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Microorganisms, Volume 1, Issue 1 (December 2013), Pages 1-198

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Editorial

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Open AccessEditorial Microorganisms—A Forum for Understanding Microbial Life in All Its Forms
Microorganisms 2013, 1(1), 1-2; doi:10.3390/microorganisms1010001
Received: 24 January 2013 / Accepted: 24 January 2013 / Published: 19 February 2013
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Abstract It is my great pleasure to welcome you to Microorganisms, a new open access journal, which is dedicated to microorganisms in all their forms and via any approach to their study. [...] Full article

Research

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Open AccessCommunication Control of a Multi-Drug-Resistant Acinetobacter baumannii Outbreak after Orthopedics Department Relocation
Microorganisms 2013, 1(1), 158-161; doi:10.3390/microorganisms1010158
Received: 6 September 2013 / Revised: 13 November 2013 / Accepted: 22 November 2013 / Published: 2 December 2013
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Abstract
Acinetobacter baumannii clinical isolates have the ability to survive in the hospital niche for prolonged time periods and to develop resistance against multiple antimicrobial agents. Therefore, A. baumannii has emerged as an important cause of nosocomial outbreaks worldwide, especially in critical-care environments [...] Read more.
Acinetobacter baumannii clinical isolates have the ability to survive in the hospital niche for prolonged time periods and to develop resistance against multiple antimicrobial agents. Therefore, A. baumannii has emerged as an important cause of nosocomial outbreaks worldwide, especially in critical-care environments such as intensive care units. In the present communication, we report a multi-drug-resistant A. baumannii outbreak that occurred in an orthopedics department in Greece after the admission of a patient previously hospitalized in the intensive care unit of a Greek tertiary care hospital. Despite the implementation of infection control measures, 29 patients were infected, significantly raising their hospitalization periods and treatment costs. Interestingly, the outbreak was put under control after the department’s previously programmed relocation. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
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Open AccessArticle Macroalgal Endophytes from the Atlantic Coast of Canada: A Potential Source of Antibiotic Natural Products?
Microorganisms 2013, 1(1), 175-187; doi:10.3390/microorganisms1010175
Received: 9 October 2013 / Revised: 8 November 2013 / Accepted: 5 December 2013 / Published: 13 December 2013
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Abstract
As the need for new and more effective antibiotics increases, untapped sources of biodiversity are being explored in an effort to provide lead structures for drug discovery. Endophytic fungi from marine macroalgae have been identified as a potential source of biologically active [...] Read more.
As the need for new and more effective antibiotics increases, untapped sources of biodiversity are being explored in an effort to provide lead structures for drug discovery. Endophytic fungi from marine macroalgae have been identified as a potential source of biologically active natural products, although data to support this is limited. To assess the antibiotic potential of temperate macroalgal endophytes we isolated endophytic fungi from algae collected in the Bay of Fundy, Canada and screened fungal extracts for the presence of antimicrobial compounds. A total of 79 endophytes were isolated from 7 species of red, 4 species of brown, and 3 species of green algae. Twenty of the endophytes were identified to the genus or species level, with the remaining isolates designated codes according to their morphology. Bioactivity screening assays performed on extracts of the fermentation broths and mycelia of the isolates revealed that 43 endophytes exhibited antibacterial activity, with 32 displaying antifungal activity. Endophytic fungi from Bay of Fundy macroalgae therefore represent a significant source of antibiotic natural products and warrant further detailed investigation. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)

