Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour

The glioblastoma brain tumour (GBM) stands out as the most aggressive and resistant-to-treatment malignancy. Nevertheless, the gut-brain connection plays a pivotal role in influencing the growth and activation of the central nervous system. In this particular investigation, we aimed to assess and characterize the gut microbial ecosystem in GBM patients, both quantitatively and qualitatively. We collected faecal samples from 15 healthy volunteers and 25 GBM patients. To delve into the microbial content, we employed PCR-DGGE, targeting the V3 region of the 16S rRNA gene, and conducted qPCR to measure the levels of crucial intestinal bacteria. For a more in-depth analysis, high-throughput sequencing was performed on a selection of 20 random faecal samples (10 from healthy individuals and 10 from GBM patients), targeting the V3+V4 region of the 16S rRNA gene. Our findings from examining the richness and diversity of the gut microbiota unveiled that GBM patients exhibited significantly higher microbial diversity compared to healthy individuals. At the phylum level, Proteobacteria saw a significant increase, while Firmicutes experienced a noteworthy decrease in the GBM group. Moving down to the family level, we observed significantly elevated levels of Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae in GBM patients, while levels of Veillonellaceae, Rikenellaceae, and Prevotellaceae were notably lower. Delving into genera statistics, we noted a substantial increase in the abundance of Parasutterella, Escherichia-Shigella, and Bacteroides, alongside significantly lower levels of Ruminococcus 2, Faecalibacterium, and Prevotella_9 in the GBM group compared to the control group. Furthermore, when examining specific species, we found a significant increase in Bacteroides vulgatus and Escherichia coli in the GBM group. These observations collectively indicate a marked dysbiosis in the gut microbial composition of GBM patients. Additionally, the GBM group exhibited notably higher levels of alpha diversity when compared to the control group. This increase in diversity suggests a significant bacterial overgrowth in the gut of GBM patients in contrast to the controls. As a result, this research opens up potential avenues to gain a better understanding of the underlying mechanisms, pathways, and potential treatments for GBM, stemming from the significant implications of gut microbial dysbiosis in these patients.

Fungal Community Composition as Affected by Litter Chemistry and Weather during Four Years of Litter Decomposition in Rainshadow Coastal Douglas-Fir Forests

Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO₂ concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry.

Molecular Analysis of Soil Bacterial Community Structures for Environmental Risk Assessment with Varieties of Genetically Modified Soybean and Hot Pepper

With the advance in gene technology, genetically modified (GM) crops have increased in recent years. GM crops offer us various benefits. However, there are potential risks of GM crops for the environment. In this study, the impacts of transgenic plants on soil microbial community structures were assessed. Two varieties of soybean (Glycine max L.) and hot pepper (Capsicum annuum L.), which introduced the herbicide-resistant gene, bar, were used in this study. The effects of GM crops on soil microbial community structures were investigated using a cultural method, the denaturing gradient gel electrophoresis (DGGE) procedure, and 16S rRNA gene sequencing on the Illumina platform. Additionally, the persistence of transgenes was monitored using a quantitative real-time PCR procedure. The cultural method, DGGE analysis, and the amplicon-based community profile indicated that soil microbial communities were not significantly different between GM and non-GM lines. The level of the bar gene in GM soybean plots greatly increased when the crops were actively growing, but thereafter gradually decreased to the initial level. Meanwhile, the level of the bar gene in GM hot pepper plots repeatedly increased and decreased according to the flowering stages. These results indicated that soil microbial community structures were not significantly affected.

Hydrogeochemical controls on As and B enrichment in the aqueous environment from the Western Tibetan Plateau: A case study from the Singe Tsangpo River Basin

Although enrichment of As and B has been extensively observed in major rivers within the Tibetan Plateau, the mechanisms regulating natural enrichment of As and B in the river basins remain poorly understood. To evaluate the hydrogeochemical controls on the As and B enrichment in the aqueous environment in the western Tibetan Plateau, samples of river waters, river sediments, and groundwater were collected within the Singe Tsangpo River basin. The results revealed significant enrichment of As and B in river water (up to 104 μg L^-1 for As and 3.2 mg/L for B), river sediment (up to 141 mg/kg for As and 79.4 mg/kg for B), and groundwater (up to 73 μg /L for As and 2.5 mg/L for B). Moreover, the decreases in the molar ratios from the Ca²⁺ /(Na⁺+K⁺) in river water and the chemical index of alteration (CIA) in the sediments accompanied with the enrichment of heavier δ¹⁸O values along the river flow path suggested that, carbonate and silicate weathering were more substantial at the upper reaches, and the dissolution of evaporites was enhanced at the lower reaches. The As and B enrichment in the river waters primarily resulted from the discharge of geothermal springs, while the carbonate weathering has facilitated the B enrichment through providing HCO₃^- for the competitive adsorption with H₃BO₃ or B(OH)₄^- . In addition, the recharge of surface water into groundwater resulted in elevated As and B concentrations in the alluvial aquifers at the lower reaches of the Singe Tsangpo River. The present study highlighted that variations in the weathering processes within the river basin could significantly contribute to the enrichment of As and B, which can improve our understanding of hydrogeochemical controls on the transport and enrichment of trace elements at the catchment scale worldwide.

