Ribosomal Ribonucleic Acid Gene Sequencing Research Articles

A new insight to adsorption and accumulation of high lead concentration by exopolymer and whole cells of lead-resistant bacterium Acinetobacter junii L. Pb1 isolated from coal mine dump

A lead-resistant bacterial strain was isolated from coal mine dump and identified as Acinetobacter junii Pb1 on basis of 16S rRNA (ribosomal ribonucleic acid) gene sequencing. The minimum inhibitory concentration of lead for the strain was 16,000mgl-1 and it showed antibiotic and multi metal resistance. In aqueous culture, at an initial lead (Pb(II)) concentration of 100 and 500mgl-1, lead adsorption and accumulation by the isolate was 100 and 60%, at pH 7 at 30°C after 48 and 120h, respectively. The two fractions of exopolysaccharide (EPS), loosely associated EPS (laEPS) and bound EPS (bEPS), and whole cells (devoid of EPS) showed high binding affinity towards Pb(II). The binding affinity of laEPS towards Pb(II) (1071mgPbg-1) was three times higher than that of bEPS (321.5mgPbg-1) and 6.5 times higher than that of whole cells (165mgPbg-1). The binding affinity of EPS and whole cells with Pb(II), reported in the current study, is considerably higher as compared to that reported in the literature, till date. SEM analysis, showed an increase in thickness of cells on exposure to Pb(II) and TEM analysis, revealed its accumulation (interior of cell) and its adsorption (with the external cell surface). The isolate was also found to be positive for indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production which helps in promoting plant growth. Thus, this study provides a new understanding towards Pb(II) uptake by A. junii Pb1, highlighting its potential on the restoration of Pb(II) contaminated repositories.

Distinct Effects of the Cervicovaginal Microbiota and Herpes Simplex Type 2 Infection on Female Genital Tract Immunology.

Genital inflammation is a key determinant of human immunodeficiency virus (HIV) transmission, and may increase HIV-susceptible target cells and alter epithelial integrity. Several genital conditions that increase HIV risk are more prevalent in African, Caribbean, and other black (ACB) women, including bacterial vaginosis and herpes simplex virus type-2 (HSV-2) infection. Therefore, we assessed the impact of the genital microbiota on mucosal immunology in ACB women and microbiome-HSV-2 interactions. Cervicovaginal secretions and endocervical cells were collected by cytobrush and Instead Softcup, respectively. T cells and dendritic cells were assessed by flow cytometry, cytokines by multiplex enzyme-linked immunosorbent assay (ELISA), and the microbiota by 16S ribosomal ribonucleic acid gene sequencing. The cervicovaginal microbiota of 51 participants were composed of community state types (CSTs) showing diversity (20/51; 39%) or predominated by Lactobacillus iners (22/51; 42%), L. crispatus (7/51; 14%), or L. gasseri (2/51; 4%). High-diversity CSTs and specific bacterial phyla (Gardnerella vaginalis and Prevotella bivia) were strongly associated with cervicovaginal inflammatory cytokines, but not with altered endocervical immune cells. However, cervical CD4+ T-cell number was associated with HSV-2 infection and a distinct cytokine profile. This suggests that the genital microbiota and HSV-2 infection may influence HIV susceptibility through independent biological mechanisms.

Neonatal Meningitis Caused by Actinomyces: A Case Report of the Most Probably New Strain

Over the past three decades, the detection and identification of the Actinomyces spp. in clinical microbiology laboratories, in addition to their recognition as pathogens in clinical settings, have proven challenging. A case of a preterm neonate who was diagnosed with meningitis caused by the Actinomyces spp. during application of a ventricular puncture for the treatment of posthemorrhagic hydrocephalus was presented. PCR tests showed that the neonate's strain exhibited 98.26% 16S ribosomal ribonucleic acid ( rRNA ) gene sequence similarity with the Actinomyces oris strain (ATCC 27044). The GenBank accession number for the nucleotide sequence is Actinomyces KX026867. This case report provides evidence that the Actinomyces spp. should be considered as a potential pathogen of neonatal meningitis, even if the strain is rarely isolated, phenotypically aberrant, and has often been poorly described.

Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform

BackgroundThe composition of the skin microbiome is predicted to play a role in the development of conditions such as atopic eczema and psoriasis. 16S rRNA gene sequencing allows the investigation of bacterial microbiota. A significant challenge in this field is development of cost effective high throughput methodologies for the robust interrogation of the skin microbiota, where biomass is low. Here we describe validation of methodologies for 16S rRNA (ribosomal ribonucleic acid) gene sequencing from the skin microbiome, using the Illumina MiSeq platform, the selection of primer to amplify regions for sequencing and we compare results with the current standard protocols..MethodsDNA was obtained from two low density mock communities of 11 diverse bacterial strains (with and without human DNA supplementation) and from swabs taken from the skin of healthy volunteers. This was amplified using primer pairs covering hypervariable regions of the 16S rRNA gene: primers 63F and 519R (V1-V3); and 347F and 803R (V3-V4). The resultant libraries were indexed for the MiSeq and Roche454 and sequenced. Both data sets were denoised, cleaned of chimeras and analysed using QIIME.ResultsThere was no significant difference in the diversity indices at the phylum and the genus level observed between the platforms. The capture of diversity using the low density mock community samples demonstrated that the primer pair spanning the V3-V4 hypervariable region had better capture when compared to the primer pair for the V1-V3 region and was robust to spiking with human DNA. The pilot data generated using the V3-V4 region from the skin of healthy volunteers was consistent with these results, even at the genus level (Staphylococcus, Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, Enhydrobacter and Deinococcus identified at similar abundances on both platforms).ConclusionsThe results suggest that the bacterial community diversity captured using the V3-V4 16S rRNA hypervariable region from sequencing using the MiSeq platform is comparable to the Roche454 GS Junior platform. These findings provide evidence that the optimised method can be used in human clinical samples of low bacterial biomass such as the investigation of the skin microbiota.

Shifts of Sediment Microbial Community Structure along a Salinized and Degraded River Continuum

ABSTRACT Wang, Y. and Wang, Z.-L., 2018. Shifts of sediment microbial community structure along a salinized and degraded river continuum. Succession of sediment microbial community along salinized and degraded river continuums where discharge declines and nutrient loading increases has received little attention. This issue was studied in a 120-km sediment continuum from upstream to estuary of the Jiyun River, northern China. Microbial community was investigated by phospholipid fatty acid (PLFA) analysis and 16S ribosomal ribonucleic acid (rRNA) gene sequencing. Microbial PLFA contents varied from 1.48 to 7.64 nmol g−1. Salinity decreased microbial, bacterial, and actinomycetic PLFA contents (p < 0.05), but had little effect on fungal PLFA contents. Dissolved organic carbon and dissolved nitrogen increased microbial, bacterial, and actinomycetic PLFAs (p < 0.05), but did not affect fungal PLFAs. Fungal PLFAs were mainly associated with the contents of sediment organic carbon (SOC) and total nitrogen (TN). ...

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters.

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

Bioproduction of Ascorbic Acid and Its Optimization by a Rhizobium sp. from Root Nodules of Sesbania cannabina

The microsymbiont was isolated from the root nodules of Sesbania cannabina (Wild.) Pers. Initially eleven strains were isolated and all were identified as Rhizobium sp. through different physiological and biochemical tests. Ascorbic acid (AsA) production by all the isolates was checked in glucose supplemented basal medium. All the strains had the capacity to produce AsA in the culture filtrate, however to different extent. The isolate S5 showed highest AsA production (160 μg mL−1) in the culture filtrate and hence subsequent experiments were carried out with S5 strain. Both the growth and AsA production phase were started simultaneously at the onset of inoculation, and reached maximum at 24 h. The optimum pH for the AsA production was 7.0. Production of AsA by the isolate was increased to a greater extent over control when the basal medium was supplemented individually with glucose (0.7 %), thiamine-hydrochloride (200 μg L−1), biotin (200 μg L−1), glycine (0.15 %) and sodium dodecyl sulfate (1.0 μg mL−1). AsA production was increased by 278.3 % at a time when all the individual best supplements were added to the basal medium. The results of the Basic Local Alignment Search Tool search of the 16S ribosomal ribonucleic acid gene sequences indicated that S5 isolate was closely related to Rhizobium sp. Moreover, it was found that root contained very negligible amount of AsA than the root nodule. The possible role of AsA production by the Rhizobium sp. in the legume-rhizobia symbiosis has been discussed.

