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Sulfamethazine (SMZ) is an important sulfonamide antibiotic. Although the concentration in the environment is small, it is harmful. The drug residues can be transferred, transformed or accumulated, affecting the growth of animals and plants. In this study, the integrated fixed-film activated sludge membrane bioreactor (IFAS-MBR) were constructed to investigate the performance and degradation mechanism of SMZ. The addition of SMZ had a significant impact on the removal of the chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N). The optimal operating conditions were hydraulic retention time (HRT) at 10 h and solid retention time (SRT) at 80 d, respectively. On this basis, the effects of different SMZ concentrations on nutrient removal, degradation, and sludge characteristics were compared. The removal efficiency of SMZ increased with the increase of SMZ concentration. The maximum removal rate was as high as 87%. The SMZ dosage also had an obvious effect on sludge characteristics. As the SMZ concentration increased, the extracellular polymer substances (EPS) concentration and the membrane resistance both decreased, which were beneficial for the reduction of membrane fouling. Finally, seven kinds of SMZ biodegradation intermediates were identified, and the possible degradation pathways were speculated. The microbial community results showed that the microbial diversity and richness in the reactor decreased after adding SMZ to the influent. The relative abundance of Bacteroidetes, Actinobacteria, Saccharibacteria and Nitrospirae increased at the phylum level. Sphingobacteria and Betaproteobacteria became dominant species at the class level. The relative abundance of norank-p-Saccharibacteria and Nitrospirae increased significantly, and norank-p-Saccharibacteria may be the dominant bacteria for SMZ degradation.

Part of the native root nodule endophytic microflora referring to members of the genera Proteobacteria and Sphingobacteria were used to test their bioefficacy as seed biopriming. These were quantified for their plant growth promoting (PGP) attributes such as IAA production, P and K-solubilization and ACC deaminase production. Results showed that significantly highest IAA was produced by E. hormaechi RCT10. The highest P-solubilization was observed with S. maltophila RCT31 it was solubilizing all the substrate tri-calcium phosphate, di-calcium phosphate, and zinc phosphate. Significantly highest K-solubilization was observed with S. maltophila RCT31 followed by E. turicensis RCT5. However, the maximum zinc solubilization was reported with S. maltophila RCT31 followed by E. turicensis RCT5. The maximum ACC deaminase was quantified in the bacterium. Results revealed that the E. hormaechi RCT10 utilized seed leechates most effectively while root exudates were maximally utilized by S. maltophila RCT31. The pots experiment proves that S. maltophila RCT31 was the most effective bacterium and it was replication vis-à-vis field experiment. In particular, S. maltophila RCT31 holds strong potential to be possibly used as a bioformulation for the medicinal legume, as an economical and eco-friendly alternative to agrochemicals.

30 Páginas.-- 6 Figuras.-- 1 Tabla, In this work, we have used a metataxonomic analysis to study the bacterial biodiversity in three types of commercial dressing and ingredients habitually used in table olive packaging. The bioinformatics analysis showed that salt samples (marine and spring) had the highest biodiversity indexes, followed by the aromatic herbs (thyme, oregano, and fennel) and finally by fermented dressing samples (garlic, pepper, and pepper paste). In salt samples, a significant high presence of Cytophagia, Sphingobacteria, Deltaproteobacteria and Halobacteria classes was observed. On the contrary, the presence of Bacilli class in fermented dressing samples was significantly higher compared to the other samples. Finally, the abundance of Gammaproteobacteria was statistically higher in the samples of herbs. At genus or family taxonomic level, Pseudomonas and diverse non-assigned genus of the Enterobacteriaceae family predominated in many samples of herbs. In fermented dressing samples, diverse genus belonging to the Enterobacteriaceae family appeared in a high relative abundance in pepper paste and garlic, and presence of Vibrio sp. was detected in pepper. However, Lactobacillus, Weisella, and Pediococcus were the predominant genera found in many of these fermented samples. Salinibacter was the most representative genus in both types of salt samples. Multivariate analysis (PCA) of the metataxonomic data sets discriminated well the samples belonging to the three different groups, showing a high proportion of sequences shared by samples-group. This survey reports for the first time the presence of new bacterial species not previously related with table olive processing, as well as the presence of others which could compromise the stability of olive packaging., The research was funded by the Spanish Government (Project OliFilm AGL-2013-48300-R: www.olifilm.science.com.es) AB-C and JB-G thanks the Spanish Ministry of Economy and Competitiveness for their FPI grant and JDC-Incorp. contract, respectively. BC-D thanks the Andalusian Ministry of Economy, Science and Innovation by her pre-doctoral contract.

The rapid start-up of the partial nitritation process in a laboratory-scale aerobic granular sludge-sequencing batch reactor was successful by controlling low dissolved oxygen and gradually increasing the influent ammonia levels. The microbial community dynamics were analyzed by high-throughput sequencing and quantitative polymerase chain reaction. The microbial communities were significantly affected by the different influent NH4+-N concentrations (77.84, 119.42, 170.31, and 252.21 mg/L) in Phases I, II, III, and IV. The sludge Shannon index in Phases I, II, III, and IV was 3.9, 4.39, 3.47, and 2.13, respectively, which was higher than that of the inoculated sludge (1.62). The dominant class transformed from Alphaproteobacteria and Gammaproteobacteria in Phase I to Betaproteobacteria in Phase IV. Furthermore, Sphingobacteria and Clostridia were the dominant bacteria in Phases III and IV. The quantitative polymerase chain reaction (qPCR) results suggested that Nitrosomonadaceae_uncultured belonging to ammonia-oxidizing bacterium was the dominant species, but the relative abundance of nitrite-oxidizing bacteria (mainly Nitrospira and Nitrobacter) was extremely rare in Phase IV. Furthermore, Thauera, Denitratisoma, and Planctomycetacia were the dominant functional nitrogen removal microbes in Phases III and IV. Some nitrogen removal pathways such as partial nitritation, denitrification, and anaerobic ammonium oxidation co-existed in the partial nitritation process.

Membrane fouling is the major bottleneck limiting widespread adoption of membrane bioreactors (MBRs), but its root causes are not yet fully understood. In this study, different fouling patterns were observed for replicate MBRs seeded with the same inoculum and maintained under identical operating conditions, with similar levels of biomass, soluble microbial products, and extracellular polymeric substances. None of these had significant correlations with membrane fouling. Exogenous colloidal particles from a real plant did not have an impact on fouling propensity. Fouling appeared to be correlated with increased abundance of specific classes of bacteria, notably Alphaproteobacteria, Sphingobacteria, and Flavobacteria. The membrane biofouling layer had a different community structure from MBR mixed liquor, showing the two dominant phyla Proteobacteria and Chloroflexi.

