16S rRNA Levels Research Articles

Temporal dynamics of total and free-living nitrogen-fixing bacterial community abundance and structure in soil with and without history of arsenic contamination during a rice growing season.

Despite the fact that the nitrogen (N) fixers act as the key regulator of ecosystem process, a detailed study of their abundance, diversity, and dynamics in arsenic (As)-contaminated rice fields is missing so far. DNA extracted from soil followed by 16S rRNA and nifH gene-based real-time qPCR, clone library analysis, and DNA sequencing were used to examine the status of the total and diazotrophic communities in two agricultural fields with and without arsenic contamination history during one rice cultivation season. In general, higher nifH and 16S rRNA gene copy numbers were observed in rice growing soils with lesser As than that with higher As. Elevated levels of 16S rRNA and nifH genes in soil is directly associated with total and nitrogen fixers abundance in the agricultural land without As contamination history through the cultivation period, but the copy number of 16S rRNA gene was decreased, and the nifH gene remained unchanged in the As-contaminated land. Additionally, Canonical Correspondence Analysis (CCA) indicated the possible suppression of nifH gene abundance by soil pH, phosphate, and As content. Increased abundance of total and Acidobacterial lineages in low As-containing soil and the detection of several uncultured groups among nifH gene sequence in higher frequency indicated the presence of novel nifH bearing bacterial groups. Conversely, the abundance of copiotrophic Proteobacterial lineages gradually increased in soil with higher As. Herein, our study demonstrated that the dynamics of free-living nitrogen-fixing bacterial communities were perturbed due to As contamination in agricultural land.

Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis.

Here we describe a new species of the genus Streptococcus that was isolated from a dairy cow with mastitis in New Zealand. Strain NZ1587T was Gram-positive, coccus-shaped and arranged as chains, catalase and coagulase negative, γ-haemolytic and negative for Lancefield carbohydrates (A-D, F and G). The 16S rRNA sequence did not match sequences in the NCBI 16S rRNA or GreenGenes databases. Taxonomic classification of strain NZ1587T was investigated using 16S rRNA and core genome phylogeny, genome-wide average nucleotide identity (ANI) and predicted DNA-DNA hybridisation (DDH) analyses. Phylogeny based on 16S rRNA was unable to resolve the taxonomic position of strain NZ1587T, however NZ1587T shared 99.4 % identity at the 16S rRNA level with a distinct branch of S. pseudoporcinus. Importantly, core genome phylogeny demonstrated that NZ1587T grouped amongst the 'pyogenic' streptococcal species and formed a distinct branch supported by a 100 % bootstrap value. In addition, average nucleotide identity and inferred DNA-DNA hybridisation analyses showed that NZ1587T represents a novel species. Biochemical profiling using the rapid ID 32 strep identification test enabled differentiation of strain NZ1587T from closely related streptococcal species. In conclusion, strain NZ1587T can be classified as a novel species, and we propose a novel taxon named Streptococcus bovimastitidis sp. nov.; the type strain is NZ1587T. NZ1587T has been deposited in the Culture Collection University of Gothenburg (CCUG 69277T) and the Belgian Co-ordinated Collections of Micro-organisms/LMG (LMG 29747).

Human papillomavirus type 8 E7 protein binds nuclear myosin 1c and downregulates the expression of pre-rRNA.

Our aim was to search for new cellular binding partners for the E6 and E7 oncogenes of beta human papillomaviruses (HPV), whose direct role in skin carcinogenesis has not been thoroughly investigated. By employing glutathione S-transferase pulldown and coimmunoprecipitation, we identified nuclear myosin 1c as a binding partner of HPV 8 E7 protein. As nuclear myosin 1c is an essential component of the RNA polymerase I transcription complex, we studied the effects of HPV 8 E7 protein expression on ribosomal RNA (rRNA) expression. Here we show that the activity of RNA polymerase I is decreased and that pre-rRNA expression is consequently reduced due to HPV 8 E7 expression. However, the expression levels of mature cytoplasmic 18S and 28S rRNA are retained. We propose that by relieving their resources from the energy-consuming process of rRNA transcription, HPV 8 E7 expressing cells might support more efficient virus replication in the differentiating epithelium.

