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Journal: FEMS microbiology letters

83

Scholarly communication is in a perpetual state of disruption. Within this, peer review of research articles remains an essential part of the formal publication process, distinguishing it from virtually all other modes of communication. In the last several years, there has been an explosive wave of innovation in peer review research, platforms, discussions, tools, and services. This is largely coupled with the ongoing and parallel evolution of scholarly communication as it adapts to rapidly changing environments, within what is widely considered as the ‘open research’ or ‘open science’ movement. Here, we summarise the current ebb and flow around changes to peer review and consider its role in a modern digital research and communications infrastructure and suggest why uptake of new models of peer review appears to have been so low compared to what is often viewed as the ‘traditional’ method of peer review. Finally, we offer some insight into the potential futures of scholarly peer review and consider what impacts this might have on the broader scholarly research ecosystem. In particular, we focus on the key traits of certification and reputation, moderation and quality control, and engagement incentives, and discuss how these interact with socio-technical aspects of peer review and academic culture.

27

The genomes of two novel Dehalococcoides mccartyi strains, DCMB5 and BTF08, enriched from the heavily organohalide-contaminated megasite around Bitterfeld (Germany), were fully sequenced and annotated. Although overall similar, the genome sequences of the two strains reveal remarkable differences in their genetic content, reflecting a specific adaptation to the contaminants at the field sites from which they were enriched. The genome of strain BTF08 encodes for 20 reductive dehalogenases, including all three of which are necessary to couple the reductive dechlorination of PCE to ethene to growth. The genes encoding trichloroethene and vinyl chloride reductive dehalogenases, tceA and vcrA, are located within mobile genetic elements, suggesting their recent horizontal acquisition. The genome of strain DCMB5 contains 23 reductive dehalogenase genes, including cbrA, which encodes a chlorobenzene reductive dehalogenase, and a gene cluster encoding arsenic resistance proteins, both corresponding to typical pollutants at its isolation site. This article is protected by copyright. All rights reserved.

Concepts: DNA, Gene, Genetics, Human genome, Virus, Genome, RNA, Horizontal gene transfer

27

L-asparaginase producing microbes are conventionally screened on phenol red L-asparagine containing plates. However, sometimes the contrast of the zone obtained (between yellow and pink) is not very sharp and distinct. In the present investigation, an improved method for screening of the microorganisms producing extracellular L- asparaginase is being reported wherein, bromothymol blue (BTB) is incorporated as pH indicator in L-asparagine containing medium instead of phenol red. Plates containing BTB at acidic pH are yellow and turn dark blue on alkaline pH. Thus, a dense dark blue zone is formed around microbial colonies producing L-asparaginase, thereby differentiating between enzyme producers and non-producers. The present method is more sensitive and accurate as compared to conventional method for screening of both fungi and bacteria producing extracellular L-asparaginase. Furthermore, BTB gives a transient green colour at neutral pH (7.0) and dark blue colour at higher pH 8.0-9.0, thereby also distinguishing the potency of microorganism for L-asparaginase production. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Concepts: Archaea, Bacteria, Microbiology, Biotechnology, PH, Green, Microorganism, PH indicator

26

Trichoderma species have been used widely as biocontrol agents for the suppression of soil-borne pathogens. However, some antagonistic mechanisms of Trichoderma are not well characterized. In this study, a series of laboratory experiments were designed to characterize the importance of mycoparasitism, exoenzymes and volatile organic compounds (VOCs) by T. harzianum T-E5 for the control of F. oxysporum f. sp. cucumerinum (FOC). We further tested if these mechanisms were inducible and upregulated in presence of FOC. The results were as follows: T-E5 heavily parasitized FOC by coiling and twisting the entire mycelium of the pathogen in dual cultures. T-E5 growing medium conditioned with deactivated FOC (T2) showed more proteins and higher cell wall-degrading enzyme activities than T1, suggesting that FOC could induce the upregulation of exoenzymes. The presence of deactivated FOC (T2') also resulted in the upregulation of VOCs that 5 and 8 different types T-E5-derived VOCs were identified from T1' and T2', respectively. Further, the excreted VOCs in T2' showed significantly higher antifungal activities against FOC than T1'. In conclusion, mycoparasitism of T-E5 against FOC involved mycelium contact and the production of complex extracellular substances. Together, these data provide clues to help further clarify the interactions between these fungi. This article is protected by copyright. All rights reserved.

Concepts: Enzyme, Fusarium oxysporum, Volatile organic compound, Organic compounds, Copyright, Volatile, Trichoderma, Trichoderma harzianum

25

Genome annotation is one of the key actions that must be undertaken in order to decypher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multi-threaded script named MEGAnnotator (Multi-threaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to prearrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline.