Improved PCR-DGGE analysis by emulsion-PCR for the determination of food geographical origin: A case study on Greek PDO "avgotaracho Mesolonghiou"

Greek avgotaracho Mesolonghiou (fish eggs from Flathead Mullet) is a highly valuable food product which holds Protected Destination of Origin status. The aim of this work was to use PCR-DGGE technique to examine whether there is a correlation between bacteria population in fish eggs and geographical origin. Cluster analysis of fish eggs from three geographical locations (Mesolonghi, Australia and Mauritania) discriminated samples according to their provenance. Moreover, we utilized emulsion-PCR amplification in DGGE analysis in order to investigate whether we could obtain further information about food products’ bacteria communities. PCR-DGGE proved to be a suitable method for fish eggs traceability, moreover emulsion PCR-DGGE provides better results. Emulsion-PCR can face up the existing limitations of conventional PCR and thus can be demonstrated as alternative molecular technique for complex and processed matrices, regarding food traceability and authentication.

•

Traceability of Greek PDO “avgotaracho Mesolonghiou” by PCR-DGGE is presented.

•

Emulsion PCR for DGGE” improves analysis of microbial communities.

•

Emulsion PCR for DGGE improves geographical traceability of food.

•

Emulsion PCR as an alternative molecular method for food traceability and authentication.

Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.

Computational analysis of successional changes in the microbial population and community diversity of the immobilized marine nitrifying bacterial consortium in a nitrifying packed bed bioreactor

Nitrifying bioreactor (NBR) connected to the recirculating aquaculture system (RAS), has a greater emphasis on the biological treatment of wastewater. Nitrifying bacterial consortium (NBC) formed bio-film on the substratum activating the NBR, and it was observed with high nitrification potential in shrimp maturation systems. Scanning Electron Microscopy (SEM) revealed the integrity of the biofilm substantiated with biomineralization. The fate of the matured bio-film population on subsequent operation under RAS, and the aggregated population at different points of RAS, including the rearing water were determined using fingerprints of Denaturing Gradient Gel Electrophoresis (DGGE). Altogether, 38 OTUs of biofilm sample and 35 OTUs of water samples represented the bacterial communities; the shared and unique OTUs indicated the diversity of the population at different time intervals in the operation of the NBR. The mathematical (range-weighted richness) and statistical (diversity indices) interpretation unveiled the OTUs based high bacterial diversity in the biofilm supporting the compositional changes and determined the distance between the community cluster. Ordination analyses indicated the population shift and stability of the activated bio-film till the matured biofilm community got established in the RAS. The DGGE with mathematical and statistical analysis revealed microbial diversity (high Shannon index, species richness and evenness), abundance (relative intensity), consecutive change in the population composition (OTUs, Rr index), and the dynamics (Δt) in the system during the operation.

Changes in microbial communities during phytoremediation of contaminated soil with phenanthrene

Although polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that affect negatively soils biology, several strategies lead to their removal such as the phytoremediation. In order to assess the potential of phytoremediation using "alfalfa" Medicago sativa as a strategy to reduce the phenanthrene on the soil, we analyzed the structure and dynamic of the microbial communities of a microcosm soil artificially contaminated with phenanthrene (2000 ppm), which was exposed to the plants. At different incubation times (7, 14, 21, 28, 42, and 56 days), a soil sample was taken from each microcosm and the residual amount of phenanthrene was quantified. Dehydrogenase activity and the count of fungi and bacteria were also estimated. Bacterial communities were characterized using PCR-DGGE, Shannon and Weaver's indexes, multivariate analysis, and rarefaction curves. It was found that phytoremediation treatment was associated with a higher richness and bacterial diversity compared with those on control soil. Although an OTUs (Operational Taxonomic Unit) succession over time was detected in both treatments, bacterial richness and diversity were conditioned by the phenanthrene concentration available and also dependent on the treatment, which were associated to different bacterial communities. In this study, phytoremediation treatment reduced the content of phenanthrene in the soil after 56 days to a 0.45% compared with the control treatment, which only reached to 4.25%. This preliminary work suggests the promoting activity of "alfalfa" plants, through rhizodegradation, to remove in soil PAHs, as well as its relevance in the activation of different ecological processes mediated by soil microorganisms.

Molecular characterization of alterations in the intestinal microbiota of patients with grade 3 hypertension

Hypertension has become a major risk factor for many diseases, including cardiovascular, cerebrovascular and kidney disorders. It has been reported that the composition of human gut microbiota is changed during the progression of cardiovascular and kidney diseases. The current study aimed to qualitatively and quantitatively compare the composition of gut microbiota between patients with hypertension and healthy controls. Fecal samples were collected from 50 patients diagnosed with grade 3 hypertension and 30 healthy controls. Touchdown PCR-denaturing gradient gel electrophoresis with primers specifically targeting the V3 region of 16S ribosomal RNA, and quantitative PCR, were performed to characterize all the samples. High-throughput sequencing of the V3-V4 regions was performed on 30 randomly selected samples. By comparing diversity and richness indices, the gut microbiome of the hypertensive individuals was found to be more diverse than that of the healthy controls. Among the main bacterial phlya that reside in the gut, Bacteroidetes, Firmicutes and Proteobacteria were dominant in all the samples; however the Firmicutes to Bacteroidetes ratio was variable, with a significant increase in the patients with hypertension compared with the healthy control group. In addition, at the genus level, there was an increased abundance of Prevotella_9, Megasphaera, Parasutterella and Escherichia-Shigella in patients with hypertension, while Bacteroides and Faecalibacterium were decreased. These results suggested that the human gut microbiota is altered in hypertension, and understanding the mechanism of these changes in microbial composition may open up new insights, and help to treat hypertension and other related diseases.