Stormwater loadings of antibiotic resistance genes in an urban stream

Antibiotic resistance presents a critical public health challenge and the transmission of antibiotic resistance via environmental pathways continues to gain attention. Factors driving the spread of antibiotic resistance genes (ARGs) in surface water and sources of ARGs in urban stormwater have not been well-characterized. In this study, five ARGs (sul1, sul2, tet(O), tet(W), and erm(F)) were quantified throughout the duration of three storm runoff events in an urban inland stream. Storm loads of all five ARGs were significantly greater than during equivalent background periods. Neither fecal indicator bacteria measured (E. coli or enterococci) was significantly correlated with sul1, sul2, or erm(F), regardless of whether ARG concentration was absolute or normalized to 16S rRNA levels. Both E. coli and enterococci were correlated with the tetracycline resistance genes, tet(O) and tet(W). Next-generation shotgun metagenomic sequencing was conducted to more thoroughly characterize the resistome (i.e., full complement of ARGs) and profile the occurrence of all ARGs described in current databases in storm runoff in order to inform future watershed monitoring and management. Between 37 and 121 different ARGs were detected in each stream sample, though the ARG profiles differed among storms. This study establishes that storm-driven transport of ARGs comprises a considerable fraction of overall downstream loadings and broadly characterizes the urban stormwater resistome to identify potential marker ARGs indicative of impact.

Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma.

It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs. We used qRT-PCR to verify the expression levels of these candidates and another seven commonly used reference genes and miRNAs. A set of 50 paired human normal esophageal tissues and squamous cell carcinoma samples were used in the analysis. We then used geNorm and NormFinder to analyze the results. DDX5, LAPTM4A, RHOA, ACTB, RNU48, miR-28-5p, miR-34a-5p, and miR-186-5p were stably expressed, indicating they are suitable for used as references in qRT-PCR analysis of esophageal squamous cell carcinoma. However, expression levels of 18s rRNA, GAPDH, P4HB, 5s rRNA, U6, and RNU6B varied greatly between esophageal normal and squamous cell carcinoma samples, indicating that they are not suitable for use as references in the qRT-PCR analysis of esophageal squamous cell carcinoma.

Gilvimarinus japonicus sp. nov., a cellulolytic and agarolytic marine bacterium isolated from coastal debris.

A cellulolytic and agarolytic bacterial strain, designated 12-2T, was isolated from a piece of cotton rope fragment washed ashore on a beach and was studied phenotypically, genotypically and phylogenetically. Analyses of 16S rRNA and gyrB gene sequences and DNA base composition suggested that the strain is a member of the genus Gilvimarinus. However, levels of 16S rRNA and gyrB gene sequence similarity between it and the type strains of Gilvimarinus species were no higher than 97.9 and 78.7 %, respectively, suggesting that the strain is distinct. Moreover, the results of DNA-DNA hybridization experiments and physiological characterization clearly differentiated the strain from its closest neighbours. The strain is therefore considered to represent a novel species of the genus Gilvimarinus, for which the name Gilvimarinus japonicus sp. nov. is proposed. The type strain is 12-2T (=NBRC 111987T=KCTC 52141T).

In Vitro Gene Silencing of the Fish Microsporidian Heterosporis saurida by RNA Interference.

Heterosporis saurida, a microsporidian parasite of lizardfish, Saurida undosquamis, causes severe economic losses in marine aquaculture. Among the novel approaches being explored for treatment of parasitic infections in aquaculture is small interfering RNA molecules. The aim of the present study was to investigate the efficiency of using siRNA to knock down expression of specific genes of H. saurida in vitro. For this purpose, siRNAs specific for ATP/ADP antiporter 1 and methionine aminopeptidase II genes were designed and tested using a previously developed in vitro cultivation model. Silencing of H. saurida target genes was assessed and the efficacy of using siRNA for inhibition of gene expression was measured by quantitative real-time polymerase chain reaction (PCR). Silencing of ATP/ADP antiporter 1 or methionine aminopeptidase II by siRNA reduced H. saurida infection levels in EK-1 cells 40% and 60%, respectively, as measured by qRT-PCR and spore counts. Combined siRNA treatment of both ATP/ADP antiporter 1 and methionine aminopeptidase II siRNAs was more effective against H. saurida infection as seen by the 16S rRNA level and spore counts. Our study concluded that siRNA could be used to advance development of novel approaches to inhibit H. saurida and provide an alternative approach to combat microsporidia.