Bacterial systems have gained wide attention for depolymerization of lignocellulosic biomass, due to their high functional diversity and adaptability. To achieve the full microbial exploitation of lignocellulosic residues and the cost-effective production of bioproducts within a biorefinery, multiple metabolic pathways and enzymes of various specificities are required. In this work, highly diverse aerobic, mesophilic bacteria enriched from Keri Lake, a pristine marsh of increased biomass degradation and natural underground oil leaks, were explored for their metabolic versatility and enzymatic potential towards lignocellulosic substrates. A high number of Pseudomonas species, obtained from enrichment cultures where organosolv lignin served as the sole carbon and energy source, were able to assimilate a range of lignin-associated aromatic compounds. Comparatively more complex bacterial consortia, including members of Actinobacteria, Proteobacteria, Bacilli, Sphingobacteria, and Flavobacteria, were also enriched from cultures with xylan or carboxymethyl cellulose as sole carbon sources. Numerous individual isolates could target diverse structural lignocellulose polysaccharides by expressing hydrolytic activities on crystalline or amorphous cellulose and xylan. Specific isolates showed increased potential for growth in lignin hydrolysates prepared from alkali pretreated agricultural wastes. The results suggest that Keri isolates represent a pool of effective lignocellulose degraders with significant potential for industrial applications in a lignocellulose biorefinery., Microbial bioprospecting; Lignocellulose biodegradation; Lignin metabolism; Cellulases; Xylanases; Ligninases; Lignin related aromatics.

The variability of culturable bacterial diversity and distribution was studied by phylogenetic analysis of 16S rRNA sequences. Seventeen water samples were examined and were collected, from different depths in the range of 5 m to 2700 m at 3 sampling sites (CTD06, CTD10 and CTD11) in the South Atlantic Ocean. Phylogenetic analysis of 16S rRNA gene sequences revealed a significant diversity of culturable bacteria. A total of 247 strains clustered into 8 classes: γ-Proteobacteria, α-Proteobacteria, Actinobacteria, Actinomycetales, Bacilli, Flavobacteria, Opitutae and Sphingobacteria. The 17 water samples were dominated by populations of strains belonging to the genus Erythrobacter (16.60%). Of the 247 strains, 10 were potential new species and might form a minor population in the deep sea. To our knowledge, this is the first report to analyze the diversity of culturable bacteria in the South Atlantic Ocean from different depths across the water column.

Microorganisms, including the bacterial populations living inside plant tissues (endophytes), and vegetation are components of constructed wetland (CW) systems playing pivotal roles in the water treatment process and in the ecosystem establishment. The present study focuses on the assessment of the culturable endophytic bacterial communities of Canna flaccida plants, the dominant plant species in a polycultured CW treating wastewater from a tourism facility. Bacterial endophytes were grouped by random amplified polymorphic DNA and identified by 16S ribosomal RNA gene sequencing. From the bacterial isolates, 103 were considered for phylogenetic analysis, falling in 25 genera within the gamma-, beta- alpha-Proteobacteria, Flavobacteria, Sphingobacteria, Actinobacteria and Bacilli classes. Forty-nine percent of the isolates belonged to the Enterobacteriaceae family, suggesting that the plants in CW systems may act as a sink of potential human pathogenic microorganisms; nevertheless their abundance on the plant tissues was reduced from the inlet (62%) to the outlet zone (38%). High diversity in terms of genera was found in C. flaccida tissues, although the number of genera common to both sampling zones was low, which suggests that the processes occurring within the CW, including the water characteristics gradient from the inlet to the outlet (e.g. total suspended solids, organics and fecal loads), had the ability to shape the diversity of the endophytic communities. (C) 2016 Elsevier All rights reserved. C.S.C. Calheiros and S.I.A. Pereira thank the grants SFRH/BPD/63204/2009 and SFRH/BPD/65134/2009, respectively, from Fundação para a Ciência e Tecnologia (FCT, Portugal), Fundo Social Europeu and Fundos Nacionais do MEC through the program QREN−POPH−Tipologia 4.1-Formação Avançada. This work was supported by National Funds from FCT−Fundação para a Ciência e a Tecnologia through project UID/Multi/50016/2013. The authors are thankful for the collaboration of Paço de Calheiros and Saint-Gobain Weber Portugal, S.A. The authors wish to thank Dr. Pedro Carvalho for reviewing the manuscript.

Bioremediation of triclosan (TCS) is a challenge because of its low bioavailability, persistence in the environment and recalcitrance to remediation efforts. Rhamnolipid (RL) was used to enhance TCS biodegradation by indigenous microbes in an aerobic water-sediment system. However, knowledge of the effects of TCS on the bacterial community and environmental factors in an RL-enhanced, TCS-degrading system are lacking. Therefore, in this study, the influence of environmental factors on RL-enhanced biodegradation of TCS was investigated by single factor experiments, and shifts in aerobic TCS-degrading bacterial populations, with and without RL, were analyzed by high-throughput sequencing technology. The results showed that aerobic biodegradation of TCS was significantly promoted by the addition of RL. Environmental conditions, which included RL addition (0.125-0.5g/L), medium concentrations of TCS (

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degradation, toxicity and the associated bacterial community structure and composition in diesel-contaminated soil. A significant reduction in total petroleum hydrocarbon (TPH) concentration was detected in both treatments; however, PS-treated soil showed more rapid degradation (87%) after 5 months together with a significant reduction in soil toxicity (EC50 = 91 mg diesel/kg). Quantitative PCR analysis revealed an increase in the number of 16S rRNA and alkB genes in the PS-amended soil. Substantial shifts in soil bacterial community were observed during the bioremediation, including an increased abundance of numerous hydrocarbon-degrading bacteria. The bacterial community shifted from dominance by Alphaproteobacteria and Gammaproteobacteria in the original soil to Actinobacteria during bioremediation. The dominance of two genera of bacteria, Sphingobacteria and Betaproteobacteria, in both NA- and PS-treated soil demonstrated changes occurring within the soil bacterial community through the incubation period. Additionally, pea straw itself was found to harbour a diverse hydrocarbonoclastic community including Luteimonas, Achromobacter, Sphingomonas, Rhodococcus and Microbacterium. At the end of the experiment, PS-amended soil exhibited reduced ecotoxicity and increased bacterial diversity as compared with the NA-treated soil. These findings suggest the rapid growth of species stimulated by the bioremediation treatment and strong selection for bacteria capable of degrading petroleum hydrocarbons during necrophytoremediation.

