16S rDNA Libraries Research Articles

Alteration in microbes changed the contents of oviposition-deterrent pheromones on the Spodoptera litura egg surface.

Microorganisms symbiotic with insects, whether permanently or temporarily, play a crucial role in the nutrition, development, reproduction, defence, and metamorphosis regulation. In some Lepidoptera, oviposition-deterrent pheromones (ODPs) on egg surface were used by pregnant females to modify the behaviour of conspecifics to avoid excessive competition for limited resources. In this study, we constructed four different Spodoptera litura groups, including, OH, OA, SH, and OA, which either feed on different hosts or grow in different environments. The 16S rDNA libraries of microbes from the egg surface of the four groups were constructed and sequenced. According to alpha and beta diversity indices, the microbes in environments and diets considerably influenced the richness, diversity, and community compositions of the microbiota on egg surfaces. The quantity of the main ODP components and the corresponding oviposition-deterrent activity among four groups were significantly differed among the four groups. The result of this study revealed that altering of microbes in environments or diets considerably changed the contents of ODP and oviposition-deterrent activity. As ODPs impart oviposition-deterrent activity towards closely related species, the findings of this study suggest that we should pay more attention to the role of symbiotic microorganisms in changing the ability of insects, especially sympatric species, to occupy the optimal niche when developing novel pest-control strategies.

Profiling of bacterial community’s dynamics inhibiting the intestinal tract of broiler chickens growing in naturally ventilated house

An experiment was conducted to evaluate the relative abundance of gastrointestinal microbial structures in different gut sections of Cobb500 broiler chickens reared in naturally ventilated houses and fed a standard diet for 35 days under the ambient environment of Oman. In this research, sequences from 1,179,068 16S rDNA analyses were grouped into 253 operational taxonomic units with a sequence similarity threshold of 97%. These units revealed the presence of seven phyla and twenty-six families. Firmicutes were found to be the dominant phylum in the duodenum (96.4%), jejunum (88.8%), ileum (96.8%), and cecum (96.8%). In contrast, Tenericutes and Thermi were the least prevalent phyla across these gut regions, accounting for between 0.01% and 0.12% of the total sequences. Actinobacteria, Bacteroidetes, and Cyanobacteria showed higher prevalence in the cecum (accounted for 6.59%, 7.42%, and 7.50%, respectively) than in duodenum, jejunum, and ileum. Lactobacillaceae were notably observed as the predominant family in the four gut segments, accounting for 73.87% in the duodenum, 43.30% in the jejunum, 77.81% in the ileum, and 46.30% in the caecum, collectively comprising a substantial portion of the sequencing data. Lachnospiraceae and Ruminococcaceae emerged as dominant families, comprising 28.61% and 30.8% of the sequencing data across all four intestinal sections, respectively. Statistical analysis of the 16S rDNA libraries showed that each section of the intestine contains a unique bacterial community with an increase in bacterial diversity parallel to age increase. The study's findings reveal the temporal dynamics of the chicken's gut microbiota in a naturally ventilated housing environment. The results obtained provide a unique perspective on the diversity of bacterial communities, highlighting significant differences in microbial composition across different segments of the intestine and offering practical insights for the management of broiler chicken health.

Grass Meal Acts as a Probiotic in Chicken

Probiotics can act as an alternative to antibiotics in animal feeding, but their use is minimal due to their expensive production. Dry grass is rich with bacteria beneficial for animal feeding and can be used as a probiotic. However, data about the quantitative dependence of the grass microbiome on environmental factors and seasons remain insufficient for preparing “grass-meal-based probiotics”. Four grass samples were collected in two geographically remote regions of Russia; their microbiome was characterized by metagenomic sequencing of 16S rDNA libraries and microbiological seeding, and biological testing of the grass meal was carried out on 6 groups of birds containing 20 Ross 308 cross broilers each for a period of 42 days. The positive control group (PC) obtained 16–25 mg/mL toltrazuril (coccidiostatic agent) and 0.5 mL/L liquid antibiotic enrostin (100 mg/mL ciprofloxacin and 106 MU/mL colistin sulfate in the commercial preparation) within the drinking water, while the negative control group (NC) obtained no medicines. Four experimental groups were fed the diet supplemented with 1% grass meal over the period of 7–42 days of life; no commercial medicines were used here. A spontaneous infection with Eimeria was registered in the NC control groups, which caused the loss of 7 chickens. No losses were registered in the PC group or the two experimental groups. In two other experimental groups, losses of coccidiosis amounted to 10% and 15%, respectively. All specimens of the grass meal demonstrated a significant effect on the average body weight gain compared to NC. Taken together, these observations support the hypothesis that the grass meal may substitute toltrazuril for protecting the chickens from parasitic invasion and increase average daily weight gain (ADG) as effectively as the antibiotic enrostin.