The role of bacteria in pine wilt disease: insights from microbiome analysis

Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient Gel Electrophoresis, 16S rRNA gene pyrosequencing, and a functional inference-based approach (PICRUSt). The bacterial community structure of the nematode was significantly different from the infected trees but closely related to the insect vector, supporting the hypothesis that the nematode microbiome might be in part inherited from the insect. Sampling location influenced mostly the tree microbiome (P < 0.05). Genes related both with plant growth promotion and phytopathogenicity were predicted for the tree microbiome. Xenobiotic degradation functions were predicted in the nematode and insect microbiomes. Phytotoxin biosynthesis was also predicted for the nematode microbiome, supporting the theory of a direct contribution of the microbiome to tree-wilting. This is the first study that simultaneously characterized the nematode, tree and insect-vector microbiomes from the same affected areas, and overall the results support the hypothesis that the PWD microbiome plays an important role in the disease's development.

Dietary supplementation of chestnut and quebracho tannins mix: Effect on caecal microbial communities and live performance of growing rabbits

The interest in antimicrobial compounds as feed additives is currently increasing. Among different options, tannins seem to have several beneficial effects when employed in animals diet. The present study aimed at investigating the influence on caecal microbial communities of the supplementation of a chestnut and quebracho tannins mix in meat rabbit's diet, also considering animals live performances. Four groups of rabbits were fed with a different diet: a control diet (C); a control diet with coccidiostat (CC), and two experimental diets with 0.3% (T0.3) and 0.6% (T0.6) chestnut and quebracho tannins mix. For microbial analysis, culture-dependent and culture-independent methods were employed. Live performances were not significantly affected by tannins mix supplementations, as well as culturable microbial loads of E. coli, Enterobacteriaceae, Bacteroides spp. and Bifidobacterium spp. C. perfringens was always under the detection limit. A consistent result was obtained by qPCR. As for PCR-DGGE analysis, the Richness and evenness (Shannon-Weiner index) of bacterial communities in caecum resulted significantly higher in control samples (C and CC) than in those from rabbit fed with tannin-containing diets. Sequencing analysis revealed that the phylum Firmicutes was less represented in samples from control groups. As for the methanogen archaeal DGGE, no significant differences were found in richness and diversity among different groups, all dominated by Methanobrevibacter spp.. This work highlights the potential antimicrobial effect of chestnut and quebracho tannins mix in an in vivo system revealed by molecular analysis.

Phosphorus source driving the soil microbial interactions and improving sugarcane development

The world demand for phosphate has gradually increased over the last decades, currently achieving alarming levels considering available rock reserves. The use of soil microorganisms, such as arbuscular mycorrhizal fungi (AMF), has been suggested as a promising alternative to improve phosphorus-use efficiency. However, the effect of the source of phosphorus on the interactions within the soil microbial community remains unclear. Here, we evaluated the links between the total dry matter content of sugarcane and the interactions within the soil microbial community under different phosphate sources, with/without AMF inoculation. The phosphate sources were Simple Superphosphate (SS, 18% of P2O5), Catalão rock phosphate (CA, 2.93% of P2O5) and Bayovar rock phosphate (BA, 14% of P2O5). The results indicated that the BA source led to the largest total dry matter content. The phosphate source affected total dry matter and the structure of the soil microbial communities. The bacterial interactions increased across sources with high percentage of P2O5, while the fungal interactions decreased. The interactions between bacterial and fungal microorganisms allowed to identify the percentage of P2O5 resulting in the highest total sugarcane dry matter. Our findings suggested the soil microbial interactions as a potential microbial indicator helping to improve the agricultural management.

Aerobic and anaerobic enrichment cultures highlight the pivotal role of facultative anaerobes in soil hydrocarbon degradation

Aliphatic and aromatic hydrocarbons are ubiquitous in the environment due to natural and anthropogenic processes. Under aerobic conditions hydrocarbons can be rapidly biodegraded but oxygenated environments often quickly become anaerobic when microbial respiration is coupled to contaminant oxidation. Most studies in literature usually focus on the initial microbial diversity of the hydrocarbon impacted environment and examine either aerobic or anaerobic conditions for enrichment. Hence, the aim of the present study was to enrich bacterial consortiums from two diesel impacted soil samples under both these conditions to assess the enrichment diversities and hydrocarbon degradation potentials. This would shed light upon how an environmental population shift would correlate to oxygen intrusion and depletion and still continue hydrocarbon degradation. Analysis of the 16S rRNA gene sequences showcases the different microbial populations that could emerge as the environmental factors change, resulting in different populations that are still capable of hydrocarbon degradation. Microbial diversity analysis also highlights the role of facultative anaerobic bacteria like Pseudomonas spp. and Citrobacter spp. in maintaining hydrocarbon degradation. This study shows that microorganisms capable of surviving under both oxic and anoxic (aerobic and anaerobic) conditions are the most crucial to the long term degradation of hydrocarbons in the environment.