A lack of consensus in the literature findings on the removal of airborne benzene by houseplants: Effect of bacterial enrichment

Removal rates of benzene and formaldehyde gas by houseplants reported by several laboratories varied by several orders of magnitude. We hypothesized that these variations were caused by differential responses of soil microbial populations to the high levels of pollutant used in the studies, and tested responses to benzene by plants and soils separately. Five houseplant species and tobacco were exposed to benzene under hydroponic conditions and the uptake rates compared. Among the test plants, Syngonium podophyllum and Chlorophytum comosum and Epipremnum aureum had the highest benzene removal rates. The effects of benzene addition on populations of soil bacteria were determined using reverse transcription quantitative PCR (RT-qPCR) assays targeting microbial genes involved in benzene degradation. The total bacterial population increased as shown by increases in the levels of eubacteria 16S rRNA, which was significantly higher in the high benzene incubations than in the low benzene incubations. Transcripts (mRNA) of genes encoding phenol monooxygenases, catechol-2,3-dioxygenase and the housekeeping gene rpoB increased in all soils incubated with high benzene concentrations. Therefore the enrichment of soils with benzene gas levels typical of experiments with houseplants in the literature artificially increased the levels of total soil bacterial populations, and especially the levels and activities of benzene-degrading bacteria.

Integrated Biosensor Assay for Rapid Uropathogen Identification and Phenotypic Antimicrobial Susceptibility Testing

BackgroundStandard diagnosis of urinary tract infection (UTI) via urine culture for pathogen identification (ID) and antimicrobial susceptibility testing (AST) takes 2–3 d. This delay results in empiric treatment and contributes to the misuse of antibiotics and the rise of resistant pathogens. A rapid diagnostic test for UTI may improve patient care and antibiotic stewardship. ObjectiveTo develop and validate an integrated biosensor assay for UTI diagnosis, including pathogen ID and AST, with determination of the minimum inhibitory concentration (MIC) for ciprofloxacin. Design, setting, and participantsUrine samples positive for Enterobacteriaceae (n=84) or culture-negative (n=23) were obtained from the Stanford Clinical Microbiology Laboratory between November 2013 and September 2014. Each sample was diluted and cultured for 5h with and without ciprofloxacin, followed by quantitative detection of bacterial 16S rRNA using a single electrochemical biosensor array functionalized with a panel of complementary DNA probes. Pathogen ID was determined using universal bacterial, Enterobacteriaceae (EB), and pathogen-specific probes. Phenotypic AST with ciprofloxacin MIC was determined using an EB probe to measure 16S rRNA levels as a function of bacterial growth. MeasurementsElectrochemical signals for pathogen ID at 6 SD over background were considered positive. An MIC signal of 0.4 log units lower than the no-antibiotic control indicated sensitivity. Results were compared to clinical microbiology reports. Results and limitationsFor pathogen ID, the assay had 98.5% sensitivity, 96.6% specificity, 93.0% positive predictive value, and 99.3% negative predictive value. For ciprofloxacin MIC the categorical and essential agreement was 97.6%. Further automation, testing of additional pathogens and antibiotics, and a full prospective study will be necessary for translation to clinical use. ConclusionsThe integrated biosensor platform achieved microbiological results including MIC comparable to standard culture in a significantly shorter assay time. Further assay automation will allow clinical translation for rapid molecular diagnosis of UTI. Patient summaryWe have developed and validated a biosensor test for rapid diagnosis of urinary tract infections. Clinical translation of this device has the potential to significantly expedite and improve treatment of urinary tract infections.

Adaptations to chronic rapamycin in mice.