Tripartite interactions comprising yeast-endobacteria systems in the gut of vector mosquitoes.

It is shown that bacteria use yeast as a niche for survival in stressful conditions, therefore yeasts may act as temporary or permanent bacterial reservoirs. Endobacteria colonise the fungal vacuole of various osmotolerant yeasts which survive and multiply in sugar-rich sources such as plant nectars. Nectar-associated yeasts are present even in the digestive system of insects and often establish mutualistic symbioses with both hosts. Research on insect microbial symbioses is increasing but bacterial-fungal interactions are yet unexplored. Here, we have focused on the endobacteria of Wickerhamomyces anomalus (formerly Pichia anomala and Candida pelliculosa), an osmotolerant yeast associated with sugar sources and the insect gut. Symbiotic strains of W. anomalus influence larval development and contribute digestive processes in adults, in addition to exerting wide antimicrobial properties for host defence in diverse insects including mosquitoes. Antiplasmodial effects of W. anomalus have been shown in the gut of the female malaria vector mosquito Anopheles stephensi. This discovery highlights the potential of utilizing yeast as a promising tool for symbiotic control of mosquito-borne diseases. In the present study, we have carried out a large Next Generation Sequencing (NGS) metagenomics analysis including W. anomalus strains associated with vector mosquitoes Anopheles, Aedes and Culex, which has highlighted wide and heterogeneous EB communities in yeast. Furthermore, we have disclosed a Matryoshka-like association in the gut of A stephensi that comprises different EB in the strain of W. anomalus WaF17.12. Our investigations started with the localization of fast-moving bacteria-like bodies within the yeast vacuole of WaF17.12. Additional microscopy analyses have validated the presence of alive intravacuolar bacteria and 16S rDNA libraries from WaF17.12 have identified a few bacterial targets. Some of these EB have been isolated and tested for lytic properties and capability to re-infect the yeast cell. Moreover, a selective competence to enter yeast cell has been shown comparing different bacteria. We suggested possible tripartite interactions among EB, W. anomalus and the host, opening new knowledge on the vector biology.

Can the Salivary Microbiome Predict Cardiovascular Diseases? Lessons Learned From the Qatari Population.

Background: Many studies have linked dysbiosis of the gut microbiome to the development of cardiovascular diseases (CVD). However, studies assessing the association between the salivary microbiome and CVD risk on a large cohort remain sparse. This study aims to identify whether a predictive salivary microbiome signature is associated with a high risk of developing CVD in the Qatari population.Methods: Saliva samples from 2,974 Qatar Genome Project (QGP) participants were collected from Qatar Biobank (QBB). Based on the CVD score, subjects were classified into low-risk (LR < 10) (n = 2491), moderate-risk (MR = 10–20) (n = 320) and high-risk (HR > 30) (n = 163). To assess the salivary microbiome (SM) composition, 16S-rDNA libraries were sequenced and analyzed using QIIME-pipeline. Machine Learning (ML) strategies were used to identify SM-based predictors of CVD risk.Results: Firmicutes and Bacteroidetes were the predominant phyla among all the subjects included. Linear Discriminant Analysis Effect Size (LEfSe) analysis revealed that Clostridiaceae and Capnocytophaga were the most significantly abundant genera in the LR group, while Lactobacillus and Rothia were significantly abundant in the HR group. ML based prediction models revealed that Desulfobulbus, Prevotella, and Tissierellaceae were the common predictors of increased risk to CVD.Conclusion: This study identified significant differences in the SM composition in HR and LR CVD subjects. This is the first study to apply ML-based prediction modeling using the SM to predict CVD in an Arab population. More studies are required to better understand the mechanisms of how those microbes contribute to CVD.

Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

BackgroundThe eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).ResultsOur data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.ConclusionsThe short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes.8KR8qv6CEcKmimx9at5UakVideo Abtract.