Analysis of Commercial Kidney Stone Probiotic Supplements

To examine the levels of Oxalobacter formigenes in probiotic supplements marketed by PRO-LAB, Ltd, Toronto, Canada, and capsules of Oxalo purchased from Sanzyme Ltd, Hyderabad, India, and to measure the ability of these preparations to degrade oxalate invitro. Probiotic supplements and pure cultures of O. formigenes were cultured in a number of media containing oxalate. Optical density at 595 nm (OD595) was used to measure bacterial growth, and ion chromatography was used to measure loss of oxalate in culture media. O. formigenes-specific and degenerate Lactobacillus primers to the oxalate decarboxylase gene (oxc) were used in polymerase chain reaction (PCR). Incubating probiotic supplements in different media did not result in the growth of oxalate-degrading organisms. PCR indicated the absence of organisms harboring the oxc gene. Culture and 16S ribosomal ribonucleic acid gene sequencing indicated the PRO-LAB supplement contained viable Lactococcus lactis subsp. lactis (GenBank accession no. KJ095656.1), whereas Oxalo contained several Bacillus species and Lactobacillus plantarum. The probiotic supplement sold over the Internet by PRO-LAB Ltd and Sanzyme Ltd did not contain identifiable O. formigenes or viable oxalate-degrading organisms, and they are unlikely tobe of benefit to calcium oxalate kidney stone patients.

English

Contamination with petroleum and its products is an environmental threat in oil producing countries. Microbes have been used to clean up petroleum contaminated environments, which has been demonstrated to be an appropriate and more practical alternative compared to the mechanical and chemical techniques. In this study, crude oil degrading indigenous bacteria were isolated from soils around the oil exploration sites in Western Uganda and their efficiency of oil biodegradation and presence of the catabolic gene xylE in the isolates to relate with their biodegradation efficiency were determined. The organisms with oil degrading activity were screened by isolating them from crude oil supplemented mineral salts medium (MSM). The isolates were tentatively identified phenotypically and confirmed genotypically by 16S ribosomal ribonucleic acid (rRNA) gene sequencing. Hydrocarbon degradation in the culture fluids was analyzed by a gas chromatography mass spectrometer (GC/MS); and amplification of catabolic gene xylE by polymerase chain reaction (PCR) was done in order to relate with the degradation activity. Forty four indigenous oil degrading bacteria were isolated and categorized into eight groups based on their morphological and biochemical properties; and were identified as belonging to the genera; Corynebacterium, Pseudomonas, Moraxella, Bacillus, Enterobacteriaceae, Nocardia, Serratia and Rhodococcus. Eight isolates that exhibited a relatively higher biodegradation activity in the first five days of incubation were selected for a detailed analysis. Based on 16S rRNA gene sequence analyses, the eight selected isolates were identical to Stenotrophomonas maltophilia, Burkholderia sp., Delftia tsuruhatensis, Pseudomonas aeruginosa, Acinetobacter sp., Curtobacterium sp. and Paenibacillus agaridevorans. The selected isolates; Ngara-T1, Kig5-1, Kig5-T2, Kig3-T3, Kig3-T4, Kas2-T7, Kas2-T5 and Gat-3 degraded the total petroleum hydrocarbons (TPHs) up to: 91.9, 79.9, 89.2, 73.1, 94.2, 83.2, 77.0 and 67.2%, respectively, by the end of 21 days of incubation as compared to 29.7% degradation in the control experiment (without bacteria). The catabolic gene xylE was detected in two of the selected isolates, Ngara T-1 and Kig5-T2. It could be concluded that the oil degrading bacteria identified in this study showed diverse and varying capacities to degrade the crude oil; with some degrading up to 90% and can be exploited for cleaning up hydrocarbon contaminated sites in western Uganda. Key words: Bacteria, bioremediation, degradation, oil, hydrocarbons, Uganda.

