Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601

Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.

Lagrangian profiles of riverine autotrophy, organic matter transformation, and micropollutants at extreme drought

On their way from inland to the ocean, flowing water bodies, their constituents and their biotic communities are exposed to complex transport and transformation processes. However, detailed process knowledge as revealed by Lagrangian measurements adjusted to travel time is rare in large rivers, in particular at hydrological extremes. To fill this gap, we investigated autotrophic processes, heterotrophic carbon utilization, and micropollutant concentrations applying a Lagrangian sampling design in a 600 km section of the River Elbe (Germany) at historically low discharge. Under base flow conditions, we expect the maximum intensity of instream processes and of point source impacts. Phytoplankton biomass and photosynthesis increased from upstream to downstream sites but maximum chlorophyll concentration was lower than at mean discharge. Concentrations of dissolved macronutrients decreased to almost complete phosphate depletion and low nitrate values. The longitudinal increase of bacterial abundance and production was less pronounced than in wetter years and bacterial community composition changed downstream. Molecular analyses revealed a longitudinal increase of many DOM components due to microbial production, whereas saturated lipid-like DOM, unsaturated aromatics and polyphenols, and some CHOS surfactants declined. In decomposition experiments, DOM components with high O/C ratios and high masses decreased whereas those with low O/C ratios, low masses, and high nitrogen content increased at all sites. Radiocarbon age analyses showed that DOC was relatively old (890-1870 years B.P.), whereas the mineralized fraction was much younger suggesting predominant oxidation of algal lysis products and exudates particularly at downstream sites. Micropollutants determining toxicity for algae (terbuthylazine, terbutryn, isoproturon and lenacil), hexachlorocyclohexanes and DDTs showed higher concentrations from the middle towards the downstream part but calculated toxicity was not negatively correlated to phytoplankton. Overall, autotrophic and heterotrophic process rates and micropollutant concentrations increased from up- to downstream reaches, but their magnitudes were not distinctly different to conditions at medium discharges.

Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

Evaluation of Two Methods to Concentrate SARS-CoV-2 from Untreated Wastewater

Use of wastewater-based epidemiology as a tool to record and manage the course of SARS-CoV-2 infections in human populations requires information about the efficiency of methods to concentrate the virus from wastewater. In the present study, we spiked untreated wastewater with quantified SARS-CoV-2 positive clinical material and enriched the virus by polyethylene glycol precipitation and ultrafiltration with Vivaspin 10 kDa MWCO columns. SARS-CoV-2 was detected and quantified by reverse transcription quantitative PCR (E- and S-gene) and droplet digital PCR. The concentration of virus with precipitation resulted in mean recoveries between 59.4% and 63.7% whereas rates from 33.0% to 42.6% after ultrafiltration of samples were demonstrated. The results suggest that the use of both methods allows an effective and practicable enrichment of SARS-CoV-2 from raw wastewater.

Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection

BACKGROUND

The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus involved in cases and case clusters of severe acute respiratory infection in the Arabian Peninsula, Tunisia, Morocco, France, Italy, Germany, and the UK. We provide a full description of a fatal case of MERS-CoV infection and associated phylogenetic analyses.

METHODS

We report data for a patient who was admitted to the Klinikum Schwabing (Munich, Germany) for severe acute respiratory infection. We did diagnostic RT-PCR and indirect immunofluorescence. From time of diagnosis, respiratory, faecal, and urine samples were obtained for virus quantification. We constructed a maximum likelihood tree of the five available complete MERS-CoV genomes.

FINDINGS

A 73-year-old man from Abu Dhabi, United Arab Emirates, was transferred to Klinikum Schwabing on March 19, 2013, on day 11 of illness. He had been diagnosed with multiple myeloma in 2008, and had received several lines of treatment. The patient died on day 18, due to septic shock. MERS-CoV was detected in two samples of bronchoalveolar fluid. Viral loads were highest in samples from the lower respiratory tract (up to 1·2 × 10(6) copies per mL). Maximum virus concentration in urine samples was 2691 RNA copies per mL on day 13; the virus was not present in the urine after renal failure on day 14. Stool samples obtained on days 12 and 16 contained the virus, with up to 1031 RNA copies per g (close to the lowest detection limit of the assay). One of two oronasal swabs obtained on day 16 were positive, but yielded little viral RNA (5370 copies per mL). No virus was detected in blood. The full virus genome was combined with four other available full genome sequences in a maximum likelihood phylogeny, correlating branch lengths with dates of isolation. The time of the common ancestor was halfway through 2011. Addition of novel genome data from an unlinked case treated 6 months previously in Essen, Germany, showed a clustering of viruses derived from Qatar and the United Arab Emirates.

INTERPRETATION

We have provided the first complete viral load profile in a case of MERS-CoV infection. MERS-CoV might have shedding patterns that are different from those of severe acute respiratory syndrome and so might need alternative diagnostic approaches.

FUNDING

European Union; German Centre for Infection Research; German Research Council; and German Ministry for Education and Research.

Evidence for novel hepaciviruses in rodents

Hepatitis C virus (HCV) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma. Research is complicated by a lack of accessible small animal models. The systematic investigation of viruses of small mammals could guide efforts to establish such models, while providing insight into viral evolutionary biology. We have assembled the so-far largest collection of small-mammal samples from around the world, qualified to be screened for bloodborne viruses, including sera and organs from 4,770 rodents (41 species); and sera from 2,939 bats (51 species). Three highly divergent rodent hepacivirus clades were detected in 27 (1.8%) of 1,465 European bank voles (Myodes glareolus) and 10 (1.9%) of 518 South African four-striped mice (Rhabdomys pumilio). Bats showed anti-HCV immunoblot reactivities but no virus detection, although the genetic relatedness suggested by the serologic results should have enabled RNA detection using the broadly reactive PCR assays developed for this study. 210 horses and 858 cats and dogs were tested, yielding further horse-associated hepaciviruses but none in dogs or cats. The rodent viruses were equidistant to HCV, exceeding by far the diversity of HCV and the canine/equine hepaciviruses taken together. Five full genomes were sequenced, representing all viral lineages. Salient genome features and distance criteria supported classification of all viruses as hepaciviruses. Quantitative RT-PCR, RNA in-situ hybridisation, and histopathology suggested hepatic tropism with liver inflammation resembling hepatitis C. Recombinant serology for two distinct hepacivirus lineages in 97 bank voles identified seroprevalence rates of 8.3 and 12.4%, respectively. Antibodies in bank vole sera neither cross-reacted with HCV, nor the heterologous bank vole hepacivirus. Co-occurrence of RNA and antibodies was found in 3 of 57 PCR-positive bank vole sera (5.3%). Our data enable new hypotheses regarding HCV evolution and encourage efforts to develop rodent surrogate models for HCV.