A study of enteric viruses in raw and treated sewage from two secondary treatment plants, which received sewage from Oslo city (plant A) and small municipalities in Hedmark county in Norway (plant B), showed high levels of noro-, adeno-, and bocavirus throughout the year. A seasonal variation was observed for adeno- and GII norovirus with higher levels during winter and bocavirus that had more positive samples during winter. The virus concentrations in raw sewage were comparable in the two plants, with medians (log10 genome copies per liter) of 6.1, 6.3, 6.0, and 4.5 for noro GI, noro GII, adeno-, and bocavirus, respectively. The level of hepatitis E virus was not determined as it was below the limit of quantification. The mean log10 virus reduction was 0.55 (plant A) and 1.44 (plant B) with the highest reduction found in the plant with longer hydraulic retention time. The adenoviruses were dominantly serotype 41, while serotype 12 appeared sporadically. Of the 102 raw and treated sewage samples that were tested, eight were positive for hepatitis E virus of which four were from treated sewage. Two of the four obtained gene sequences from hepatitis E virus originated from the rural sewage samples and showed high similarity with a genotype 3 strain of hepatitis E virus detected in local piglets. Two other hepatitis E virus sequences obtained from urban sewage samples showed high similarities with genotype 3 strains isolated from urban sewage in Spain and a human genotype 1 isolate from India. The study gives information on the levels of noroviruses in raw and treated sewage, which is valuable to risk assessment, information indicating that some infections with hepatitis E viruses in Norway have a regional origin and that human bocavirus 2 and 3 are prevalent in the Norwegian population.
To understand better the link between atmospheric CO2 concentrations and climate over geological time, records of past CO2 are reconstructed from geochemical proxies. Although these records have provided us with a broad picture of CO2 variation throughout the Phanerozoic eon (the past 544 Myr), inconsistencies and gaps remain that still need to be resolved. Here I present a continuous 300-Myr record of stomatal abundance from fossil leaves of four genera of plants that are closely related to the present-day Ginkgo tree. Using the known relationship between leaf stomatal abundance and growing season CO2 concentrations, I reconstruct past atmospheric CO2 concentrations. For the past 300 Myr, only two intervals of low CO2 (2,000 p.p.m.v.) concentrations. These results are consistent with some reconstructions of past CO2 (refs 1, 2) and palaeotemperature records, but suggest that CO2 reconstructions based on carbon isotope proxies may be compromised by episodic outbursts of isotopically light methane. These results support the role of water vapour, methane and CO2 in greenhouse climate warming over the past 300 Myr.
Comment In: Nature. 2001 May 17;411(6835):247-811357108
Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the "stability profiles" of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world.
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Numeric abundance, identity and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six-wetlands of European Northern Russia (pH 3.9-4.7) varied from 0.04 to 0.60 µg CH4 g(-1) peat h(-1). The number of cells revealed by hybridization with fluorochrome-labeled probes M84 + M705 specific for type I methanotrophs was 0.05-2.16 x 10(5) cells g(-1) dry peat, i.e. 0.4-12.5% of the total number of methanotrophs and 0.004-0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93-99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonaspaludis and Methylovulum miyakonense, respectively. Only Methylomonaspaludum SH10 was capable of growth in acidic media (pH range for growth 3.8-7.2 with the optimum at pH 5.8-6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5-8.0 with the optimum at pH 6.5-7.5).
Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface.