Review

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Open AccessReview Understanding Bioluminescence in Dinoflagellates—How Far Have We Come?
Microorganisms 2013, 1(1), 3-25; doi:10.3390/microorganisms1010003
Received: 3 May 2013 / Revised: 20 August 2013 / Accepted: 24 August 2013 / Published: 5 September 2013
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Abstract
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to [...] Read more.
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms’ lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions that need to be addressed to advance this research field. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Circadian Rhythms in Dinoflagellates: What Is the Purpose of Synthesis and Destruction of Proteins?
Microorganisms 2013, 1(1), 26-32; doi:10.3390/microorganisms1010026
Received: 21 June 2013 / Revised: 26 August 2013 / Accepted: 9 September 2013 / Published: 18 September 2013
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Abstract
There is a prominent circadian rhythm of bioluminescence in many species of light-emitting dinoflagellates. In Lingulodinium polyedrum a daily synthesis and destruction of proteins is used to regulate activity. Experiments indicate that the amino acids from the degradation are conserved and incorporated [...] Read more.
There is a prominent circadian rhythm of bioluminescence in many species of light-emitting dinoflagellates. In Lingulodinium polyedrum a daily synthesis and destruction of proteins is used to regulate activity. Experiments indicate that the amino acids from the degradation are conserved and incorporated into the resynthesized protein in the subsequent cycle. A different species, Pyrocystis lunula, also exhibits a rhythm of bioluminescence, but the luciferase is not destroyed and resynthesized each cycle. This paper posits that synthesis and destruction constitutes a cellular mechanism to conserve nitrogen in an environment where the resource is limiting. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions
Microorganisms 2013, 1(1), 33-57; doi:10.3390/microorganisms1010033
Received: 2 July 2013 / Revised: 2 September 2013 / Accepted: 8 October 2013 / Published: 21 October 2013
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Abstract
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of [...] Read more.
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhis marina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5′ oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview The Genus Neoceratium (Planktonic Dinoflagellates) as a Potential Indicator of Ocean Warming
Microorganisms 2013, 1(1), 58-70; doi:10.3390/microorganisms1010058
Received: 14 August 2013 / Revised: 25 September 2013 / Accepted: 10 October 2013 / Published: 25 October 2013
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Abstract
Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end [...] Read more.
Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end of the 19th century. It has already been described as a good candidate to monitor water masses and describe ocean circulation. We argue that the sensitivity displayed by Neoceratium to water temperature also makes it relevant as an indicator of ocean warming. The advantages and interests of using Neoceratium species to monitor climate change on a large scale are reassessed in view of recent advances in understanding their biology and ecology. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Transcription and Maturation of mRNA in Dinoflagellates
Microorganisms 2013, 1(1), 71-99; doi:10.3390/microorganisms1010071
Received: 22 July 2013 / Revised: 10 September 2013 / Accepted: 14 October 2013 / Published: 1 November 2013
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Abstract
Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many [...] Read more.
Dinoflagellates are of great importance to the marine ecosystem, yet scant details of how gene expression is regulated at the transcriptional level are available. Transcription is of interest in the context of the chromatin structure in the dinoflagellates as it shows many differences from more typical eukaryotic cells. Here we canvas recent transcriptome profiles to identify the molecular building blocks available for the construction of the transcriptional machinery and contrast these with those used by other systems. Dinoflagellates display a clear paucity of specific transcription factors, although surprisingly, the rest of the basic transcriptional machinery is not markedly different from what is found in the close relatives to the dinoflagellates. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara
Microorganisms 2013, 1(1), 100-121; doi:10.3390/microorganisms1010100
Received: 27 September 2013 / Revised: 18 October 2013 / Accepted: 24 October 2013 / Published: 1 November 2013
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Abstract
The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. [...] Read more.
The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. One of the processes investigated in greater detail was developed for modified vaccinia virus Ankara (MVA). MVA is highly attenuated for human recipients and an efficient vector for reactogenic expression of foreign genes. Because direct cell-to-cell spread is one important mechanism for vaccinia virus replication, cultivation of MVA in bioreactors is facilitated if cell aggregates are induced after infection. This dependency may be the mechanism behind our observation that a novel viral genotype (MVA-CR) accumulates with serial passage in suspension cultures. Sequencing of a major part of the genomic DNA of the new strain revealed point mutations in three genes. We hypothesize that these changes confer an advantage because they may allow a greater fraction of MVA-CR viruses to escape the host cells for infection of distant targets. Production and purification of MVA-based vaccines may be simplified by this combination of designed avian cell line, chemically defined media and the novel virus strain. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