Microbial Profile of the Leachate from Mexico City’s Bordo Poniente Composting Plant: An Inoculum to Digest Organic Waste

In recent years, municipal solid waste (MSW) management has become a complex problem worldwide. Similarly, Mexico City is facing such a situation for the management and treatment of organic fraction of municipal solid waste (OFMSW). Therefore, in this work, we investigated whether leachate from the composting plant, Bordo Poniente, located in Mexico City can be used as an inoculum for the treatment of OFMSW using thermophilic anaerobic digestion (AD) with a hydraulic retention time of 30 days. We analyzed the physicochemical properties of the leachate and performed a biochemical methane potential test. Archaeal and bacterial diversity was also identified using high throughput DNA sequencing of 16S rDNA libraries. Methane yield was 0.29 m3 CH4/kg VSadded in the positive control and 0.16 m3 CH4/kg VSadded in the treatment group. The phylum, Bacteroidetes, and genus, Methanosarcina, prevailed in the leachate. However, in thermophilic conditions, the microbial communities changed, and the phylum, Firmicutes, genera, Methanoculleus, and candidate genus, vadinCA11, were dominant in the treatment group. We concluded that the leachate contains a suitable initial charge of many active bacteria and methanogenic archaea which contribute to the AD process, hence it can be used as an inoculum for the treatment of OFMSW.

Influence of moderate beer consumption on human gut microbiota and its impact on fasting glucose and β-cell function.

Beer is a beverage that has been consumed worldwide for thousands of years due to social, religious, and cultural reasons; it contains polyphenolic compounds as well as phenolic acids with a potential positive effect on human health. This study aimed to explore the impact of moderate beer consumption on human health and gut microbiota diversity. Three hundred fifty-five mL of non-alcoholic beer (NAB) or alcoholic beer (AB) were consumed daily by the participants for 30 days in each study. Anthropometric measures, blood samples for biochemistry, and fecal samples for microbiota analysis were collected on Day 1 and Day 30. Microbial diversity was characterized by high-throughput sequencing of 16S rDNA libraries, and data were analyzed using the QIIME pipeline. We found that NAB and AB have effects on the composition of the gut microbiota, favoring the proliferation of Bacteroidetes with respect to Firmicutes. No increase in weight, waist, and hip parameters was observed, and the liver and lipid profile values were not modified for NAB. In addition, the consumption of NAB induced a decrease in fasting blood serum glucose and an increase in functional β cells, while, on the other hand, there was an increase in blood serum glucose and a decrease in functional β cells with the consumption of AB. In general, beer consumption neither changed anthropometric values, nor affected liver function. Although the glucose values decreased with NAB or increased with AB, they remained within the normal range. Our conclusion is that moderate consumption of NAB has a positive effect on human health via supplementation of biological active polyphenol and phenolic acids, and by enrichment of the gut microbiota diversity with beneficial bacteria, while the presence of alcohol in AB interferes with this effect. More work should be done on this topic before general conclusions are drawn.

The Study of Microbial Diversity in Mangrove Wetland Ecological System Based on a 16S rDNA Library

The microbial resources in mangrove wetland ecological system are abundant because of their special characteristics. However traditional methods of isolation and culture alone cannot analyze the microbial diversity fully and so, in this study, a 16S rDNA library was constructed to analyze microbial diversity in the Fugong mangrove of the Jiulong River Estuary, Fujian Province, China. The total sediment DNA was extracted, a 16S rDNA library constructed, and the clones analyzed using the restriction fragment length polymorphism (RFLP) method. The 16S rDNA sequences of 50 clones which had a higher display frequency in the RFLP analysis were blasted with the sequences in GenBank. The results showed that the highest similarity of the sequence in clones was 100%, while the lowest was 88%. The dominant microbes from mangrove sediments in the 16S rDNA library belonged to the Proteobacteria (70%) including α-proteobacteria (6.0%), γ-proteobacteria (22.0%), δ-proteobacteria (10.0%) and ε-proteobacteria (32.0%). The other microbes were Bacteroidetes (8.0%), Planctomycetacia (2.0%), Actinobacteria (2.0%) and Verrucomicrobia (2.0%). Additional uncultured microorganisms as well as those whose classification information was unclear were also detected (16.0%). The results of this study indicated that more objective and comprehensive information of microbial diversity in mangrove wetland ecological system had been obtained. There is abundant microbial diversity and a large amount of unknown microbial resources in mangrove wetland ecological system, which could have a very important potential, and so there should be more research to explore and utilize these microbial and functional gene resources in mangrove wetland ecological system.

Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

An accurate bacterial DNA quantification assay for HTS library preparation of human biological samples.

Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS). A qPCR method was optimized using universal 16S rDNA primers, and a commercially available bacterial community DNA standard was used to develop a precise standard curve. Following qPCR optimization, 16S rDNA libraries from saliva, vaginal and menstrual secretions, urine, and fecal matter were amplified and evaluated at various DNA concentrations; successful HTS data were generated with as low as 20 pg of bacterial DNA. Changes in bacterial DNA quantity did not impact observed relative abundances of major bacterial taxa, but relative abundance changes of minor taxa were observed. Accurate quantification of microbial DNA resulted in consistent, successful library preparations for HTS analysis.

Characterization of culturable bacteria from pulp and paper industry wastewater, with the potential for degradation of cellulose, starch, and lipids

The search for microbial enzymatic activities applied to wastewater treatment is an important task in environmental biotechnology. Microbial enzymes have been previously explored in hostile habitats. They are increasingly important in extreme habitats; biological wastewater from the pulp and paper mill industry can harbor microorganisms with valuable enzymatic capabilities that can improve the efficiency for the same process of depuration. This study was performed to characterize and evaluate cellulolytic, amylolytic, and lipolytic activities of bacteria isolated from a pulp and paper effluent. The enzymatic activities were evaluated by the formation of a clear halo around the colonies in defined substrate media. By the use of a sequence analysis of 16S rDNA libraries, isolates were identified. The 16S rDNA libraries belong to the Bacillus subtilis, B. megaterium, B. licheniformis, B. pumilus, B. thuringiensis, B. cereus, Chryseobacterium daecheongense, and Microbacterium sediminis (an alkali-tolerant bacteria which has only been isolated from deep-sea sediment). B. cereus was the best strain for cellulose and lipase activities; moreover, C. daecheongense was best for amylase activity. The present study shows that the aerated lagoons from the pulp and paper industry are a promising source of bacterial with different enzyme activities. This data is relevant for industrial applications.

Moss habitats distinctly affect their associated bacterial community structures as revealed by the high-throughput sequencing method

To better understand the factors that influence the distribution of bacteria associated with mosses, the communities inhabiting in five moss species from two different habitats in Beijing Songshan National Nature Reserve were investigated using the high-throughput sequencing method. The sequencing was performed based on the bacterial 16S rRNA and 16S rDNA libraries. Results showed that there are abundant bacteria inhabiting in all the mosses sampled. The taxonomic analysis of these bacteria showed that they mainly consisted of those in the phyla Proteobacteria and Actinobacteria, and seldom were from phylum Armatimonadetes, Bacteroidetes and Firmicutes. The hierarchical cluster tree, based on the OTU level, divided the bacteria associated with all samples into two branches according to the habitat types of the host (terrestrial and aquatic). The PCoA diagram further divided the bacterial compositions into four groups according to both types of habitats and the data sources (DNA and RNA). There were larger differences in the bacterial community composition in the mosses collected from aquatic habitat than those of terrestrial one, whether at the DNA or RNA level. Thus, this survey supposed that the habitat where the host was growing was a relevant factor influencing bacterial community composition. In addition, the bacterial community detected at the RNA level was more sensitive to the habitat of the growing host, which could also be proved by the significantly differences in the predicted function by PICRUSt and the metabolically active dominant genera between different groups. This study expands the knowledge about the interactions between mosses and microbes.

Pellicle formation, microbial succession and lactic acid utilisation during the aerobic deteriorating process of Sichuan pickle

AbstractThe pellicles formation, microbial changes and lactic acid utilisation during the aerobic deterioration of Sichuan pickle were discussed in this study. By plate counting, chemical detection and HPLC analysis, the aerobic deterioration of Sichuan pickle was featured by microbial growth, pellicle formation, lactic acid decrease and pH elevation. Bacteria dominated in pellicles and the pellicles present morphological change from smooth to wrinkly along with the aerobic deteriorating process. Nine species of bacteria were identified and responsible for the pellicle formation. Combined with Lactobacillus plantarum, eight pellicle‐forming bacteria were the dominant lactic acid consuming organisms in deteriorating Sichuan pickle. Especially under the harsh acid condition of the early deteriorating period, Lb. plantarum, pellicle‐forming bacteria Bacillus amyloliquefaciens, B. subtilis and Citrobacter freundii participated in the pellicles, utilised lactic acid and increased the brine pH effectively. Sequence analysis of 16S rDNA libraries suggested that the resulting pH of 4.8–5.0 initiated the growth of more undesirable organisms, and the pellicle bacterial diversity changed greatly compared with that in the early deteriorating period. The study indicated the important role of pellicles in the initiation of Sichuan pickle's aerobic deterioration and enhanced our ability to understand and potentially control the aerobic deterioration.