Rapamycin inhibits mechanistic (or mammalian) target of rapamycin (mTOR) that promotes protein production in cells by facilitating ribosome biogenesis (RiBi) and eIF4E-mediated 5'cap mRNA translation. Chronic treatment with encapsulated rapamycin (eRapa) extended health and life span for wild-type and cancer-prone mice. Yet, the long-term consequences of chronic eRapa treatment are not known at the organ level. Here, we report our observations of chronic eRapa treatment on mTORC1 signaling and RiBi in mouse colon and visceral adipose. As expected, chronic eRapa treatment decreased detection of phosphorylated mTORC1/S6K substrate, ribosomal protein (rpS6) in colon and fat. However, in colon, contrary to expectations, there was an upregulation of 18S rRNA and some ribosomal protein genes (RPGs) suggesting increased RiBi. Among RPGs, eRapa increases rpl22l1 mRNA but not its paralog rpl22. Furthermore, there was an increase in the cap-binding protein, eIF4E relative to its repressor 4E-BP1 suggesting increased translation. By comparison, in fat, there was a decrease in the level of 18S rRNA (opposite to colon), while overall mRNAs encoding ribosomal protein genes appeared to increase, including rpl22, but not rpl22l1 (opposite to colon). In fat, there was a decrease in eIF4E relative to actin (opposite to colon) but also an increase in the eIF4E/4E-BP1 ratio likely due to reductions in 4E-BP1 at our lower eRapa dose (similar to colon). Thus, in contrast to predictions of decreased protein production seen in cell-based studies, we provide evidence that colon from chronically treated mice exhibited an adaptive ‘pseudo-anabolic’ state, which is only partially present in fat, which might relate to differing tissue levels of rapamycin, cell-type-specific responses, and/or strain differences.

Dietary Olive and Perilla Oils Affect Liver Mitochondrial DNA Methylation in Large Yellow Croakers1–3

Background: Substantial progress has been made in nutritional epigenetics, but little is known regarding whether mitochondrial DNA (mtDNA) methylation is involved in this process.Objective: The objective of this study was to determine whether dietary lipid sources [various fatty acids (FAs)] modify mtDNA methylation.Methods: A total of 600 large yellow croakers (Larimichthys crocea) with an average initial weight of 151 ± 4 g were fed 1 of 5 diets (3 replicate cages/treatment) containing either fish oil (FO) (control), palmitic acid, olive oil (OO), sunflower oil, or perilla oil (PO) as the dietary lipid source (12% dry weight of the diet) for 70 d. Pyrosequencing was used to determine the effects of dietary lipid sources (FAs) on mtDNA methylation.Results: Mitochondrial arginine transfer RNA and NAD(H) dehydrogenase 4L encoding region methylation in the liver was higher in the OO (9.5% ± 0.52%; P < 0.05) and PO (7.3% ± 0.33%; P < 0.05) groups than in the FO (5.9% ± 0.42%) group, whereas 12S ribosomal RNA (rRNA) methylation in the liver was lower in the OO group (2.7% ± 0.22%) than in the FO group (4.2% ± 0.73%) (P < 0.05). Additionally, fish fed the OO diet had lower liver mRNA levels of ND3 (P < 0.05), ND4L (P < 0.05), ND6 (P < 0.05), 12S rRNA (P < 0.05), and 16S rRNA (P < 0.05) than those fed the FO diet, whereas fish fed the PO diet had lower liver mRNA levels of 16S rRNA than those fed the FO diet (P < 0.05). Moreover, fish fed the OO (P < 0.05) or PO (P < 0.05) diet had lower liver mitochondrial complex I activity than did those fed the FO diet.Conclusions: These findings provide the first evidence, to our knowledge, that dietary lipid sources influence mitochondrial function through mtDNA methylation in large yellow croakers.

Quantitative RT-PCR assay for high-throughput screening (HTS) of drugs against the growth of Cryptosporidium parvum in vitro.

Our laboratory has previously developed a qRT-PCR assay to assess drug efficacy on the growth of Cryptosporidium parvum in vitro by detecting the levels of parasite 18S rRNA. This approach displayed up to four orders of magnitude of linear dynamic range and was much less labor-intensive than the traditional microscopic methods. However, conventional qRT-PCR protocol is not very amendable to high-throughput analysis when total RNA needs to be purified by lengthy, multi-step procedures. Recently, several commercial reagents are available for preparing cell lysates that could be directly used in downstream qRT-PCR analysis (e.g., Ambion Cell-to-cDNA kit and Bio-Rad iScript sample preparation reagent). Using these reagents, we are able to adapt the qRT-PCR assay into high-throughput screening of drugs in vitro (i.e., 96-well and 384-well formats for the cultivation of parasites and qRT-PCR detection, respectively). This qRT-PCR protocol is able to give a >150-fold linear dynamic range using samples isolated from cells infected with various numbers of parasites. The new assay is also validated by the NIH-recommended intra-plate, inter-plate, and inter-day uniformity tests. The robustness and effectiveness of the assay are also confirmed by evaluating the anti-cryptosporidial efficacy of paromomycin and by a small scale screening of compounds.