A case of autochthonous human Dirofilaria infection, Germany, March 2014

In March 2014, an infection with the nematode Dirofilaria repens was diagnosed in a German citizen in the federal state of Saxony-Anhalt. The patient had developed an itching subcutaneous nodule containing a female worm, which was identified as D. repens by 12S ribosomal ribonucleic acid (rRNA) gene sequencing. Autochthonous human D. repens infections have not been described in Germany so far, but this finding is consistent with the recent detection of D. repens in mosquitoes from east Germany.

Different susceptibilities of bacterial community to silver nanoparticles in wastewater treatment systems

The release of silver (Ag) nanoparticles (NPs) into sewage streams has heightened concerns about potential adverse impacts on wastewater treatment processes. Here, we show that the rate constants of both biological nitrification and organic oxidation decreased exponentially with an increase in the Ag NP concentration, but nitrification was more severely inhibited than the organic oxidation even at low Ag NP concentrations (<1 mg Ag L−1) in batch experiments. The long-term exposure effects of Ag NPs on activated sludge bacteria were evaluated in sequencing batch reactors (SBRs) fed with two different substrates favoring heterotrophic and autotrophic bacteria. From a continuous operation for 50 days, it was found that heterotrophic bacteria in the organic removal process have higher tolerance to Ag NPs than do nitrifying bacteria. The effects of Ag NPs on the microbial community in both SBRs were analyzed using 16S ribosomal ribonucleic acid (rRNA) gene sequences obtained from pyrosequencing. The results showed that the level of microbial susceptibility is different for each type of microorganism and that the microbial diversity decreased dramatically after continuous exposure to Ag NPs for 50 days, resulting in a decrease of wastewater treatment efficiency.

Ammonia stimulates growth and nitrite-oxidizing activity of Nitrobacter winogradskyi

The aim of this study was to obtain a nitrite-oxidizing bacterium with high nitrite oxidation activity for controlling nitrite levels. A nitrite-oxidizing bacterium, ZS-1, was isolated from the water of a coastal Pseudosciaena crocea-rearing pond. The strain was identified as Nitrobacter winogradskyi based on the phylogenetic analyses of the 16S ribosomal ribonucleic acid gene and nxrA sequence of ZS-1. Under aerobic condition, the nitrite-oxidizing activity of ZS-1 did not change considerably in the range of pH 7–9, but was strongly inhibited by lower (pH = 6) and higher (pH = 10) pH values. The optimum temperature range is 25–32 °C. Lower temperature made the adaptive phase of ZS-1 longer but did not affect its maximum nitrite oxidization rate. The nitrite-oxidizing activity of ZS-1 started to be inhibited by ammonia and nitrate when the concentrations of ammonia and nitrate reached 25 mg L−1 and 100 mg L−1, respectively. The inhibition was stronger with higher concentration of ammonia or nitrate. The nitrite-oxidizing activity of ZS-1, however, was not inhibited by high concentration of nitrite (500 mg L−1). The nitrite-oxidizing activity of ZS-1 was increased by low ammonia concentration (1 mg L−1 to 10 mg L−1).

Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice.

Background:Endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. Bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. One of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. Hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes.Objective:The objective of this study was to examine the effect of endophytic bacteria from mangrove tree (Rhizophora apiculata Blume) for their efficacy in promoting seedling growth in rice.Materials and Methods:Eight endophytic bacterial isolates (EBIs) isolated from twig and petiole tissues of the mangrove were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequence homology. Separately, surface sterilized paddy seeds were treated with cell-free broth and cell suspension of the EBIs. Rice seedlings were analyzed by various bioassays and data was recorded.Results:The gene sequences of the isolates were closely related to two genera namely, Bacillus and Pantoea. Inoculation of EBIs from R. apiculata with rice seeds resulted in accelerated root and shoot growth with significant increase in chlorophyll content. Among the isolates, Pantoea ananatis (1MSE1) and Bacillus amyloliquefaciens (3MPE1) had shown predominance of activity. Endophytic invasion was recognized by the non-host by rapid accumulation of reactive oxygen species (ROS) and was counteracted by the production of hydrogen peroxide (H2O2) and lipid peroxide. The results demonstrated that EBIs from mangrove tree can increase the fitness of the rice seedlings under controlled conditions.Conclusion:These research findings could be useful to enhance the seedling growth and could serve as foundation in further research on enhancing the growth of the rice crop using endophytic bacteria.