Phylogenetic diversity of microorganisms associated with three marine sponges from Mien Trung sea of Vietnam

Using culture - independent technique, hypervariable V4 region of 16S rDNA library sequencing by MiSEq, the baterial communities of three host sponges Rhabdastrella sp. DN, Spheciospongia sp. QT and Clathria sp. NT from Mien Trung sea were characterized. The phylogenetic analysis showed that bacterial community structures of the three investigated sponges similar to each other regarding 10 common phyla, although abundance of these phyla was different for each sponge. Phylum Thaumarchaeota was rich component for three sponges, especially in NT sponge (31.89%). In this sponge, 3 phyla Planctomycetes, Verrucomicrobia and Firmicutes were undetected in other 2 sponge samples. Phyla Cyanobacteria was observed only in DN sponge. The obtained amplicons were assigned in different taxonomic levels (class, order, family and genus) based on Silva database. At class level, Gammaproteobacteria was abundant in three sponges; and Caldilineae, Marine-group I were dominant in DN; mealwile, in QT other dominant classes were Marine-group I and Betaproteobacteria. For NT, they were Cytophaga and Deferribacteres. In general, all three sponges harbored abundant and genetically diverse microbial associated consortia and they shared several common bacterial operational taxonomic units, although with different abundance.

Composition and pathogenic potential of a microbial bioremediation product used for crude oil degradation.

A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales. The MBP was most susceptible to ciprofloxacin, doxycycline, gentamicin, and meropenam. MBP exposure of human HT29 and A549 cells caused significant cytotoxicity, and bacterial growth and adherence. An acellular MBP filtrate was also cytotoxic to HT29, but not A549. Both MBP and filtrate exposures elevated the neutrophil chemoattractant IL-8. In endotracheal murine exposures, bacterial pulmonary clearance was complete after one-week. Elevation of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, and chemokines KC and MCP-1 occurred between 2h and 48h post-exposure, followed by restoration to baseline levels at 96h. Cytokine/chemokine signalling was accompanied by elevated blood neutrophils and monocytes at 4h and 48h, respectively. Peripheral acute phase response markers were maximal at 24h. All indicators examined returned to baseline values by 168h. In contrast to HT29, but similar to A549 observations, MBP filtrate did not induce significant murine effects with the indicators examined. The results demonstrated the potentially complex nature of MBPs and transient immunological effects during exposure. Products containing microbes should be scrutinized for pathogenic components and subjected to characterisation and quality validation prior to commercial release.

Nonylphenol biodegradation characterizations and bacterial composition analysis of an effective consortium NP-M2

Nonylphenol (NP), ubiquitously detected as the degradation product of nonionic surfactants nonylphenol polyethoxylates, has been reported as an endocrine disrupter. However, most pure microorganisms can degrade only limited species of NP with low degradation efficiencies. To establish a microbial consortium that can effectively degrade different forms of NP, in this study, we isolated a facultative microbial consortium NP-M2 and characterized the biodegradation of NP by it. NP-M2 could degrade 75.61% and 89.75% of 1000 mg/L NP within 48 h and 8 days, respectively; an efficiency higher than that of any other consortium or pure microorganism reported so far. The addition of yeast extract promoted the biodegradation more significantly than that of glucose. Moreover, surface-active compounds secreted into the extracellular environment were hypothesized to promote high-efficiency metabolism of NP. The detoxification of NP by this consortium was determined. The degradation pathway was hypothesized to be initiated by oxidization of the benzene ring, followed by step-wise side-chain biodegradation. The bacterial composition of NP-M2 was determined using 16S rDNA library, and the consortium was found to mainly comprise members of the Sphingomonas, Pseudomonas, Alicycliphilus, and Acidovorax genera, with the former two accounting for 86.86% of the consortium. The high degradation efficiency of NP-M2 indicated that it could be a promising candidate for NP bioremediation in situ.