Thermus parvatiensis RL(T) sp. nov., Isolated from a Hot Water Spring, Located Atop the Himalayan Ranges at Manikaran, India.

A Gram negative, yellow pigmented, rod shaped bacterium designated as RL(T) was isolated from a hot water spring (90-98°C) located at Manikaran in Northern India. The isolate grows at 60-80°C (optimum, 70°C) and at pH 7.0-9.0 (optimum pH 7.2). Phylogenetic analysis of 16S rRNA gene sequences and levels of DNA-DNA relatedness together indicate that the new isolate represents a novel species of the genus Thermus with closest affinity to Thermus thermophilus HB8(T) (99.5%) followed by Thermus arciformis (96.4%). A comparative analysis of partial sequences of housekeeping genes (HKG) further revealed that strain RL(T) is a novel species belonging to the genus Thermus. The melting G+C content of strain RL(T) was calculated as 68.7mol%. The DNA-DNA relatedness value of strain RL(T) with its nearest neighbours (>97%) was found to be less than 70% indicating that strain RL(T) represents a novel species of the genus Thermus. MK-8 was the predominant respiratory quinone. The presence of characteristic phospholipid and glycolipid further confirmed that strain RL(T) belongs to the genus Thermus. The predominant fatty acids of strain RL(T) were iso-C17:0 (23.67%) and iso-C15:0 (24.50%). The results obtained after DNA-DNA hybridization, biochemical and physiological tests clearly distinguished strain RL(T) from its closely related species. Thus, strain RL(T) represents a novel species of the genus Thermus for which the name Thermus parvatiensis is proposed (=DSM 21745(T)= MTCC 8932(T)).

The Human Mitochondrial DEAD-Box Protein DDX28 Resides in RNA Granules and Functions in Mitoribosome Assembly

Human mitochondrial ribosomes are specialized in the synthesis of 13 proteins, which are fundamental components of the oxidative phosphorylation system. The pathway of mitoribosome biogenesis, the compartmentalization of the process, and factors involved remain largely unknown. Here, we have identified the DEAD-box protein DDX28 as an RNA granule component essential for the biogenesis of the mitoribosome large subunit (mt-LSU). DDX28 interacts with the 16S rRNA and the mt-LSU. RNAi-mediated DDX28 silencing in HEK293T cells does not affect mitochondrial mRNA stability or 16S rRNA processing or modification. However, it leads to reduced levels of 16S rRNA and mt-LSU proteins, impaired mt-LSU assembly, deeply attenuated mitochondrial protein synthesis, and consequent failure to assemble oxidative phosphorylation complexes. Our findings identify DDX28 as essential during the early stages of mitoribosome mt-LSU biogenesis, a process that takes place mainly near the mitochondrial nucleoids, in the compartment defined by the RNA granules.

Expression of gyrB and 16S ribosomal RNA genes as indicators of growth and physiological activities of Legionella pneumophila.

To determine whether the DNA gyrase (gyrB) and 16S ribosomal RNA (16S rRNA) genes can be used as indicators of the biological activities of Legionella pneumophila, the expression levels were estimated. The ratio of mRNA/DNA in gyrB was 0.7 in mid log phase and decreased drastically after the log phase. For 16S rRNA, the ratio was highest in mid log phase (7.0×10(3)), and the value that was about 10% of that in the log phase was maintained for six days. The rRNA may be vital in the resting or active but nonculturable cells that are not growing but physiologically active. The expression levels of gyrB mRNA and 16S rRNA can be used as indicators of the growth activity and the physiological activity of L. pneumophila, respectively. Therefore, by measurement of these indicators, we can evaluate the activities of Legionella cells in various environments.