Endosymbiotic bacteria are extremely common and diverse in arthropods. Cardinium, maternally transmitted intracellular bacteria, can contribute to the fitness of the host and can manipulate its reproduction by feminization, cytoplasmic incompatibility, and thelytokous parthenogenesis. Non-marine ostracods can reproduce asexually as well as sexually. We studied the presence of Cardinium in non-marine ostracods collected from 43 sites in Turkey between 2014 and 2017. The presence of Cardinium in 64 specimens belonging to 24 ostracod species were tested by PCR protocol using 16S rRNA-specific primers. A total of 59 specimens belonging to 22 species showed positive result for the presence of Cardinium, with the sequences of the partial 16S rRNA assigned to the bacteria. Results showed that that majority (92 %) of ostracod species tested were found to be infected by Cardinium. It appears that the bacteria can be seen in both sexes depending on species. We report the first evidence of the presence of Cardinium in non-marine ostracods.

The biological activated carbon (BAC) is a popular advanced water treatment to the provision of safe water supply. A bench–scale device was designed to gain a better insight into microbial diversity and community structure of BAC biofilm by using high–throughput sequencing method. Both samples of BAC biofilm (the first, third and fifth month) and water (inlet water and outlet water of carbon filter, outlet water of backwashing) were analyzed to evaluate the impact of carbon filter depth, running time and backwash process. The results showed that the microbial diversity of biofilm decreased generally with the increase of carbon filter depth and biofilm reached a steady–state at the top layer of BAC after three months’ running. Proteobacteria (71.02%–95.61%) was found to be dominant bacteria both in biofilms and water samples. As one of opportunistic pathogen, the Pseudomonas aeruginosa in the outlet water of device (1.20%) was about eight times higher than that in the inlet water of device (0.16%) at the genus level after five–month operation. To maintain the safety of drinking water, the backwash used in this test could significantly remove Sphingobacteria (from 8.69% to 5.09%, p

Extracellular polymeric substances (EPSs), which composed of different organic components, play an important role in the formation of mucilaginous cyanobacterial bloom. However, how the phylogeny of microbial community coupling with the degradation of EPS matrixes remains unclear. A better understanding of the dynamic process not only give insight into the carbon cycling in the phycosphere, but also provide a new approach for controlling the cyanobacteria bloom. In this study, fractionated EPSs were prepared as a carbon source to enrich different particle size microorganisms. Changes of organic components in EPSs and microbial communities in the degradation process were investigated using Fluorescence excitation and emission matrix (EEM) and Illumina sequencing. The results showed that it is the change of organic components in the degradation process that causes the microbial community to follow a certain succession law. Size-fractionated microorganisms exhibited different hydrolytic activities when interacting with macromolecules, but they did not present different phylogenetic compositions. The changes of humic-like C1 and tryptophan-like C3 in EPSs were significantly correlated to the variations of microbial community composition and diversity. Tightly-bound EPSs (TB-EPSs) contained more low molecular single carbon compounds and were more easily utilized by more diverse microorganisms. Betaproteobacteria, Firmicute, Alphaproteobacteria, Sphingobacteria and Actinobacter were significantly correlated with the changes of organic maters through the humification process. Meanwhile, loosely-bound EPSs (LB-EPSs), which composed of more macromolecules, were more affiliated to a functional organized microbial community. When Gammaproteobacteria and Betaproteobacteria were involved in LB-EPS degradation as indicators, the polysaccharide structures changed dramatically. And the content of some small molecules was briefly increased during the degradation process. Therefore, in order to prevent algal bloom from reducing cellular aggregation by decreasing viscous EPSs, specialized microbial communities should be considered in the phycosphere.

High-yielding microalgae present an important commodity to sustainably satisfy burgeoning food, feed and biofuel demands. Because algae-associated bacteria can significantly enhance or reduce yields, we isolated, identified and selected highly-effective “probiotic” bacterial strains associated with Nannochloropsis oceanica, a high-yielding microalga rich in eicosapentaenoic acid (EPA). Xenic algae growth was significantly enhanced by co-cultivation with ten isolated bacteria that improved culture density and biomass by 2.2- and 1.56-fold, respectively (1.39 × 108 cells mL−1; 0.82 g L−1). EPA contents increased up to 2.25-fold (to 39.68% of total fatty acids). Added probiotic bacteria possessed multiple growth-stimulating characteristics, including atmospheric nitrogen fixation, growth hormone production and phosphorous solubilization. Core N. oceanica-dominant bacterial microbiomes at different cultivation scales included Sphingobacteria, Flavobacteria (Bacteroidetes), and α, γ-Proteobacteria, and added probiotic bacteria could be maintained. We conclude that the supplementation with probiotic algae-associated bacteria can significantly enhance biomass and EPA production of N. oceanica.

Summary Nitrogen-fixing cyanobacteria in the genus Trichodesmium play a critical role in the productivity of the tropical and subtropical oligotrophic oceans. The ecological success of these populations is likely associated with the diverse microbial interactions occurring within the Trichodesmium holobiont, especially between Trichodesmium and heterotrophic bacterial epibionts. Yet, the composition of the Trichodesmium holobiont and the processes governing microbial assemblage are not well documented. Here, we used high-resolution 16S rDNA amplicon sequencing to examine the diversity of Trichodesmium and associated epibionts across different ocean regions and colony morphologies (puffs and rafts). Trichodesmium Clade I (i.e., T. thiebautii-like) dominated the colonies in all ocean basins regardless of morphology, although the Trichodesmium community structure significantly varied between morphologies in some regions. On average, Alphaproteobacteria (i.e., Thalassobius), Gammaproteobacteria (i.e., Pseudoalteromonas), Sphingobacteria (i.e., Microscilla and Vibrio) and Flavobacteria dominated the epibiont communities, but community composition and structure significantly differed between regions. Epibionts from the two colony morphologies were taxonomically and functionally distinct in the North Atlantic and North Pacific. These findings suggest that the colony types might define two distinct niches and that epibiont assemblage might be driven in part by selective processes, where epibionts are selected according to their influence on colony metabolism.

Effluents from paper mills are highly toxic and are a major source of aquatic pollution. In this study, we collected water and sediment samples to examine the microbial communities using denaturing gradient gel electrophoresis and identified bacterial taxa greatly affected by paper mill pollution using next-generation sequencing data. Our results indicated that bacterial communities in downstream sediments were similar to those in paper mill discharge sites, indicating obvious effects of pollution, while bacterial communities in downstream water samples showed similar profiles to those in upstream sites, both being quite different from the bacterial communities in paper mill discharge sites. This was possibly because of the short contact period. In addition, bacterial communities in the estuary were quite different from those in other water and sediment samples, which was owing to the special habitat type. Considering the storage of paper mill pollutants in sediment and the significant effect on shifts in bacterial communities, we selected Clostridia and Epsilonproteobacteria at the class level and Fusibacter and Desulfobulbus at the genus level as bacterial indicators of paper mill pollution. To monitor the remediation of polluted aquatic environments, we propose Sphingobacteria, Alphaproteobacteria, Actinobacteria, Subdivision3, Planctomycetacia and Verrucomicrobiae at the class level and Bacillus, Steroidobacter, Nocardioides, Terrimonas, Pirellula and Methylibium at the genus level.