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

Myxobacteria harbor an enormous potential for new bioactive secondary metabolites and therefore the isolation of in particular new groups is of great interest. The diversity of myxobacteria present in two ecological habitats, namely sand from Kiritimati Island and German compost, was evaluated by both cultivation‐based and cultivation‐independent methods. Phylogenetic analyses of the strains in comparison with 16S rRNA gene sequences from cultured and uncultured material in GenBank revealed a great potential of undescribed myxobacteria in both sampling sites. Several OTUs (operational taxonomic units) represent unknown taxa and were detected by clone bank analyses, but not by cultivation. Clone bank analyses indicated that the myxobacterial community is predominantly indigenous. The 16S rDNA libraries from the two samples were generated from total community DNA with myxobacterial specific forward and universal reverse primer sets. The clones were partially sequenced. Cultivation was successful for exclusively bacteriolytic, but not for cellulolytic myxobacteria and revealed 42 strains from the genera Corallococcus, Myxococcus, and Polyangium. The genera of Myxococcaceae family were represented by both approaches. But, even in this well studied family, as well as in the suborders Sorangiineae and Nannocystineae, a considerable number of clones were assigned to, if any, uncultivated organisms. Our study shows an overrepresentation of the genera Myxococcus spp. and Corallococcus spp. with standard cultivation methods. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by exclusively cultivation‐independent approaches. Especially, clades which are exclusively represented by clones are of high interest with regard to the cultivation of new bioactive secondary metabolite producers.

Aerobic biofilm reactor for treating a commercial formulation of the herbicides 2,4-D and dicamba: Biodegradation kinetics and biofilm bacterial diversity

A microbial community, able to use 2,4-D (2,4-dichlorophenoxyacetic acid) and dicamba (3,6-dichloro-2-methoxybenzoic acid) as carbon and energy sources, was selected in a continuously operated packed-bed column (PBC). Both active compounds are present in the Banvel herbicide. The predominant cultivable microorganisms isolated belong to the genera Burkholderia, Dyella, Mycobacterium, and Microbacterium. The presence of the catabolic genes tfdACD encoding enzymes involved in the 2,4-D metabolic pathway was evaluated for the bacterial isolates, with positive results for all of them. To evaluate the ability of the entire microbial community to degrade these herbicides in aerobic conditions a horizontal multistage-packed-bed reactor (HMPBR) was constructed. The reactor has four zones packed with fragments of volcanic rock, interspaced with four unpacked aerated zones. The continuous reactor, inoculated with the isolated microbial consortium, was run at increasing Banvel loading rates always operating in an aerobic environment and under steady-state conditions. In no case, 2,4-D or its main aromatic derivatives were detected in reactor's effluent, while dicamba was substantially degraded only at low loading rates. The highest degradation efficiencies of the herbicides were 100% for 2,4-D and 84% for dicamba. COD determinations showed that other components present in the commercial formulation of the herbicide were also removed. To evaluate changes in the diversity of the microbial consortium, massive semiconductor sequencing of 16S rDNA libraries was made. A remarkable variation in the bacterial diversity at phylum level, was observed in biofilm samples obtained from distinct packed bed zones of the reactor, and at different operating conditions.

Study on As Uptake and Rhizobacteria of Two as Hyperaccumulators Forward to As Phytoremediation

As a strategy of arsenic-containing mine tailing soil, the application of arsenic hyper-accumulator plants such as Pteris vittata shows high potential. Previous studies suggest that the arsenic uptake by P. vittata is largely determined by arsenic speciation, which is strongly influenced by microbial activities. In this study, two arsenic hyper-accumulators, P. vittata that is a subtropical plant and Pteris multifida that has been found in northeastern Japan, were selected and the their rhizobacteria were investigated. Pot experiments of P. vittata and P. multifida cultivation were performed. The concentration of total arsenic in the plant samples was monitored by inductively coupled plasma - mass spectrometry. Microbes in the rhizosphere samples were investigated by 16S rDNA library analysis and arsenic resistant bacteria isolation. The results showed that both ferns accumulated As, while P. multifida was more resistant to cold weather. Two ferns presented different rhizobacterial communities and cultivatable bacteria number, but bacteria that contain As(III) oxidase gene or As(III) oxidation activity were confirmed in both rhizosphere samples. The results of present study suggested that the cultivation of ferns changed the microbial communities in soil (rhizosphere), and microbial activity in the rhizosphere played a role in As(III) oxidation. Since ferns absorbs As(III) and As(V) in different efficiency, this study provided hints when linking microbial As transformation to As uptake by ferns which is important when designing pre-treatment procedures of phytoremediation.