Concepts: DNA, Genetics, Bacteria, Organism, Human Genome Project, Virus, Genome, Genomics

24

Listeria monocytogenes possesses the highest number of leucine-rich repeat (LRR) containing proteins among all gram-positive bacteria; these LRR-containing molecules are known as the “internalin” family. To understand the functions of largely uncharacterized LRR-containing molecules, we constructed seven deletion mutants in L. monocytogenes H7858 strain targeting genes in this family and tested their virulence. Among the seven mutants, the ΔLMOh7858_0369 strain and the ΔLMOh7858_2546 strain showed significantly impaired invasiveness to HepG2 cells. We further tested the virulence of these two strains in the intravascular sepsis model using BALB/c mice. Interestingly, the ΔLMOh7858_0369 strain showed significant reduction in organ colonization, bacteremia, and invasion of the brain compared to the parental wild type strain. Host immune responses to listerial intravascular infection were measured at 24 h and 72 h post infection. Transcript levels of several proinflammatory cytokines and chemokines were significantly lower when induced by the ΔlmOh7858_0369 strain than when induced by wild type. These results suggest that the putative LRR-containing protein encoded by LMOh7858_0369 might be a novel virulence factor of the L. monocytogenes H7858 strain.

Concepts: Immune system, Inflammation, DNA, Protein, Gene, Bacteria, Microbiology, Listeria

24

The heavy dependence on petroleum-derived fuel has raised concerns about energy sustainability and climate change, which have prompted researchers to explore fuel production from renewable sources. 1-Butanol and isobutanol are promising biofuels that have favorable properties and can also serve as solvents or chemical feedstocks. Microbial production of these alcohols provides great opportunities to access a wide spectrum of renewable resources. In recent years, research has improved the native 1-butanol production and has engineered isobutanol production in various organisms to explore metabolic diversity and a broad range of substrates. This review focuses on progress in metabolic engineering for the production of these two compounds using various resources.

Concepts: Metabolism, Enzyme, Natural resource, Habitat conservation, Renewable energy, Alternative energy, Renewable resource, Natural capital

24

Two isolates belonging to Aspergillus section Fumigati were recovered from German soil on itraconazole containing agar media. Phylogenetic analysis and phenotypic characterization of both isolates show that they represent a novel species named Aspergillus oerlinghausenensis (holotype CBS H-22119(HT), ex-type CBS 139183(T) = IBT 33878 = DTO 316-A3). The species is phylogenetically related to Aspergillus fischeri and Aspergillus fumigatus. Aspergillus oerlinghausenensis can be differentiated from A. fischeri by its higher growth rate at 50°C. Furthermore, A. oerlinghausenensis is proto-heterothallic as only the MAT1-1 idiomorph was detected, while A. fischeri is homothallic. The species differs from A. fumigatus by a weak sporulation on malt extract agar at 25°C, a floccose colony texture on Czapek yeast extract agar and malt extract agar and subglobose instead of subclavate vesicles. The cyp51A promoter region of A. oerlinghausenensis deviates from the previously reported cyp51A promoter regions in A. fumigatus and potentially presents a novel azole-resistance conferring modification. Due to the close relationship of A. oerlinghausenensis with A. fischeri and A. fumigatus, this species is placed in a good position for comparative studies involving these species.

Concepts: DNA, Gene, Promoter, Aspergillus, Aspergillus fumigatus

23

Traditional methods for the production of food grade pigments from fungus Monascus spp. are mostly relying on submerged fermentation. However, cell bound nature and intracellular accumulation of pigments in Monascus spp is the major hurdle in pigment production by submerged fermentation. The present study focused on the investigation of the effect of the antifungal agent, fluconazole on red pigment production from Monascus purpureus (NMCC-PF01). At the optimized concentration of fluconazole (30 μg/ml), pigment production was found to be enhanced by 88% after 96 h and it remained constant even after further incubation up to 168 h. An ergosterol, a sterol specific for fungi was also extracted and estimated as a function of fungal growth. The concentration of ergosterol in fluconazole-treated fermentation broth was reduced by 49% as compared to control broth. Thus it could be responsible for facilitating the release of intracellular and cell bound pigments. Nevertheless, the role of cell transporters in transporting out the red pigments cannot be ignored and deserves further attention. Qualitative analysis of red pigment by TLC, UV spectroscopy and mass spectrometric analysis (ESIMS) has confirmed the presence of well-known pigment, Rubropunctamine. In addition, this fermentation process produces citrinin-free pigments. This novel approach will be useful to facilitate increased pigment production by the release of intracellular or cell bound Monascus pigments.

Concepts: Bacteria, Enzyme, Fungus, Pigment, Vermilion, Ergosterol, Antifungal drug, Monascus purpureus

22

Methane seepages are widespread in the Black Sea. However, microbiological research has been carried out only at the continental shelf seeps. The present work dealt with coastal gas seepages of the Kalamit Bay (Black Sea). High-throughput 16S rRNA gene sequencing and radiotracer analysis (14С and 35S) were used to determine the composition of the microbial community and the rates of microbial sulfate reduction and methane oxidation. The phylum Proteobacteria, represented mainly by sulfate reducers of the class Deltaproteobacteria, was the predominant in sequence dataset. Bacteroidetes and Planctomycetes were other numerous phyla. Among archaea, the phylum Woesearchaeota and Marine Benthic Group B were predominant in the upper horizons. Relative abundance of Euryarchaeota of the families Methanomicrobiacea and Methanosarcinaceae (including ANME-3 archaea) increased in deeper sediment layers. Sulfate reduction rate (up to 2.9 mmol/L×day) was considerably higher than the rate of anaerobic methane oxidation (up to 43.4 μmol/L×day), which indicated insignificant contribution of anaerobic methane oxidation to the total sulfide production.