Comparison of oral microbiota in orthodontic patients and healthy individuals

Orthodontic treatments often include dental displacement using a fixed retainer such as braces, which may result in the accumulation of plaque that provides a suitable environment for microorganisms to cause oral infection. So, this study was designed to investigate the microbial diversity among orthodontic patients and healthy individuals.

METHODS

Fifty individuals i.e. 30 orthodontic patients and 20 normal individuals were included in this study. Samples were collected during the midterm of orthodontic treatment (10-12 months). Saliva samples were collected and total DNA was isolated. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) with universal primers targeting the V3 region of 16s rRNA was used to study the bacterial diversity among different orthodontic and control groups. After DGGE profile analysis, the predominant product bands from the gel were excised, cloned, and sequenced to confirm the taxonomic identity followed by its quantification by using real-time PCR with gene-specific primers.

RESULTS

Both orthodontic treatment and control groups formed two distinct clustering profiles, but the Shannon-Weaver index (H') indicated greater microbial diversity in the orthodontic group (P = 0.08). Sequence analysis and real-time PCR revealed a greater number of Pseudomonas spp. in the orthodontic group, while there was no significant difference in Streptococcal spp.

CONCLUSION

This study suggested alterations in the oral microbiota following orthodontic treatment would provide diagnostic tools to identify prevalent microbes associated with oral infections that may prove useful for developing future therapies.

Effects of floodgates operation on nitrogen transformation in a lake based on structural equation modeling analysis

Floodgates operation is one of the primary means of flood control in lake development. However, knowledge on the linkages between floodgates operation and nitrogen transformation during the flood season is limited. In this study, water samples from six sampling sites along Lake Xingkai watershed were collected before and after floodgates operation. The causal relationships between environmental factors, bacterioplankton community composition and nitrogen fractions were determined during flood season. We found that concentrations of nitrogen fractions decreased significantly when the floodgates were opened, while the concentrations of total nitrogen (TN) and NO₃^- increased when the floodgates had been shut for a period. Further, we proposed a possible mechanism that the influence of floodgates operation on nitrogen transformation was largely mediated through changes in dissolved organic matter, dissolved oxygen and bacterioplankton community composition as revealed by structural equation modeling (SEM). We conclude that floodgates operation has a high risk for future eutrophication of downstream watershed, although it can reduce nitrogen content temporarily. Therefore, the environmental impacts of floodgates operation should be carefully evaluated before the floodwaters were discharged into downstream watershed.

Vancomycin and ceftriaxone can damage intestinal microbiota and affect the development of the intestinal tract and immune system to different degrees in neonatal mice

This study aimed to determine how antibiotic-driven intestinal dysbiosis impairs the development and differentiation of the digestive tract and immune organs of host animals. BALB/C neonatal mice were orally administered ceftriaxone or vancomycin from postnatal day 1 to day 21 and sacrificed on day 21. The diversity and abundance of the intestinal bacteria, morphological changes and barrier function of intestinal tract, and the splenic CD4+CD25+Foxp3+ T cells were investigated. The gut microbiota and intestinal tissue were damaged, and the numbers of Ki67-, Muc2- and ZO-1-positive cells were significantly decreased in the antibiotic treatment groups. Furthermore, the administration of ceftriaxone, but not vancomycin, led to a significant reduction in the abundance of splenic CD4+CD25+Foxp3+ T cells. Each antibiotic caused intestinal dysbiosis and characteristically influenced the regeneration of intestinal epithelial cells, formation of the intestinal mucus layer and tight junctions, and differentiation of splenic Foxp3+ Treg cells of the neonatal mice before any clinical side effects were observed. The potent ability of each antibiotic to affect the makeup of intestinal commensal microbiota may be a key determinant of the spectrum of antibiotics and influence the health of the host animal, at least partly.

Can phosphorus application and cover cropping alter arbuscular mycorrhizal fungal communities and soybean performance after a five-year phosphorus-unfertilized crop rotational system?

Background

Understanding diversity of arbuscular mycorrhizal fungi (AMF) is important for optimizing their role for phosphorus (P) nutrition of soybeans (Glycine max (L.) Merr.) in P-limited soils. However, it is not clear how soybean growth and P nutrition is related to AMF colonization and diversity of AMF communities in a continuous P-unfertilized cover cropping system. Thus, we investigated the impact of P-application and cover cropping on the interaction among AMF colonization, AMF diversity in soybean roots, soybean growth and P nutrition under a five-year P-unfertilized crop rotation.

Methods

In this study, we established three cover crop systems (wheat, red clover and oilseed rape) or bare fallow in rotation with soybean. The P-application rates before the seeding of soybeans were 52.5 and 157.5 kg ha^-1 in 2014 and 2015, respectively. We measured AMF colonization in soybean roots, soybean growth parameters such as aboveground plant biomass, P uptake at the flowering stage and grain yields at the maturity stage in both years. AMF community structure in soybean roots was characterized by specific amplification of small subunit rDNA.

Results

The increase in the root colonization at the flowering stage was small as a result of P-application. Cover cropping did not affect the aboveground biomass and P uptake of soybean in both years, but the P-application had positive effects on the soybean performance such as plant P uptake, biomass and grain yield in 2015. AMF communities colonizing soybean roots were also significantly influenced by P-application throughout the two years. Moreover, the diversity of AMF communities in roots was significantly influenced by P-application and cover cropping in both years, and was positively correlated with the soybean biomass, P uptake and grain yield throughout the two years.