A case study of the effects of rearing yellow mealworm (Tenebrio molitor L.) in a closed artificial ecosystem on their associated microbial communities is presented. Two groups of T. molitor larvae were reared, one in a controlled environment agricultural ecosystem and another one in an open environment (as a control). Microbial community structures of larval midgut, larval homogenate and frass samples of both groups, and a sample of feed, which was made through the fermentation of plant wastes, were tested by 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiota differences among the two groups and the feed revealed that the diversities of microbial communities in all samples of both groups decreased compared with the feed, with the lowest in midgut of the both groups. Compared with the three samples from the closed ecosystem, those from the open environment had higher abundances of Bacillus, Lactococcus, Weissella, Escherichia and Clostridiaceae. Enterococcus and some unclassified Enterobacteriaceae were identified as the predominant bacteria in samples from the closed ecosystem. The classes Acidobacteria, Planctomycetacia and Sphingobacteria were found in feed, but almost disappeared in the samples of both groups. Possible metabolic and immune effects of the above differences in associated microbial communities on larval growth are discussed. With the aim of improving the rearing efficiency of T. molitor in such a controlled environment agricultural ecosystem, follow-up study would focus on microbial isolation from the midgut of T. molitor for the preparation of probiotics as well as measures of microbial pathogen control.

Bacterial community composition within the highly arsenic (As) contaminated groundwater from Kolsur, West Bengal was analyzed over a period of 3 years using 16S rRNA gene clone library and Denaturing Gradient Gel Electrophoresis (DGGE). Molecular phylogenetic study revealed abundance of α-Proteobacteria (56%) and Firmicutes (29%) along with members of β-Proteobacteria, Verrucomicrobia and Sphingobacteria as relatively minor groups. Along with consistent physicochemical environment, a stable microbial community structure comprising of bacterial genera Agrobacterium-Rhizobium, Ochrobactrum, Pseudomonas, Anoxybacillus and Penibacillus was recorded over the three years study period. Presence of cytosolic arsenate reductase (arsC) gene was observed within the microbial community. Phylogenetic analyses revealed that all the arsC sequences were closely related to the same gene from γ-proteobacterial members while the community was consisted of mainly α-proteobacterial groups. Such phylogenetic incongruence between 16S rRNA and arsC genes possibly indicated horizontal gene transfer (HGT) of the ars genes within the groundwater community. Overall, the study reported a nearly stable geomicrobial environment and genetic determinant related to As homeostasis gene, and provided a better insight on biogeochemistry of As contaminated aquifer of West Bengal.

This study aims to ameliorate effects of packing carriers, filling ratio, temperature and limited aeration on hydrolysis performance in a chemical industrial park wastewater treatment plant. Illumina-MiSeq sequencing was applied to compare microbial community structure between biofilm attached on carriers and activated sludge in a full-scale hydrolysis tank. Packing carriers intensified the plentifulness of microbial community, enriched hydrolytic bacteria (Betaproteobacteria, Gammaproteobacteria, Sphingobacteria, Clostridia, Bacteroidia), and enhanced biodegradability of organics in the wastewater. Rising carriers filling ratio increased first-order kinetic constant of hydrolysis from 0.015 to 0.080 h−1, and decreased fractions inert to hydrolysis. Rising temperature stimulated enzymatic activity for hydrolysis with activation energy of 80.22 kJ/mol. Limited aeration further enriched hydrolytic bacteria, inhibited sulfate-reducing bacteria and intensified biodegradability of organic substances. Variations of fluorescent organic substances and ammonia nitrogen release during hydrolysis confirmed that hydrolysis was strengthened by packing carriers, increasing filling ratio, enhancing temperature and introducing limited aeration. Packing carriers and limited aeration were techno-economic methods for enhancing hydrolysis performance in the chemical industrial park wastewater treatment plant by enriching hydrolytic bacteria and stimulating their activities.

Simultaneous nitrification and denitrification (SND) in a model distribution pipe (DP) fed with actual reclaimed water was studied in this experiment. The water quality, microbial activity, bacteria community as well as the surfaces of biofilm were analysed and observed along the model DP, which had been operated for more than three years. The results exhibited that the nitrogen loss appeared in 65.6 % of the samples and an observable increase in pH value and a measurable decrease in organic carbon occurred along the flow course. The highest nitrification activity arose at the forepart of DP, which indicated nitrifiers of biofilm in DP appeared low susceptible to residual chlorine. Meanwhile, the higher denitrification activity was inclined to appear in the middle section of DP and the obvious gas pores existed on the biofilm surfaces of DP. Finally, the clone analysis revealed that Nitrospirae and Nitrosomonadales were the dominant nitrifiers while some potential denitrifiers such as Pseudomonas, Flavobacteria, Sphingobacteria, and Acinetobacter were also detected along the model DP. Briefly, SND could happen in the DP fed with the reclaimed water even under a certain amount of residual chlorine existed in the influent. A complicated microbial community, including typical nitrifiers and denitrifiers, was involved in the biofilm system of the DP, which played a key role in SND. The paper revealed that the end-water quality tended to stable after a long delivery for reclaimed water due to SND, which is helpful to the designers and managers of the water resource.

Truffle fungi, luxurious food items with captivating aromas, are highly valued in the culinary world. However, truffles are perishable and their aroma undergoes deep changes upon storage. Additionally, truffle aroma might be partially derived from microbes. Hence, we investigated here the influence of storage on two factors, namely the volatile profile and bacterial community composition in the black truffle Tuber aestivum. The possible linkage among those factors was further explored. Our results demonstrate important changes in the volatile profiles of truffles over nine days of storage at room temperature. In the same time frame, dominant bacterial classes characteristic of fresh truffles (α-Proteobacteria, β-Proteobacteria, and Sphingobacteria classes) were gradually replaced by food spoilage bacteria (γ-Proteobacteria and Bacilli classes). Freshness and spoilage volatile markers (i.e. dimethyl sulfide (DMS), butan-2-one, 2- and, 2- and 3-methylbutan-1-ol, and 2-phenylethan-1-ol) were identified. Lastly, network analysis showed correlations between those markers and specific bacterial classes typical of fresh and spoiled truffles. Overall, our results demonstrate the profound effect of storage on the aroma and bacterial community composition of truffles and highlight how the gradual replacement of the commensal microbiome by spoilage microbes mirrors shifts in aroma profile and the possible loss of fresh truffle flavor.

Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.

Soil microorganisms may respond to metal stress by a shift in the microbial community from metal sensitive to metal resistant microorganisms. We assessed the bacterial community from low (2–20 mg kg −1 ), medium (200–400 mg kg −1 ), high (500–900 mg kg −1 ) and very high (>900 mg kg −1 ) uranium soils at Ranger Uranium Mine in northern Australia through pyrosequencing. Proteobacteria (28.85%) was the most abundant phylum at these sites, followed by Actinobacteria (9.31%), Acidobacteria (7.33%), Verrucomicrobia (2.11%), Firmicutes (2.02%), Chloroflexi (1.11%), Cyanobacteria (0.93%), Planctomycetes (0.82%), Bacteroidetes (0.46%) and Candidate_division_WS3 ( Latescibacteria ) (0.21%). However, 46.79% of bacteria were unclassified. Bacteria at low U soils differed from soils with elevated uranium. Bacterial OTUs closely related to Kitasatospora spp., Sphingobacteria spp. and Rhodobium spp. were only present at higher uranium concentrations and the bacterial community also changed with seasonal and temporal changes in soil uranium and physicochemical variables. This study using next generation sequencing in association with environmental variables at a uranium mine has laid a foundation for further studies of soil-microbe-metal interactions which may be useful for developing sustainable management and rehabilitation strategies. Furthermore, bacterial species associated with higher uranium may serve as useful indicators of uranium contamination in the wet-dry tropics.

The travelling population is increasing globally year on year. International tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014, of which 53% and 54% respectively accounted for air transport. The water on board aircraft is sourced from surface or ground water, piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. The purpose of this study was to ascertain the microbial, chemical (pH, Total and Free chlorine) and physical (temperature) quality of water from two aircraft, long- and short-haul, as well as from the original water source and the water service vehicle. A total of 154 water samples were collected and analysed. Long-haul flights were found to be significantly poorer in terms of microbial quality than short haul flights (p = 0.015). Furthermore, correlation and regression analysis showed that the water service vehicle was a significant source of increased microbial load in aircraft. Microbial diversity was also demonstrated, with 37 bacterial species identified belonging to eight classes: γ-Proteobacteria, β-Proteobacteria, α-Proteobacteria, Bacilli, Actinobacteria, Flavobacteria, Sphingobacteria and Cytophaga, using phenotypic and 16S rDNA sequence-based analysis. We present a novel quantified study of aircraft-related potable water supplies.

This study aimed to investigate the dynamics of bacterial and eukaryotic community associated with stability during vermicomposting of pelletized dewatered sludge (PDS). For this, dewatered sludge was pelletized to the particle sizes of 4.5 mm and 14.5 mm and then vermicomposted for 60 days using earthworms Bimastus parvus . Physicochemical results showed that vermicomposting resulted in the decrements of organic matter, total nitrogen, ammonia-nitrogen and dissolve organic carbon and the increments of electrical conductivity, nitrate-nitrogen and available phosphorous. Principal component analysis of physicochemical and enzymatic characteristics revealed that the active decomposition stage occurred on day 20 and subsequent stable stage began from day 50–60 of vermicomposting. Moreover, the small PDS displayed a fast speed of stabilization than the large one. PCR and denatured gradient gel electrophoresis (DGGE) assay for communities of 16S rDNA and 18S rDNA ascertained that the microbes of the Flavobacteria and the Sphingobacteria and the Cercozoa predominated in vermicomposting system. This study suggests that earthworms combined with the diversified microbes could rapidly stabilize the fresh PDS within 60 days.

Periphyton-based bioreactors are widely accepted for removing various pollutants from wastewater; however, the slow start-up and low efficiency in widely fluctuating temperatures limit its application. A spiral periphyton bioreactor (SPR) was developed and its COD removal capability and the associated microbial communities were investigated. This SPR can be easily backwashed to stimulate periphyton growth and efficiently remove COD at temperatures ranging from 4 to 30 °C. The species richness and evenness of the periphyton community increased during domestication, while its functional diversity and organic carbon metabolic vitality were higher after 30 days domestication. Cyanobacteria were the main components of the SPR and produced an aerobic environment, while Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria and Sphingobacteria were the microorganisms responsible for COD removal. This study provides valuable insights into changes in pivotal microorganisms of the periphyton community during domestication, and indicates that SPR is simple to operate and efficient in COD removal.

Brominated flame retardants (BFRs) are a group of widely used compounds that, due to their limited biodegradability, exhibit excessive persistence in the environment. The persistence and high toxicity of these compounds to the natural biota causes great environmental concern. We investigated the biodegradation of the BFR dibromoneopentyl glycol (DBNPG) under continuous culture conditions using a miniature membrane bioreactor (mMBR) to assess its feasibility as a bioremediation approach. This system demonstrated long-term, stable biodegradation of DBNPG (>90 days), with an average removal rate of about 50%. Pyrosequencing of the 16S rRNA gene of the microorganisms involved in this process revealed the dominance of reads affiliated with the genus Brevundimonas of the Alphaproteobacteria class during the different mMBR operational stages. The bacterial community was also dominated by reads affiliated with the Sinorhizobium and Sphingopyxis genera within the Alphaproteobacteria class and the Sediminibacterium genus of the Sphingobacteria class. Real-time PCR used to analyze possible changes in the population dynamics of these four dominant groups revealed their consistent presence throughout the long-term mMBR biodegradation activity. Two genera, Brevundimonas and Sphingopyxis, were found to increase in abundance during the acclimation period and then remained relatively stable, forming the main parts of the consortium over the prolonged active stage.

We analysed the genetic properties of non-rhizobial root nodule endophytes (NRE) isolated from indigenous legumes in Flanders. In total, 654 isolates were obtained from 30 different plant species within the Faboideae legume subfamily. Partial sequencing of the 16S rRNA gene revealed a large diversity of different taxa from the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmibacteria, Flavobacteria and Sphingobacteria. Many of the isolates belonged to the genera Bacillus (17.9%) and Pseudomonas (15.9%). No symbiosis (nodC) or nitrogen fixation related genes (nifH) could be detected amongst the isolates, which indicate the endophytic nature of the bacteria. Statistical analysis grouped the investigated plant species into six clusters according to the presence of particular NRE. However, no correlations could be found within these six clusters towards plant tribes or ecoregions the plants had been sampled from. Cluster analysis of the ecoregions according to the presence of NRE, revealed correlations between bacterial genera and those areas. However, groups present in the ecoregions did not correlate with the groups present in the different plant clusters. When combining our previous study on rhizobial diversity recovered from the same sampling campaign (De Meyer et al., 2011) with the current study, 84.1% of the isolates belonged to the traditional rhizobia groups and only 15.9% were NRE. The Loamy ecoregion yielded the lowest number of culturable NRE (8.04%) and the Campine ecoregion the highest number (24.19%). The present study highlights the frequent presence of these NRE in root nodules. The occurrence of certain rhizobia was correlated with the presence of particular NRE, suggesting their presence may not be accidental, however their functions remain unclear at this point.