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Open AccessReview An Updated List of Generic Names in the Thoracosphaeraceae
Microorganisms 2013, 1(1), 122-136; doi:10.3390/microorganisms1010122
Received: 28 August 2013 / Revised: 12 September 2013 / Accepted: 23 October 2013 / Published: 1 November 2013
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Abstract
Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first [...] Read more.
Calcareous dinophytes produce exoskeletal calcified structures during their life history (a unique character among the alveolates) and are subsumed under the Thoracosphaeraceae as part of the Peridiniales. We provide a brief synopsis about the taxonomic history of the group, from the first descriptions of fossils in the 19th century through to the results of molecular phylogenetics studies undertaken during the past two decades. Delimitation and circumscription of the Thoracosphaeraceae are challenging, as they comprise both phototrophic (presumably including endosymbiotic) as well as heterotrophic (and even parasitic) dinophytes from marine and freshwater environments, respectively. However, calcareous structures are not known from all members of the Thoracosphaeraceae, and the corresponding species and groups are considered to have lost the capacity to calcify. Five years ago, a taxonomic list of 99 generic names assigned to the Thoracosphaeraceae was published, and we update this compendium with 19 additional names based on recent studies. Full article
(This article belongs to the Special Issue Biology of Dinoflagellates: Advances in the Last 25 Years (1987-2012))
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Open AccessReview A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)
Microorganisms 2013, 1(1), 137-157; doi:10.3390/microorganisms1010137
Received: 26 September 2013 / Revised: 5 November 2013 / Accepted: 8 November 2013 / Published: 20 November 2013
Cited by 2 | PDF Full-text (2506 KB) | HTML Full-text | XML Full-text
Abstract
With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on [...] Read more.
With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
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Open AccessReview Molecular Quantification and Genetic Diversity of Toxigenic Fusarium Species in Northern Europe as Compared to Those in Southern Europe
Microorganisms 2013, 1(1), 162-174; doi:10.3390/microorganisms1010162
Received: 27 September 2013 / Revised: 5 November 2013 / Accepted: 25 November 2013 / Published: 3 December 2013
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Abstract
Fusarium species produce important mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV) and T-2/HT-2-toxins in cereals. The highest DON and T-2/HT-2 toxin levels in northern Europe have been found in oats. About 12%–24% of Finnish oat samples in 2012 contained >1.75 mg·kg−1 [...] Read more.
Fusarium species produce important mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV) and T-2/HT-2-toxins in cereals. The highest DON and T-2/HT-2 toxin levels in northern Europe have been found in oats. About 12%–24% of Finnish oat samples in 2012 contained >1.75 mg·kg−1 of DON, which belongs to type B trichothecenes. Fusarium graminearum is the most important DON producer in northern Europe and Asia and it has been displacing the closely related F. culmorum in northern Europe. The 3ADON chemotype of F. graminearum is dominant in most northern areas, while the 15ADON chemotype of F. graminearum is predominating in Central and southern Europe. We suggest that the northern population of F. graminearum may be more specialized to oats than the southern population. Only low levels of F. culmorum DNA were found in a few oat samples and no correlation was found between F. culmorum DNA and DON levels. DNA levels of F. graminearum were in all cases in agreement with DON levels in 2011 and 2012, when DON was measured by gas chromatography-mass spectrometry (GC-MS). When the RIDA® QUICK SCAN kit results (DON) were compared to DNA levels of F. graminearum, the variation was much higher. The homogenization of the oats flour by grinding oats with 1 mm sieve seems to be connected to this variation. There was a significant correlation between the combined T-2 and HT-2 and the combined DNA levels of F. langsethiae and F. sporotrichioides in Finland in 2010–2012. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
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Open AccessReview Temporal Variation of Mycotoxin Producing Fungi in Norwegian Cereals
Microorganisms 2013, 1(1), 188-198; doi:10.3390/microorganisms1010188
Received: 1 October 2013 / Revised: 19 November 2013 / Accepted: 10 December 2013 / Published: 17 December 2013
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Abstract
Spring barley is grown on about half of the Norwegian cereal area. The rest of the area is equally divided between wheat and oats. Most years the domestic production provides 70%–80% of the domestic market for bread wheat. Barley and oats are [...] Read more.
Spring barley is grown on about half of the Norwegian cereal area. The rest of the area is equally divided between wheat and oats. Most years the domestic production provides 70%–80% of the domestic market for bread wheat. Barley and oats are mainly grown for animal feed. During the years 2008–2012, severe epidemics of Fusarium head blight have led to increased mycotoxin contamination of cereals. During that period, precipitation was above normal during anthesis and grain maturation. The most important mycotoxin producers have been F. avenaceum, F. culmorum, F. graminearum and F. langsethiae. Increased deoxynivalenol contamination of Norwegian cereals during recent years is due to severe F. graminearum epidemics. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)

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