Discussion

Our results indicated that P-application rather than cover cropping may be a key factor for improving soybean growth performance with respect to AMF diversity in P-limited cover cropping systems. Additionally, AMF diversity in roots can potentially contribute to soybean P nutrition even in the P-fertilized cover crop rotational system. Therefore, further investigation into the interaction of AMF diversity, P-application and cover cropping is required for the development of more effective P management practices on soybean growth performance.

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought

Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are also nitrogen limited and depend on plant associated diazotrophs as their source of ‘new’ nitrogen. A 4-year study was conducted to investigate the structure and composition of the rhizosphere diazotroph assemblages associated with 5 distinct plant zones in one such salt marsh. A period of greatly restricted tidal inundation and precipitation, as well as two periods of drought (June–July 2004, and May 2007) occurred during the study. DGGE of nifH PCR amplicons from rhizosphere samples, Principal Components Analysis of the resulting banding patterns, and unconstrained ordination analysis of taxonomic data and environmental parameters were conducted. Diazotroph assemblages were organized into 5 distinct groups (R² = 0.41, p value < 0.001) whose presence varied with the environmental conditions of the marsh. Diazotroph assemblage group detection differed during and after the drought event, indicating that persistent diazotrophs maintained populations that provided reduced supplies of new nitrogen for vegetation during the periods of drought.

Bacterial microbiota of Aedes aegypti mosquito larvae is altered by intoxication with Bacillus thuringiensis israelensis

Background

Insect microbiota is a dynamic microbial community that can actively participate in defense against pathogens. Bacillus thuringiensis (Bt) is a natural entomopathogen widely used as a bioinsecticide for pest control. Although Bt’s mode of action has been extensively studied, whether the presence of microbiota is mandatory for Bt to effectively kill the insect is still under debate. An association between a higher tolerance and a modified microbiota was already evidenced but a critical point remained to be solved: is the modified microbiota a cause or a consequence of a higher tolerance to Bt?

Methods

In this study we focused on the mosquito species Aedes aegypti, as no work has been performed on Diptera on this topic to date, and on B. thuringiensis israelensis (Bti), which is used worldwide for mosquito control. To avoid using antibiotics to cure bacterial microbiota, mosquito larvae were exposed to an hourly increasing dose of Bti during 25 hours to separate the most susceptible larvae dying quickly from more tolerant individuals, with longer survival.

Results

Denaturing gradient gel electrophoresis (DGGE) fingerprinting revealed that mosquito larval bacterial microbiota was strongly affected by Bti infection after only a few hours of exposure. Bacterial microbiota from the most tolerant larvae showed the lowest diversity but the highest inter-individual differences. The proportion of Bti in the host tissue was reduced in the most tolerant larvae as compared to the most susceptible ones, suggesting an active control of Bti infection by the host.

Conclusions

Here we show that a modified microbiota is associated with a higher tolerance of mosquitoes to Bti, but that it is rather a consequence of Bti infection than the cause of the higher tolerance. This study paves the way to future investigations aiming at unraveling the role of host immunity, inter-species bacterial competition and kinetics of host colonization by Bti that could be at the basis of the phenotype observed in this study.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2741-8) contains supplementary material, which is available to authorized users.

Comparison of automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques for analysing the influence of diet on ruminal bacterial diversity

The objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design. Bacterial pellets (LAB and SAB) were isolated at 2 h post-feeding for DNA extraction and analysed by ARISA and DGGE. The number of peaks in individual samples ranged from 48 to 99 for LAB and from 41 to 95 for SAB with ARISA, and values of DGGE-bands ranged from 27 to 50 for LAB and from 18 to 45 for SAB. The LAB samples from high concentrate-fed animals tended (p < 0.10) to show greater peak numbers and Shannon index values than those isolated from high forage-fed animals with ARISA, but no differences were identified with DGGE. The SAB samples from high concentrate-fed animals had lower (p < 0.05) peak numbers and Shannon index values than those from animals fed high-forage diets with ARISA, but only a trend was noticed for these parameters with DGGE (p < 0.10). The ARISA detected that animals fed alfalfa hay diets showed lower (p < 0.05) SAB diversity than those fed grass hay diets, but no differences were observed with DGGE. No effect of forage type on LAB diversity was detected by any technique. In this study, ARISA detected some changes in ruminal bacterial communities that were not detected by DGGE, and therefore ARISA was considered more appropriate for assessing bacterial diversity of ruminal bacterial pellets. The results highlight the impact of the fingerprinting technique used to draw conclusions on dietary factors affecting bacterial diversity in ruminal bacterial pellets.

Bioremediation of PAH-contaminated farmland: field experiment

The agricultural soil contaminated by polycyclic aromatic hydrocarbons (PAHs) is gradually emerging and becoming serious in China with the rapid development of economy. To reduce the risk of PAHs in agricultural soil and guarantee the food safety, the biological agent that Mycobacterium gilvum immobilized on modified peanut shell powder enhanced remediation of polycyclic aromatic hydrocarbon-contaminated vegetable farmland was investigated under the conditions of the field experiment. The results indicated that adding biological agent could promote PAH degradation in the soil, especially high-ring PAHs. The degradation rates of PAHs in the soil could be further improved to 16.5-43.5 %, respectively, compared with the soil without the biological agent. Adding the biological agent could significantly improve soil dehydrogenase activity and microbial diversity. It also could reduce the enrichment of PAHs in mustard planted in the polluted field, which indicated that the biological treatments might be less ecological risk. The work suggested that adding the biological agent might be a promising in situ bioremediation strategy for PAH-contaminated farmland field.

Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients

The gut microbiota has a crucial effect on human health and physiology. Hypothyroid Hashimoto's thyroiditis (HT) is an autoimmune disorder manifested with environmental and genetic factors. However, it is hypothesized that intestinal microbes might play a vital role in the pathogenesis of HT. The aim of current was to investigate and characterize the gut microbial composition of HT patients both quantitatively and qualitatively. The fecal samples from 29 HT patients and 12 healthy individuals were collected. The PCR-DGGE targeted V3 site of 16S rRNA gene and real time PCR for Bifidobacterium Lactobacillus, Bacteroides vulgatus and Clostridium leptum were performed. Pyrosequencing of 16S rRNA gene with V4 location was performed on 20 randomly selected samples. The comparative analysis of diversity and richness indices revealed diversification of gut microbiota in HT as compared to control. The statistical data elucidate the alterations in phyla of HT patients which was also affirmed at the family level. We observed the declined abundance of Prevotella_9 and Dialister, while elevated genera of the diseased group included Escherichia-Shigella and Parasutterella. The alteration in gut microbial configuration was also monitored at the species level, which showed an increased abundance of E. coli in HT. Therefore, the current study is in agreement with the hypothesis that HT patients have intestinal microbial dysbiosis. The taxa statistics at species-level along with each gut microbial community were modified in HT. Thus, the current study may offer the new insights into the treatment of HT patients, disease pathway, and mechanism.

Application of Denaturing Gradient Gel Electrophoresis to the Analysis of Bacterial Communities Associated With Asymptomatic and Symptomatic Pericoronitis

PURPOSE

Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities associated with asymptomatic and symptomatic pericoronitis. The aim of the study was to compare the fingerprinting patterns of these 2 clinical conditions.

MATERIALS AND METHODS

The microbiota of mandibular third molar pockets associated with asymptomatic or symptomatic pericoronitis cases were collected and profiled by the polymerase chain reaction DGGE method. Banding patterns were compared by cluster analysis techniques.

RESULTS

Thirteen symptomatic pericoronitis and 7 asymptomatic pericoronitis samples were collected. Comparative analysis of the 2 clinical conditions showed bands that were common to the symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique to the clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles was 23.8 ± 4.2 (range, 19 to 34) for samples from symptomatic cases and 24.1 ± 2.4 (range, 21 to 29) for those from asymptomatic cases. Cluster analysis and multidimensional scaling analysis of the DGGE banding pattern showed a distinction in the similarity of banding patterns according to the presence or absence of symptoms.

CONCLUSIONS

These results suggest that the diversity of pericoronal pocket microbiota in asymptomatic pericoronitis cases differs markedly from that of symptomatic cases.

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance

Bio-treatment of flotation wastewater has been proven to be both effective and economical, as a treatment method. Despite this, little is known regarding the effects of toxic organic floatation reagents such as Dianilinodithiophosphoric acid (DDA), on the microbial community performance or dynamics, which are critical to the effective performance of the bio-treatment reactor. A submerged membrane bioreactor (sMBR) was constructed to continuously treat simulated wastewater contaminated with DDA, an organic flotation reagent that is now considered a significant pollutant. The performance of the sMBR system was investigated at different DDA loading concentrations, with assessment of the effects of DDA on the microbial communities within the sMBR, in particular the biodiversity and succession within the microbial community. Results showed that, with increased DDA loadings, the performance of the sMBR was initially negatively affected, but the system adapted efficiently and consistently reached a COD removal rate of up to 80%. Increased DDA loading concentrations had an adverse effect on the activity of both the activated sludge and microbial communities, resulting in a large alteration in microbial dynamics, especially during the start-up stage and the high DDA loading stage. Strains capable of adapting to the presence of DDA, capable of degrading DDA or utilizing its byproducts, were enriched within the sMBR community, such as Zoogloea, Clostridium, Sideroxydans lithotrophicus, Thiobacillus, Thauera amino aromatica and Alicycliphilus denitrificans.

Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain

Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

Streptomyces effect on the bacterial microbiota associated to Crassostrea sikamea oyster

AIM

To determine the composition and diversity of the microbiota associated to Crassostrea sikamea treated during 30 days with Streptomyces strains N7 and RL8.

METHODS AND RESULTS

DNA was extracted from oysters followed by 16S rRNA gene amplification and pyrosequencing. The highest and lowest species diversity richness was observed in the initial and final control group, whereas Streptomyces-treated oysters exhibited intermediate values. Proteobacteria was the most abundant phylum (81·4-95·1%), followed by Bacteroidetes, Actinobacteria and Firmicutes. The genera Anderseniella, Oceanicola, Roseovarius, Ruegeria, Sulfitobacter, Granulosicoccus and Marinicella encompassed the core microbiota of all experimental groups. The genus Bacteriovorax was detected in all groups except in the final control and the depurated N7, whereas Vibrio remained undetected in all Streptomyces-treated groups. RL8 was the only group that harboured the genus Streptomyces in its microbiota. Principal component analysis showed that Streptomyces strains significantly changed oyster microbiota with respect to the initial and final control.