Summary Bacillus thuringiensis subsp. israelensis (Bti) is the most widely used biopesticide against mosquitoes and blackflies, with a history of high specificity and efficacy. High doses of Bti have been suggested for extended vector control in some environments; however, the effects of Bti application on the native microfauna in the environment are poorly understood. Two Bti (VectoBac G) treatments (high = 48·1 kg ha−1; low = 0·6 kg ha−1), in addition to an untreated control, were assigned to replicate 300 L microcosms. Culex abundance, phytoplankton biomass, sestonic particulates and nutrients were reduced significantly in the high Bti treatment. These changes affected other physicochemical variables in the water column during the 44-day field study. Bacterial communities present in the water column were assessed by Illumina sequencing of 16S rRNA genes. The most abundant aquatic bacteria in microcosms subject to a low dose of Bti and untreated control, Cyanobacteria, Cytophagales, Cyclobacteriaceae (phylum Bacteroidetes) and Sphingomonas (class Alphaproteobacteria), were suppressed in microcosms subject to a high dose of Bti. Bacteria in the high Bti treatment were dominated by Mucilaginibacter, Sediminibacterium (phylum Sphingobacteria) and Polaromonas (class Betaproteobacteria) and were more diverse than in the other treatments. Synthesis and applications. The biotic and abiotic changes resulting from a biopesticide application that significantly reduced mosquito abundance by more than 50% persisted longer than the period during which larval mosquito numbers were reduced. This warranted further investigation into the ecosystem-level effects of Bti application rates used routinely for mosquito control. Application rates greater than the label rate for a Bti biopesticide can reduce mosquito abundance for an extended period of time and therefore lessen the operational cost of repeated application, but they could exceed manufacturer's recommendations and might violate country-specific regulations governing biopesticide applications in natural habitats. Results of our study suggest that the widespread adoption of Bti application above the recommended label rate should be discouraged in habitats where algal abundance and its effect on primary production, microbial communities and nutrient cycling could affect the functioning of aquatic food webs.

The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.

Triclosan (TCS) is a broad-spectrum synthetic antimicrobial agent that is toxic to microbes and other aquatic organisms. Constructed wetlands (CWs) are now popular in TCS removal. However, knowledge on the effects of TCS on the bacterial community and microbial removal mechanism in CWs is lacking. The effects of TCS (60 μg L− 1) on bacterial communities in batch-loaded CWs with emergent (Typha angustifolia), submerged (Hydrilla verticillata), and floating plant (Salvinia natans) were analyzed by 454 pyrosequencing technology. After six periods of experiment, the TCS removal efficiencies were over 90% in CWs, and negative effects of TCS on bacterial community richness and diversity were observed. Moreover, plant species effect existed. Bacterial strains that contributed to TCS biodegradation in CWs were successfully identified. In TCS-treated T. angustifolia and H. verticillata CWs, beta-Proteobacteria increased by 16.63% and 18.20%, respectively. In TCS-treated S. natans CWs, delta- and gamma-Proteobacteria and Sphingobacteria increased by 9.36%, 19.49%, and 31.37%, respectively, and could relate to TCS biodegradation. TCS affected the development of certain bacteria, and eventually, the bacterial community structures in CWs. This research provided ecologically relevant information on bacterial community and microbial removal mechanism in CWs under TCS treatment.

In this study, bacteria (8 species and 5 genera) belonging to the classes Betaproteobacteria, Gammaproteobacteria, and Sphingobacteria were isolated from root nodules of the multipurpose legume Clitoria ternatea L. and identified on the basis of partial 16S rRNA sequencing. The root nodule bacteria were subjected to phenotypic clustering and diversity studies using biochemical kits, including Hi-Media Carbokit™, Enterobacteriaceae™ identification kit, ERIC–PCR, and 16S ARDRA. All the strains showed growth on Ashby’s N-free media over 7 generations, indicative of presumptive nitrogen fixation and further confirmed by amplification of the nifH gene. None of the strains showed the capability to renodulate the host plant, neither alone nor in combination with standard rhizobial strains, which was further confirmed by the absence of nodC bands in PCR assay. The results clearly indicate the common existence of nonrhizobial microflora inside the root nodules of legumes, which were thought to be colonized only by rhizobia and were responsible for N2fixation in leguminous crops. However, with the recent discovery of nodule endophytes from a variety of legumes, as also observed here, it can be assumed that symbiotic rhizobia are not all alone and that these invasive endophytes belonging to various bacterial genera are more than just opportunistic colonizers of specialized nodule niche.

The mucous skin of amphibians provides a habitat for microorganisms which may interact with their hosts and thereby affect their condition and health. Cultivation-independent analyses of the bacterial communities based on the detection of PCR-amplified bacterial 16S rRNA genes provides a direct approach to characterize their diversity. In the present pilot study we utilized this approach in combination with a high-throughput DNA sequencing technology (454 pyrosequencing), to characterize the bacterial community structure of the skin of three newt species (Lissotriton vulgaris, Ichthyosaura alpestris, Triturus cristatus), collected near Braunschweig, Germany. 16S rDNA sequences were obtained from 19 unique samples. On average, 6113 amplicon sequences were obtained per sample and these could phylogenetically be assigned to a total of 1615 different operational taxonomic units (OTUs). Altogether, most samples were rather similar in their dominant bacterial taxa. Most represented were Betaproteobacteria (46%; mostly Janthinobacterium), Gammaproteobacteria (28%; mostly Pseudomonas), Flavobacteria (phylum Bacteroidetes: 19%, mostly Flavobacterium), and Sphingobacteria (Bacteroidetes: 5%, mostly Pedobacter). We found no significant differences between the three newt species, or between hemi-nested vs. non-nested PCR, but a strong difference among sampling dates (15 and 17 April 2013) which might be explained by the ongoing transition of the newts from their terrestrial to aquatic phase which coincided with this period, or by differences between sexes as these were unevenly sampled on the two dates. 16S rRNA gene sequences retrieved in this study in several cases were identical or very similar to those previously found on the skin of North American salamanders.