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Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
A strictly anaerobic, mesophilic, syntrophic, alkane-degrading strain, L81T, was isolated from a biofilm sampled from a black smoker chimney at the Loki's Castle vent field. Cells were straight, rod-shaped, Gram-positive-staining and motile. Growth was observed at pH?6.2-9.5, 14-42?°C and 0.5-6?% (w/w) NaCl, with optima at pH?7.0-8.2, 37?°C and 3% (w/w) NaCl. Proteinaceous substrates, sugars, organic acids and hydrocarbons were utilized for growth. Thiosulfate was used as an external electron acceptor during growth on crude oil. Strain L81T was capable of syntrophic hydrocarbon degradation when co-cultured with a methanogenic archaeon, designated strain LG6, isolated from the same enrichment. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain L81T is affiliated with the family Lachnospiraceae, and is most closely related to the type strains of Natranaerovirga pectinivora (92?% sequence similarity) and Natranaerovirga hydrolytica (90%). The major cellular fatty acids of strain L81T were C15?:?0, anteiso-C15?:?0 and C16?:?0, and the profile was distinct from those of the species of the genus Natranaerovirga. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, four unidentified glycolipids and two unidentified phosphoglycolipids. The G+C content of genomic DNA was determined to be 31.7?mol%. Based on our phenotypic, phylogenetic and chemotaxonomic results, strain L81T is considered to represent a novel species of a new genus of the family Lachnospiraceae, for which we propose the name Abyssivirga alkaniphila gen. nov., sp. nov. The type strain of Abyssivirga alkaniphila is L81T (=DSM 29592T=JCM 30920T). We also provide emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
Commercial inactivated parenteral influenza vaccines reduced febrile (> or = 38 degrees C) respiratory illness by 53% (95% CL: 41-63%) during a 3 week outbreak in 1998 when A/Sydney/5/97(H3N2)-like influenza viruses were shown to be the predominant etiological agents and an older antigenic variant, A/Nanchang/933/95, served as the vaccine virus. The calculatory efficacy for preventing virologically diagnosed influenza infections was 57% (95% CL: 40-68%). The study population consisted of 1374 young male military conscripts. Vaccination coverage on a voluntary basis was 67%. Vaccination was ineffective in preventing febrile illness during a second epidemic wave lasting 2 weeks when mainly adenoviruses were shown to have been circulating in the garrison. Out of the 36 nasopharyngeal aspirates positive for influenza A by antigen detection, 18 A/Sydney/5/97-like strains (10 from non-vaccinated and eight from vaccinated subjects) and two A/Nanchang/933/95-like strains (both from non-vaccinated subjects) were isolated in MDCK cell cultures. Intraepidemic variation was detected among the A/Sydney/5/97-like field strains in their HA1 sequences and reactivity in HI tests, but no evidence was obtained that this variation would have been of significance to the virus in breaking through the vaccination-induced immunity.
In the ancient Lake Baikal, Russia, amphipod crustaceans have undergone a spectacular adaptive radiation, resulting in a diverse community of species. A survey of microsporidian parasites inhabiting endemic and non-endemic amphipod host species at the margins of Lake Baikal indicates that the endemic amphipods harbour many microsporidian parasite groups associated with amphipods elsewhere in Eurasia. While these parasites may have undergone a degree of adaptive radiation within the lake, there is little evidence of host specificity. Furthermore, a lack of reciprocal monophyly indicates that exchanges of microsporidia between Baikalian and non-Baikalian hosts have occurred frequently in the past and may be ongoing. Conversely, limitations to parasite exchange between Baikalian and non-Baikalian host populations at the margins of the lake are implied by differences in parasite prevalence and lack of shared microsporidian haplotypes between the two host communities. While amphipod hosts have speciated sympatrically within Lake Baikal, the parasites appear instead to have accumulated, moving into the lake from external amphipod populations on multiple occasions to exploit the large and diverse community of endemic amphipods in Lake Baikal.
Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates.
Actinobaculum schaalii can cause urinary tract infections and septicemia but is difficult to identify by cultivation. To obtain a fast diagnosis and identify A. schaalii, we developed a TaqMan real-time quantitative PCR. Routine urine samples were obtained from 177 hospitalized patients and 75 outpatients in Viborg County, Denmark, in 2008-2009. The PCR detected A. schaalii in 22% of samples from patients >60 years of age. This assay showed that A. schaalii is more common than implied by routine cultivation. In 90% of PCR-positive urine samples, other common uropathogens were identified. This finding suggests that A. schaalii is a common, undetected, bacterial pathogen. Our results suggest that A. schaalii may be a more common pathogen than previously thought, especially in patients with unexplained chronic urinary tract infections, who are often treated with trimethoprim or ciprofloxacin, to which A. schaalii is resistant.