Advancement in the routine identification of anaerobic bacteria by MALDI-TOF mass spectrometry

We evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) Biotyper as a tool for the identification of anaerobic bacteria compared with 500 base-pair (bp) 16S ribosomal ribonucleic acid (rRNA) gene sequencing analysis, which is considered to be the "gold standard" method. A total of 484 anaerobic bacteria were retrieved from the clinical specimens of 318 pediatric patients. Molecular identification resulted in 18 genera and 51 species. The most prevalent genus was Clostridium (76.85 %), with 70 % C. difficile isolates. The concordance and sensitivity determined by MALDI-TOF MS for C. difficile, the most prevalent species isolated, was 94.08 %, whereas the specificity was 100 %. For the other anaerobes, the sensitivity and specificity were 94.07 % and 81.82 %, respectively, with a concordance of 93.15 %. Low performance was observed for Propionibacterium acnes and Fusobacterium nucleatum, for which a dedicated pretreatment procedure should likely be set up. MALDI-TOF MS was shown to be a valid alternative for the fast and reliable identification of the most clinically relevant anaerobic bacteria; moreover, it is less time-consuming, the cost for reagents is minimized, and it does not require dedicated personnel.

Sulfonamide resistance in a disseminated infection caused by Nocardia wallacei: a case report

IntroductionNocardial infections, although rare, are challenging for clinicians to treat. Recent contradictory reports of sulfonamide resistance have raised concerns about using this drug to treat nocardial infections.Case presentationA 62-year-old immunocompetent Caucasian woman showed disseminated pulmonary nodules and a brain abscess by chest computed tomography and brain magnetic resonance imaging, respectively. Multidrug-resistant Nocardia wallacei was cultured from a stereotactic brain biopsy and confirmed by 16S ribosomal ribonucleic acid gene sequencing. After the first-line treatment failed, a long course of trimethoprim-sulfamethoxazole was prescribed with no evidence of recurrence. To the best of our knowledge, this is the first report of a Nocardia wallacei disseminated infection in an immunocompetent patient, and it is the first detailed description of successful treatment with trimethoprim-sulfamethoxazole despite the resistance observed in vitro.ConclusionSpecies identification of clinical isolates is critical for diagnosis, a prediction of antimicrobial susceptibility and epidemiological tracking. In the case of Nocardia wallacei, the clinical outcome suggests that sulfonamides can be used for treatment despite ambiguous results from in vitro susceptibility tests.

Anaerobic ammonium oxidation (anammox) bacteria and sulfide‐dependent denitrifiers coexist in the water column of a meromictic south‐alpine lake

In addition to organotrophic denitrification, alternative pathways, such as anaerobic ammonium oxidation (anammox) or sulfide‐dependent denitrification may be important modes for the removal of fixed nitrogen (N) from lakes. We used Lake Lugano as a model system with which to assess possible controls on the concurrence of multiple suboxic N2 production pathways in a lacustrine water column. In the northern basin of Lake Lugano, concentration gradients of dissolved inorganic N toward the hypolimnetic redox transition zone (RTZ) indicate ammonium oxidation and nitrate reduction occurring in close vicinity. Ammonium reaches undetectable levels 15 m below the depth of oxygen disappearance, indicating its anaerobic consumption. The presence of anammox bacteria was confirmed by 16S ribosomal ribonucleic acid gene sequencing. Quantitative polymerase chain reaction revealed a maximum in anammox bacterial abundance at the same water depth where ammonium becomes exhausted. 15N‐labeling experiments indicate that anammox activity within the Lake Lugano RTZ can contribute up to ∼ 30% of total N2 production. Incubation experiments with various potential electron donors—glucose, acetate, Mn(II), Fe(II), and H2S—revealed that N2 formation was sulfide‐dependent and that organotrophic denitrification is only of minor importance for the elimination of fixed N from the Lake Lugano north basin. Maximum potential rates of anammox and chemolithotrophic denitrification were comparatively low but consistent with nutrient fluxes calculated from concentration gradients. This study provides evidence for the coexistence of anammox bacteria and sulfide‐dependent denitrifiers in the stratified water column of a lacustrine environment.