Modification of the anoxic–oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic–oxic–settling–anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased.

The endophytic bacterial diversity of drunken horse grass (DHG) (Achnatherum inebrians) growing in native habitat station in Xinjiang Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of DHG, a pair of bacterial PCR primers was selected to specifically amplify bacterial 16S rDNA sequences directly from DHG root tissues. Among 249 positive clones in the 16S rDNA library of endophytes, 57 OTUs were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Flavobacteria, Actinobacteria, Sphingobacteria, and uncultured bacteria. The dominant group was Proteobacteria, whie the most numerous genus was Bacillus. More than 8.00% of the total clones showed a high similarity to uncultured bacteria, suggesting that nonculturable bacteria make a significant part of DHG endophytic bacterial community. To our knowledge, this is the first report that endophytic bacteria associated with DHG are revealed by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in DHG.

Only 1% of marine bacteria are currently culturable using standard laboratory procedures, and this is a major obstacle for our understanding of the biology of marine microorganisms and for the discovery of novel microbial natural products. Therefore, the purpose of this study was to investigate if improved cultivation conditions, including the use of an alternative gelling agent and supplementation with signaling molecules, improve the culturability of bacteria from seawater. Replacing agar with gellan gum improved viable counts 3- to 40-fold, depending on medium composition and incubation conditions, with a maximum of 6.6% culturability relative to direct cell counts. Through V4 amplicon sequencing we found that culturable diversity was also affected by a change in gelling agent, facilitating the growth of orders not culturable on agar-based substrates. Community analyses showed that communities grown on gellan gum substrates were significantly different from communities grown on agar and that they covered a larger fraction of the seawater community. Other factors, such as incubation temperature and time, had less obvious effects on viable counts and culturable diversity. Supplementation with acylated homoserine lactones (AHLs) did not have a positive effect on total viable counts or a strong effect on culturable diversity. However, low concentrations of AHLs increased the relative abundance of sphingobacteria. Hence, with alternative growth substrates, it is possible to significantly increase the number and diversity of cultured marine bacteria. IMPORTANCE Serious challenges to human health, such as the occurrence and spread of antibiotic resistance and an aging human population in need of bioactive pharmaceuticals, have revitalized the search for natural microbial products. The marine environment, representing the largest ecosystem in the biosphere, harbors an immense and virtually untapped microbial diversity producing unique bioactive compounds. However, we are currently able to cultivate only a minute fraction of this diversity. The lack of cultivated microbes is hampering not only bioprospecting efforts but also our general understanding of marine microbes. In this study, we present a means to increase the number and diversity of cultured bacteria from seawater, showing that relatively simple changes to medium components may facilitate the isolation and growth of hitherto unknown bacterial orders.

Proteins and peptides are key components of the labile dissolved organic matter (DOM) pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A 13C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a two-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP). The decomposition rate of AVFA in the bottom hypoxic seawater (0.018-0.035 μM h-1) was twice as fast as that in the surface normoxic seawater (0.011-0.017 μM h-1). SIP experiments indicated that incorporation of 13C was highest among the Flavobacteria, Sphingobacteria, Alphaproteobacteria, Acidimicrobiia, Verrucomicrobiae, Cyanobacteria, and Actinobacteria in surface waters. In contrast, highest 13C-enrichment was mainly observed in several Alphaproteobacteria (Thalassococcus, Rhodobacteraceae, Ruegeria) and Gammaproteobacteria genera (Colwellia, Balneatrix, Thalassomonas) in the bottom water. These data suggest that a more diverse group of both oligotrophic and copiotrophic bacteria may be involved in metabolizing labile organic matter such as peptides in normoxic coastal waters, and several copiotrophic genera belonging to Alphaproteobacteria and Gammaproteobacteria and known to be widely distributed may contribute to faster peptide decomposition in the hypoxic waters.

Although the presence of endosymbiotic rickettsial bacteria, specifically Candidatus Megaira, has been reported in diverse habitats and a wide range of eukaryotic hosts, it remains unclear how broadly Ca. Megaira are distributed in a single host species. In this study we seek to address whether Ca. Megaira are present in most, if not all isolates, of the parasitic ciliate Ichthyophthirius multifiliis. Conserved regions of bacterial 16S rRNA genes were either PCR amplified, or assembled from deep sequencing data, from 18 isolates/populations of I. multifiliis sampled worldwide (Brazil, Taiwan, and USA). We found that rickettsial rRNA sequences belonging to three out of four Ca. Megaira subclades could be consistently detected in all I. multifiliis samples. I. multifiliis collected from local fish farms tend to be inhabited by the same subclade of Ca. Megaira, whereas those derived from pet fish are often inhabited by more than one subclade of Ca. Megaira. Distributions of Ca. Megaira in I. multifiliis thus better reflect the travel history, but not the phylogeny, of I. multifiliis. In summary, our results suggest that I. multifiliis may be dependent on this endosymbiotic relationship, and the association between Ca. Megaira and I. multifiliis is more diverse than previously thought.

The goal of this study was to investigate the effectiveness of a membrane-aerated biofilm reactor (MABR), a representative of counter-current substrate diffusion geometry, in mitigating nitrous oxide (N2O) emission. Two laboratory-scale reactors with the same dimensions but distinct biofilm geometries, i.e., a MABR and a conventional biofilm reactor (CBR) employing co-current substrate diffusion geometry, were operated to determine depth profiles of dissolved oxygen (DO), nitrous oxide (N2O), functional gene abundance and microbial community structure. Surficial nitrogen removal rate was slightly higher in the MABR (11.0 ± 0.80 g-N/(m2 day) than in the CBR (9.71 ± 0.94 g-N/(m2 day), while total organic carbon removal efficiencies were comparable (96.9 ± 1.0% for MABR and 98.0 ± 0.8% for CBR). In stark contrast, the dissolved N2O concentration in the MABR was two orders of magnitude lower (0.011 ± 0.001 mg N2O-N/L) than that in the CBR (1.38 ± 0.25 mg N2O-N/L), resulting in distinct N2O emission factors (0.0058 ± 0.0005% in the MABR vs. 0.72 ± 0.13% in the CBR). Analysis on local net N2O production and consumption rates unveiled that zones for N2O production and consumption were adjacent in the MABR biofilm. Real-time quantitative PCR indicated higher abundance of denitrifying genes, especially nitrous oxide reductase (nosZ) genes, in the MABR versus the CBR. Analyses of the microbial community composition via 16S rRNA gene amplicon sequencing revealed the abundant presence of the genera Thauera (31.2 ± 11%), Rhizobium (10.9 ± 6.6%), Stenotrophomonas (6.8 ± 2.7%), Sphingobacteria (3.2 ± 1.1%) and Brevundimonas (2.5 ± 1.0%) as potential N2O-reducing bacteria in the MABR.