CONCLUSIONS

Crassostrea sikamea treated with Streptomyces showed high species diversity and a microbiota composition shift, characterized by keeping the predator genus Bacteriovorax and decreasing the pathogenic Vibrio.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first culture-independent study showing the effect of Streptomyces over the oyster microbiota. It also sheds light about the potential use of Streptomyces to improve mollusc health and safety for consumers after the depuration process.

Feasibility of using a microalgal-bacterial consortium for treatment of toxic coke wastewater with concomitant production of microbial lipids

This study examined the feasibility of using an algal-bacterial process for removal of phenol and NH₄⁺-N from differently diluted coke wastewater with simultaneous production of biomass. Under illumination, microalgal-bacterial (MSB) cultures performed complete phenol degradation at all dilutions of coke wastewater while sole microalgal culture (MSA) degraded a maximum of 27.3% of phenol (initial concentration: 24.0mgL^-1) from 5-fold diluted wastewater. Furthermore, the MSB culture had the highest rate of NH₄⁺-N removal (8.3mgL^-1d^-1) and fatty acid production (20mgL^-1d^-1) which were 2.3- and 1.5-fold higher than those observed in the MSA cultures, probably due to decreases in toxic organic pollutants. Multivariate analyses indicated that co-cultivation of activated sludge was directly correlated with the elevated removals of phenol and NH₄⁺-N. In the presence of sludge, adequate dilution of the coke wastewater can maximize the effect of bacteria on NH₄⁺-N removal and biomass production.

Diazinon dissipation in pesticide-contaminated paddy soil: kinetic modeling and isolation of a degrading mixed bacterial culture

Dissipation kinetics of diazinon was investigated in soils culled from a paddy field with a long history of the pesticide application. Goodness of fit statistical indices derived from several fitted mono- and bi-exponential kinetic models revealed a bi-phasic pattern of the diazinon dissipation curve at 15 and 150 mg kg^-1 spiking levels, which could be described best by the first-order double exponential decay (FODED) model. Parameters obtained from this model were able to describe the enhanced dissipation of diazinon as the result of repeated soil applications, where a larger fraction of the pesticide readily available in the solution phase was dissipated with a fast rate. Cluster and principal component analysis (PCA) of denaturing gradient gel electrophoresis (DGGE) obtained from soil bacterial populations revealed that they were only affected at the 150 mg kg^-1 diazinon concentration. This was also supported by the phylogenetic tree obtained from sequences of the main gel bands. Accordingly, bacterial populations belonging to Proteobacteria were enriched in the soil following three treatments with diazinon at 150 mg kg^-1. The Shannon's index revealed a nonsignificant increase (P ≤ 0.05) in overall diversity of soil bacteria following diazinon application. Diazinon-degrading bacteria were isolated from the paddy soils in a mineral salt medium. Results showed that the isolated mixed culture was able to remove 90% of the pesticide at two concentrations of 50 and 100 mg L^-1 by 16.81 and 19.60 days, respectively. Sequencing the DGGE bands confirmed the role of Betaproteobacteria as the main components of the isolated mixed culture in the degradation of diazinon.

Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics

OBJECTIVE

To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages.

METHODS

The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database.

RESULTS

Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways.

CONCLUSION

Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

Effects on intestinal microbiota and immune genes of Solea senegalensis after suspension of the administration of Shewanella putrefaciens Pdp11

The interaction host-intestinal microbiota is essential for the immunological homeostasis of the host. Probiotics, prebiotics and synbiotics are promising tools for the manipulation of the intestinal microbiota towards beneficial effects to the host. The objective of this study was to evaluate the modulation effect on the intestinal microbiota and the transcription of genes involved in the immune response in head kidney of Solea senegalensis after administration of diet supplemented with the prebiotic alginate and the probiotic Shewanella putrefaciens Pdp11 CECT 7627 (SpPdp11). The results showed higher adaptability to dietary changes in the intestinal microbiota of fish fed diet with alginate and SpPdp11 together compared to those fish that received an alginate-supplemented diet. The alginate-supplemented diet produced up-regulation of genes encoding proteins involved in immunological responses, such as complement, lysozyme G and transferrin, and oxidative stress, such as NADPH oxidase and glutation peroxidase. On the other hand, the administration of alginate combined with SpPdp11 resulted in a significant increase of the transcription of genes encoding for glutation peroxidase and HSP70, indicating a potential protective effect of SpPdp11 against oxidative stress. In addition, these effects were maintained after the suspension of the probiotic treatment. The relationship between the modulation of the intestinal microbiota and the expression of genes with protective effect against the oxidative stress was demonstrated by the Principal Components Analysis.