Robinsoniella peoriensis infection following surgery for scoliosis: a case report

IntroductionRobinsoniella peoriensis was recently identified as a Gram-positive, spore-forming, anaerobic bacillus originally isolated from swine manure storage pits. Seven isolates have been subsequently reported from human sources.Case presentationWe report the case of an infection caused by R. peoriensis in a 45-year-old Caucasian woman after posterior instrumentation correction of idiopathic thoracolumbar scoliosis. The identification was made by culture of samples inoculated onto blood agar and chocolate agar and was confirmed by 16 S ribosomal ribonucleic acid gene sequencing.ConclusionsWe discuss similar cases suggesting that R. peoriensis is responsible for health care-associated infections with the colonic flora as a potential source of infection.

Quantification of ammonia oxidation rates and ammonia‐oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean

Ammonia‐oxidizing microorganisms compete with phytoplankton for reduced nitrogen in the euphotic zone and provide oxidized nitrogen to other microbes present in the sea. We report 15NH4+ oxidation rate measurements made at 5–20‐m resolution using an in situ array and quantification of ammonia‐oxidizing archaea (AOA) and ammonia‐oxidizing bacteria (AOB) in corresponding samples from the upper water column and oxygen minimum zone (OMZ) of the Gulf of California (GOC) and eastern tropical North Pacific Ocean (ETNP). 15NH4+ oxidation rates varied substantially with depth and between stations: they were greatest at the base of the euphotic zone, and maximum rates were up to 28‐fold greater than rates measured within 5–10 m. Pyrosequencing and quantitative polymerase chain reactions (QPCR) indicated that AOA were present throughout the water column at all latitudes and always outnumbered AOB. AOB constituted only 39 of 432,240 16S ribosomal ribonucleic acid gene sequences produced via pyrosequencing but were more abundant at greater depths and higher latitudes. 15NH4+ oxidation rates were correlated with AOA abundance at some stations and were detectable in 96% of samples, including depths where oxygen concentrations were &lt; 5 µmol kg−1 and depths within the euphotic zone, where up to 42% of ammonia oxidation occurred. Ammonia is rapidly oxidized within discrete depth intervals in the GOC and ETNP; while pyrosequencing and QPCR demonstrate that AOB are confined to deeper portions of the water column, AOA appear to be active within the euphotic zone, where they may quickly respond to nitrogen inputs.

Studies on bioflocculant production by Methylobacterium sp. Obi isolated from a freshwater environment in South Africa

A bioflocculant-producing bacterium isolated from river water was identified asMethylobacterium sp. Obi by 16S ribosomal ribonucleic acid (rRNA) gene sequencing. The nucleotide sequence was deposited in the Genbank with accession number HQ537130. The bioflocculant secreted by the isolate showed a peak flocculating activity of 72% in 1 g/L kaolin suspension supplemented with CaCl2. The bioflocculant yield was maximal when glucose and peptone were used as carbon and nitrogen sources respectively, at an optimum pH of 7. Calcium was the most effective cation in stimulating bioflocculating activity. Chemical analyses of the purified bioflocculant revealed it to be a polysaccharide. Key words: Freshwater, Methylobacterium sp. Obi, bioflocculant, flocculating activity, polysaccharides.

Carbon dioxide fixation by Chlorella sp. USTB-01 with a fermentor-helical combined photobioreactor

A promising microalgal strain isolated from fresh water, which can grow both autotrophically on inorganic carbon under lighting and heterotrophically on organic carbon without lighting, was identified as Chlorella sp. USTB-01 with the phylogenetic analysis based on 18S ribosomal ribonucleic acid (rRNA) gene sequences. In the heterotrophic batch culture, more than 20.0 g·L−1 of cell dry weight concentration (DWC) of Chlorella sp. USTB-01 was obtained at day 5, and which was used directly to seed the autotrophic culture. A novel fermentor-helical combined photobioreactor was established and used to cultivate Chlorella sp. USTB-01 for the fixation of carbon dioxide (CO2). It showed that the autotrophic growth of Chlorella sp. USTB-01 in the combined photobioreactor was more effective than that in the fermentor alone and the maximum DWC of 2.5 g·L−1 was obtained at day 6. The highest CO2 fixation of 95% appeared on day 1 in the exponential growth phases of Chlorella sp. USTB-01 and 49.8% protein was found in the harvested microalgal cells.