Diatom-dominated phytoplankton blooms in neritic seas are typically terminated by aggregation. Despite extensive studies, it is still unknown how temperature controls aggregation. Therefore, we studied aggregation in a 750 liter mesocosm experiment under simulated in situ conditions during a spring diatom bloom in the southern North Sea at Helgoland Roads. In the early phase, at the peak, and in the late phase, aggregation was examined in rolling tanks at the ambient temperature (6°C) and at 11°C. In a second set of rolling tanks, cells of Thalassiosira rotula were added to examine how this readily aggregating diatom affects aggregation. In the treatments with the natural phytoplankton, a significant effect of temperature on aggregation was detected only in the late bloom, when the aggregate area increased at 11°C relative to 6°C. In contrast, in the T. rotula–supplemented treatments, aggregation was enhanced by the elevated temperature at the peak but not in the late bloom. The aggregate area per microgram particulate organic carbon, a normalized measure to assess the aggregation potential, indicated that the aggregation potential in the natural phytoplankton community decreased from the peak to the late bloom, independent of temperature. This was presumably due to the reduced stickiness of the particles and lower concentrations of transparent exopolymer particles in the late phase. In the T. rotula–supplemented treatments, aggregation potential increased from the peak to the late bloom at the ambient temperature, whereas it decreased at the elevated temperature. Flavobacteria and Sphingobacteria of the Bacteroidetes phylum and Gammaproteobacteria were the dominant bacterial groups colonizing the aggregates.

Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC.

Gut bacteria play important roles in the biology of insects. In this study, gut bacterial communities were investigated in the rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), which is a serious pest in rice growing-areas of the United States and some Asian countries. Overwintered female adults were collected from rice plants in five geographic locations: Beaumont, TX; Colt, AR; and Biggs, CA; in the United States, and Tanghai of Hebei and Yueqing of Zhejiang in China. Using polymerase chain reaction, bacterial 16S rRNA clone libraries were constructed. From the libraries, we identified 19 bacterial phylotypes (operational taxonomic units, OTUs). Of them, only 3–5 OTUs were identified in each population, except in the Beaumont weevils, which had 10 OTUs. The OTUs were affiliated with the bacteria in six classes of four phyla: α-, β-, γ-proteobacteria, Bacilli, Sphingobacteria, and Actinobacteria, with the γ-proteobacteria being the richest. Bacteria of the genera Pantoea and Wolbachia were detected in all weevil populations examined. There were also some bacteria that were specifically detected in certain locations but had a high relative abundance, such as the ones matched to Enterobacter oryzae, Lactococcus lactis, and Rickettsia felis. Geographic variations were found among bacterial communities in their richness, diversity, and evenness. This was the first study depicting a detailed profile of bacterial communities in L. oryzophilus, and the results provide important information for future studies on the bacterial functions, mutual interactions, and use for developing a biocontrol technique against this weevil.

This article presents an analysis of the microbial community growing on a stainless steel plate. A sample from this plate has been tested for the rpoC gene. Dominant biofilm species (clones) were identified with the help of molecular cloning and nucleotide sequencing of a 16S rRNA gene fragment. The activities of planktonic microorganisms and biofilm microorganisms attached to the plate were compared. Seven of nineteen sequences (37%) were found to belong to the Sphingobacteria group. Analysis of 16S rRNA gene sequences cloned from natural biofilms sampled from Lake Baikal showed a great variety of microorganisms in the biofilm. The following taxonomic groups were revealed among them: sphingobacteria, α-proteobacteria, cyanobacteria, verrucomicrobia, bacilli, γ-proteobacteria, flavobacteria, and β-proteobacteria. This kind of analysis was done in Lake Baikal for the first time.

The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.

The river Glera in Northern-Iceland presents a convenient model for the evaluation of anthropogenic effects on sub-Arctic river microbiota. The river originates in a pristine valley, flows past a landfill site where leachate merges into the river, and subsequently through a small urban area. Our aim was to characterize the river microbiota in both its pristine and anthropogenically impacted state, particularly focusing on prospective surfactant degraders whose activity in the river water might contribute to the river's self-purification capacity. We sampled river water and riverbed sediment at 10 sampling sites that spanned the river from its pristine source to the estuary for culturable bacteria and extractable DNA. A few other biotopes in the catchment area were also sampled. A confirmed pure and viable culture collection of 170 isolates was generated and partially analyzed for identification by 16S rRNA gene sequencing, and for biodegradation of selected surfactants as well as glycans, protein and triglyceride. Protein-degrading pseudomonads are strongly represented in the culture collection, many of whom can also degrade selected surfactants. The collection also contains other members of the Gammaproteobacteria as well as the Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, Flavobacteria, and Sphingobacteria. Several isolates of all classes, except the Betaproteobacteria, displayed biodegradative activity.

Aims A structural and functional study has been carried out in the rice production area of the Guadalquivir marshes in southern Spain aiming to increase knowledge of rice rhizosphere structure and function for further application on integrated management practices. Methods and Results Rhizosphere bacterial structure (analysis of 16S rRNA partial sequences from total soil DNA), metabolic diversity (analysed by Biolog FF for fungal community and GN for microbial community) and a screening for putative plant growth–promoting rhizobacteria (PGPR) to identify potential isolates for development of local biofertilizers, and biodiversity of culturable micro-organisms (analysis of 16S rRNA partial sequences) from four areas differing in salinity and Magnaporthe oryzae incidence in two moments of the crop cycle were studied. Results indicate that the dominant taxon in libraries from the four areas was Proteobacteria. Metabolic diversity was higher in areas affected only by salinity or incidence of Magnaporthe than in the control or area affected by both stresses. It seems that rice plants selected, in their rhizosphere, micro-organisms able to affect plant hormonal balance under all conditions, and this activity relied in different bacterial genera depending on the environmental stress. Conclusions Bacterial genera for each stress, as well as generalist strains, were found present in all the studied areas. Potential molecular markers and taxonomic markers (Sphingobacteria for salt and Thermococci for Magnaporthe) of the different stress situations have been highlighted, and Class Verrucomicrobiae could be a marker for nonstressed areas. In addition, putative PGPR strains isolated in this study could be used as biofertilizers. Significance and Impact of the Study Rice paddies are great ecologically important ecosystems. The results are very relevant as they may be included in the process of rice production, improving crop conditions with less environmental impact.