Community structures and antagonistic activities of the bacteria associated with surface-sterilized pepper plants grown in different field soils

Endophytic bacteria may act individually or in consortia in controlling certain plant diseases. In this study, pepper plants (Capsicum annuum L. cv. Nokkwang) were cultivated in glasshouse conditions using field soils collected from two different geographic locations, Deokso (DS) and Gwangyang (GY) in Korea. Community structure and antifungal activity of pepper endophytic bacteria were analyzed using culture-independent (PCR-DGGE) and culture-dependent (plating) methods, respectively. Dissimilarities were observed between DGGE profiles of DS and GY samples at all plant tissues. However, sequencing of the major DGGE bands revealed an enrichment of Firmicutes in the leaves of plants propagated in either soil. Similar results were observed with the culturable assays. Firmicutes dominated the isolates from both leaf samples, DS leaf (100 %) and GY leaf (83.3 %), although the genus compositions of DS leaf and GY leaf isolates were different. We assessed the antifungal activity of each isolate recovered to better understand the potential role that these endophytic bacteria may play. Of the 27 representative isolates from DS plant samples, 17 isolates (63.0 %) had antagonistic activity against at least one of the fungi tested. Seventeen isolates from GY plant samples (58.6 %) displayed antagonistic properties. The results show that the endophytic communities differ in the same plant species when propagated in different soils. Exploring the internal tissues of plants growing in diverse soil environments could be a way to find potential candidates for biocontrol agents.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms

The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency.

Geomicrobiological Features of Ferruginous Sediments from Lake Towuti, Indonesia

Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site-a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae, Chloroflexi, and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.

Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure

In situ biofilm sampling is a key step for the study of natural biofilms and using methodologies that reflect natural diversity is necessary to guarantee representative sampling. Here, we focalise on the impact of the type of substrata on which biofilms grow on bacterial and fungal communities’ structure. The indirect molecular approach, Denaturing Gel Gradient Electrophoresis (DGGE) of a gene fragment coding for either 16S rRNA or 28S rRNA, for bacteria or fungi respectively, was used to evaluate the variability of microbial community structures among different biofilm substrata: natural (pebbles, live plants, wood and sediment), or artificial (glass, Plexiglas^® and sterile wood), in a small river (the Loiret, France). Multivariate statistics, band richness and diversity indexes (Shannon and Simpson) were used to highlight variations in community structure between substrata. Results showed variations of bacterial and fungal diversity between different substrata according to substratum properties/origin (natural or artificial, organic or inorganic) but there was no optimal substratum for sampling, and artificial substrata were not significantly less applicable than natural substrata. Pooling 4 different substrata types allowed a higher bacterial and fungal biodiversity recovery. Point contact sampling may thus gain in robustness by increasing the number of substrata considered. Fungal species richness was similar to the bacterial one on most substrata which suggested they should be more frequently considered in riverine biofilm studies.

Effects of microcystin-LR on gut microflora in different gut regions of mice

To reveal the toxicological effects of the hepatotoxic microcystin-leucine arginine (MC-LR) on gut microbial community composition in different gut regions, we conducted a subchronic exposure of BALB/c mice to MC-LR via intragastric administration. Denaturing gradient gel electrophoresis (DGGE) was employed to profile the shifts of microbes after MC-LR treatment in the jejuno-ileum, caecum and colon. DGGE profiles analysis showed that MC-LR increased the microbial species richness (number of microbial bands) in the caecum and colon as well as microbial diversity (Shannon-Wiener index) in the caecum. The cluster analysis of DGGE profiles indicated that the microbial structures in the caecum and colon shifted significantly after MC-LR treatment, while that in the jejuno-ileum did not. All the relatively decreased gut microbes belonged to Clostridia in the Firmicutes phylum, and most of them were Lachnospiraceae. The increased ones derived from a variety of microbes including species from Porphyromonadaceae and Prevotellaceae in the Bacteroidetes phylum, as well as Lachnospiraceae and Ruminococcaceae in the Firmicutes phylum, and among which, the increase of Barnesiella in Porphyromonadaceae was most remarkable. In conclusion, subchronic exposure to MC-LR could disturb the balance of gut microbes in mice, and its toxicological effects varied between the jejuno-ileum and the other two gut regions.

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus

Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects’ tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects’ tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD.

Functional and structural responses of soil N-cycling microbial communities to the herbicide mesotrione: a dose-effect microcosm approach

Microbial communities driving the nitrogen cycle contribute to ecosystem services such as crop production and air, soil, and water quality. The responses to herbicide stress of ammonia-oxidizing and ammonia-denitrifying microbial communities were investigated by an analysis of changes in structure-function relationships. Their potential activities, abundances (quantitative PCR), and genetic structure (denaturing gradient gel electrophoresis) were assessed in a microcosm experiment. The application rate (1 × FR, 0.45 μg g(-1) soil) of the mesotrione herbicide did not strongly affect soil N-nutrient dynamics or microbial community structure and abundances. Doses of the commercial product Callisto® (10 × FR and 100 × FR) or pure mesotrione (100 × FR) exceeding field rates induced short-term inhibition of nitrification and a lasting stimulation of denitrification. These effects could play a part in the increase in soil ammonium content and decrease in nitrate contents observed in treated soils. These functional impacts were mainly correlated with abundance shifts of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) or denitrifying bacteria. The sustained restoration of nitrification activity, from day 42 in the 100 × FR-treated soils, was likely promoted by changes in the community size and composition of AOB, which suggests a leading role, rather than AOA, for soil nitrification restoration after herbicide stress. This ecotoxicological community approach provides a nonesuch multiparameter assessment of responses of N-cycling microbial guilds to pesticide stress.