressed to non-detectable levels by Cu-NP exposure, and two unidentified bacterial clones from the Firmicutes phylum were sensitive (not detected) to Cu, but were present in Ag and control fish. Unique changes in zebrafish microbiome caused by exposure to Ag-NP and Cu-NP indicate that NP ingestion could affect digestive system function and organism health.

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

Disruption of homeostasis between the host immune system and the intestinal microbiota leads to inflammatory bowel disease (IBD). Whether IBD is instigated by individual species or disruptions of entire microbial communities remains controversial. We characterized the fecal microbial communities in the recently described T-bet(-/-) ×Rag2(-/-) ulcerative colitis (TRUC) model driven by T-bet deficiency in the innate immune system. 16S rRNA-based analysis of TRUC and Rag2(-/-) mice revealed distinctive communities that correlate with host genotype. The presence of Klebsiella pneumoniae and Proteus mirabilis correlates with colitis in TRUC animals, and these TRUC-derived strains can elicit colitis in Rag2(-/-) and WT adults but require a maternally transmitted endogenous microbial community for maximal intestinal inflammation. Cross-fostering experiments indicated a role for these organisms in maternal transmission of disease. Our findings illustrate how gut microbial communities work in concert with specific culturable colitogenic agents to cause IBD.

Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure

The subsurface at the Oak Ridge Field Research Center represents an extreme and diverse geochemical environment that places different stresses on the endogenous microbial communities, including low pH, elevated nitrate concentrations, and the occurrence of heavy metals and radionuclides, including hexavalent uranium [U(VI)]. The in situ immobilization of U(VI) in the aquifer can be achieved through microbial reduction to relatively insoluble U(IV). However, a high redox potential due to the presence of nitrate and the toxicity of heavy metals will impede this process. Our aim is to test biostimulation of the endogenous microbial communities to improve nitrate reduction and subsequent U(VI) reduction under conditions of elevated heavy metals. Column experiments were used to test the possibility of using biostimulation via the addition of ethanol as a carbon source to improve nitrate reduction in the presence of elevated aqueous nickel. We subsequently analyzed the composition of the microbial communities that became established and their potential for U(VI) reduction and its in situ immobilization. Phylogenetic analysis revealed that the microbial population changed from heavy metal sensitive members of the actinobacteria, alpha- and gamma-proteobacteria to a community dominated by heavy metal resistant (nickel, cadmium, zinc, and cobalt resistant), nitrate reducing beta- and gamma-proteobacteria, and sulfate reducing Clostridiaceae. Coincidentally, synchrotron X-ray absorption spectroscopy analyses indicated that the resulting redox conditions favored U(VI) reduction transformation to insoluble U(IV) species associated with soil minerals and biomass. This study shows that the necessary genetic information to adapt to the implemented nickel stress resides in the endogenous microbial population present at the Oak Ridge FRC site, which changed from a community generally found under oligotrophic conditions to a community able to withstand the stress imposed by heavy metals, while efficiently reducing nitrate as electron donor. Once nitrate was reduced efficient reduction and in situ immobilization of uranium was observed. This study provides evidence that stimulating the metabolism of the endogenous bacterial population at the Oak Ridge FRC site by adding ethanol, a suitable carbon source, results in efficient nitrate reduction under conditions of elevated nickel, and a decrease of the redox potential such that sulfate and iron reducing bacteria are able to thrive and create conditions favorable for the reduction and in situ immobilization of uranium. Since we have found that the remediation potential resides within the endogenous microbial community, we believe it will be feasible to conduct field tests. Biostimulation of endogenous bacteria provides an efficient tool for the successful in situ remediation of mixed-waste sites, particularly those co-contaminated with heavy metals, nitrate and radionuclides, as found in the United States and other countries as environmental legacies of the nuclear age.

Monitoring of the microbial community of a sequencing batch reactor bioaugmented to improve its phosphorus removal capabilities

The acclimatisation of an activated sludge to enhanced biological phosphorus removal conditions was followed after and without bioaugmentation with a low amount of phosphorus-accumulating sludge. Phosphorus removal yields were monitored by conventional analytical methods and microbial communities evolutions were followed by a finger printing molecular technique (PCR-SSCP). While the benefit of the bioaugmentation seems real at the level of the reactor parameters, bioaugmentation speeded up the installation of good and stable phosphorus removal yield, the establishment of the inoculated microbial community in the bioaugmented reactor is still unclear. Both the bioaugmented and the control microbial communities evolved in a similar way to end up with apparently comparable populations. At the time of the experiment, the results suggest that the microbial community inoculated for the bioaugmentation did not establish in the reactor but compensated for phosphorus accumulation until the acclimatisation of an endogenous microbial community arose.

Microcalorimetry as a tool to detect changes in soil microbial biomass

High levels of heavy metals such as Cu, Zn and Pb have been found in soils to which composted municipal waste have been added over long periods of time. The impact of heavy metals on the endogenous microbial community was studied by measuring total microbial biomass and biomass activity in soils which contained either low or high heavy metal concentrations. Methods used were fumigation‐incubation, ATP extraction and microcalorimetry. The total amount of microbial biomass was not correlated with the total extractable amounts of heavy metals (extraction with aqua regia) nor with the NH4OAc‐EDTA extractable amounts. Neither the apparent growth rate constants of glucose‐amended soils, as estimated by microcalorimetry, nor the ATP contents were correlated with the amounts of heavy metals present. In contrast, the ratio of the heat evolved 2 hours after glucose addition to the ATP content increased with increasing concentrations of heavy metals. This ratio is a parameter which is inversely proportional to the e...

Composition of the product of algal culture in the liquid phase of animal slurry

AbstractThe composition of the product of algal culture in the liquid phase of slurry has been examined. The material consists of cells of the cultured alga (Chlorella vulgaris) together with those of the endogenous microbial community, and contains approximately 42% true protein, 23% carbohydrate, 16% lipid and 9% nucleic acid. The protein is deficient in the sulphur amino acids but rich in lysine. The latter feature appears to be related to the presence of hexanoic acid in slurry. The endogenous microorganisms do not make a significant direct contribution to the composition of material harvested after algal culture. Light and temperature have only slight effects upon composition of the harvested material.