Fecal microbes, short chain fatty acids, and colorectal cancer across racial/ethnic groups

To investigate differences in microbes and short chain fatty acid (SCFA) levels in stool samples from Hispanic and non-Hispanic African American, American Indian, and White participants. Stool samples from twenty participants were subjected to analysis for relative levels of viable bacteria and for SCFA levels. Additionally, the samples were subjected to 16S rRNA gene pyrosequencing for identification of bacteria present in the stool. We used a metagenome functional prediction technique to analyze genome copy numbers and estimate the abundance of butyrate kinase in all samples. We found that African Americans had significantly lower levels of acetate, butyrate, and total SCFAs than all other racial/ethnic groups. We also found that participant microbial profiles differed by racial/ethnic group. African Americans had significantly more Firmicutes than Whites, with enriched Ruminococcaceae. The Firmicutes/Bacteroidetes ratio was also significantly higher for African Americans than for Whites (P = 0.049). We found Clostridium levels to be significantly and inversely related to total SCFA levels (P = 0.019) and we found Bacteroides to be positively associated (P = 0.027) and Clostridium to be negatively associated (P = 0.012) with levels of butyrate. We also identified a correlation between copy number for a butyrate kinase predicted from 16S rRNA gene abundance and levels of butyrate in stool. The identified differences in gut flora and SCFA levels may relate to colorectal cancer mortality differentials and may be useful as targets for future clinical and behavioral interventions.

Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture

This study evaluated the chronic impact of tetracycline on biomass with enriched nitrifying community sustained in a lab-scale activated sludge system. For this purpose, a fill and draw reactor fed with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia was sustained at a sludge age of 15 days. At steady-state, the reactor operation was continued with a daily tetracycline dosing of 50 mg/L for more than 40 days, with periodic monitoring of the microbial composition, the nitrifying bacteria abundance, as well as the amoA and 16S rRNA gene activity, using molecular techniques. Changes in the kinetics of nitrification were quantified by modelling concentration profiles of major nitrogen fractions and oxygen uptake rate profiles derived from parallel batch experiments. Activated sludge modeling results indicated inhibitory impact of tetracycline on the growth of nitrifiers with a significant increase of the half saturation coefficients in corresponding rate equations. Tetracycline also inactivated biomass components of the enriched culture at a gradually increasing rate with time of exposure, leading to total collapse of nitrification. Molecular analyses revealed significant changes in the composition of the microbial community throughout the observation period. They also showed that continuous exposure to tetracycline inflicted significant reduction in amoA mRNA and 16S rRNA levels directly affecting nitrification. The chronic impact was much more pronounced on the ammonia oxidizing bacteria (AOB) community. These observations explained the basis of numerical changes identified in the growth kinetics of nitrifiers under stress conditions.

Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 73:211-224 (2014) - DOI: https://doi.org/10.3354/ame01718 Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea Jana Vojvoda1,2,*, Dominique Lamy1,3, Eva Sintes1, Juan A. L. Garcia1, Valentina Turk2, Gerhard J. Herndl1,4 1Department of Limnology and Oceanography, Center of Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria 2National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia 3Université Pierre et Marie Curie, UMR BOREA, UPMC/MNHN/CNRS UMR 7208/IRD-207/UCBN, 61 rue Buffon, 75005 Paris, France 4Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), 1790AB Den Burg, The Netherlands *Corresponding author: janavojvoda@gmail.com ABSTRACT: The structure and activity of prokaryotic communities were determined in marine snow and in the ambient water of the northern Adriatic Sea in different seasons (autumn, spring and summer). The seasonal variation in the composition of marine-snow-associated and ambient-water bacterial communities was assessed by T-RFLP (Terminal Restriction Fragment Length Polymorphism) on the 16S rRNA gene (16S rDNA) and 16S rRNA transcript (16S rRNA) level. On the 16S rDNA level, the bacterial community composition of the marine snow and ambient water was similar in summer and autumn, but not in spring. In contrast, on the 16S rRNA level, indicative of the active bacterial community, the marine-snow-associated bacterial community was different from that of the ambient-water, and different from the bacterial community on the 16S rDNA level, except in autumn. To phylogenetically characterize the bacterial and archaeal community composition associated with marine snow and the ambient water, clone libraries of 16S rDNA and 16S rRNA were constructed from 2 contrasting seasons. Phylogenetic profiling revealed a higher similarity among bacterial communities in summer compared to late autumn. Certain bacterial and archaeal groups were exclusively associated with summer or autumn marine snow, suggesting that marine-snow-associated prokaryotic communities are subjected to successional changes similar to ambient-water communities. Moreover, the presence of bacterial groups enriched in marine snow including Vibrionales and sulphate-reducing bacteria is consistent with niche partitioning and metabolic adaptations of the particle-associated microbiota. KEY WORDS: Marine snow · Free-living bacteria · Marine snow-associated bacteria · Archaea · T-RFLP · 16S rRNA · 16S rDNA · Northern Adriatic Sea Full text in pdf format Supplementary material PreviousNextCite this article as: Vojvoda J, Lamy D, Sintes E, Garcia JAL, Turk V, Herndl GJ (2014) Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea. Aquat Microb Ecol 73:211-224. https://doi.org/10.3354/ame01718 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 73, No. 3. Online publication date: November 11, 2014 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2014 Inter-Research.

Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 73:185-194 (2014) - DOI: https://doi.org/10.3354/ame01716 Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters Raphaël Lami1,2,3,*, David L. Kirchman1 1University of Delaware, School of Marine Science and Policy, Lewes, Delaware 19958, USA 2Sorbonne Universités, UPMC Univ Paris 06, USR 3579, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France 3CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France *Corresponding author: raphael.lami@obs-banyuls.fr ABSTRACT: Proteorhodopsins (PR) are phylogenetically widespread and highly expressed proton pumps in marine bacterial communities, including in the SAR11 clade, one of the most common clades in the oceans. The relationships between PR expression, light and cell activity remain unclear, especially in natural environments. We examined these relationships during 3 diurnal studies in spring, summer and fall in Delaware coastal waters. The abundance of genes and transcripts of SAR11 PR, SAR11 16S rRNA and total bacterial 16S rRNA were monitored using a quantitative PCR approach. We found that the expression of SAR11 PR was 2.5-fold higher during the day than at night. However, SAR11 16S rRNA levels remained constant during the day and night on all cruises, suggesting that the growth-related activity of SAR11 was not directly affected by sunlight. There was a tight correlation between expression of PR in SAR11 and photosynthetically active radiation, but not with other environmental parameters. Our data support the hypothesis that light affects PR expression by SAR11 populations, but the energy from PR appears to contribute relatively little to supporting bacterial growth-related activity in marine waters. KEY WORDS: Marine bacteria · SAR11 · Proteorhodopsin · Quantitative PCR Full text in pdf format NextCite this article as: Lami R, Kirchman DL (2014) Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters. Aquat Microb Ecol 73:185-194. https://doi.org/10.3354/ame01716 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 73, No. 3. Online publication date: November 11, 2014 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2014 Inter-Research.

Expanding the verrucomicrobial methanotrophic world: description of three novel species of Methylacidimicrobium gen. nov.

Methanotrophic Verrucomicrobia have been found in geothermal environments characterized by high temperatures and low pH values. However, it has recently been hypothesized that methanotrophic Verrucomicrobia could be present under a broader range of environmental conditions. Here we describe the isolation and characterization of three new species of mesophilic acidophilic verrucomicrobial methanotrophs from a volcanic soil in Italy. The three new species showed 97% to 98% 16S rRNA gene identity to each other but were related only distantly (89% to 90% on the 16S rRNA level) to the thermophilic genus Methylacidiphilum. We propose the new genus Methylacidimicrobium, including the novel species Methylacidimicrobium fagopyrum, Methylacidimicrobium tartarophylax, and Methylacidimicrobium cyclopophantes. These mesophilic Methylacidimicrobium spp. were more acid tolerant than their thermophilic relatives; the most tolerant species, M. tartarophylax, still grew at pH 0.5. The variation in growth temperature optima (35 to 44°C) and maximum growth rates (µmax; 0.013 to 0.040 h(-1)) suggested that all species were adapted to a specific niche within the geothermal environment. All three species grew autotrophically using the Calvin cycle. The cells of all species contained glycogen particles and electron-dense particles in their cytoplasm as visualized by electron microscopy. In addition, the cells of one of the species (M. fagopyrum) contained intracytoplasmic membrane stacks. The discovery of these three new species and their growth characteristics expands the known diversity of verrucomicrobial methanotrophs and shows that they are present in many more ecosystems than previously assumed.