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What we know about Tubulavirales, i.e. filamentous phages, essentially comes from Gram-negative-infecting Inoviridae. However, metagenomics recently suggests filamentous phages are much more widespread and diverse. Here, we report the complete sequence and functional annotation of CAK1, a 6.6 kb filamentous phage that was shown to chronically infect Clostridium beijerinckii 30 years ago and only represents the second filamentous phage cultivated on a Gram-positive bacterium. CAK1 has a typical filamentous phage modular genome with no homologs in databases and we were interested to compare it with a pig gut filamentous phage metagenomics dataset that we previously assembled and for which many filamentous phages were predicted to infect Clostridium species by bioinformatics means. CAK1 is distantly related to nine of these sequences, two of which have been predicted as Clostridium -associated. In itself, this small cluster of CAK1-connected sequences sheds light on the diversity of filamentous phages that putatively infect Clostridium species, and probably many other Gram-positive genera. [ABSTRACT FROM AUTHOR]

Acid stress is an environmental problem for plants and fresh water cyanobacteria like the filamentous, heterocyst forming species Anabaena sp. PCC 7120 (hereafter Anabaena sp.). Heterocyst differentiation, cell–cell communication and nitrogen fixation has been deeply studied in this model organism, but little is known about the cellular response of Anabaena sp. to decreased pH values, causing acid stress. ATP-binding cassette (ABC) transporters are involved in acid stress response in other bacteria, by exporting proteins responsible for survival under acidification. The genome of Anabaena sp. encodes numerous ABC transporter components, whose function is not known yet. Here, we describe the function of the gene all5304 encoding a protein with homology to membrane fusion proteins of tripartite efflux pumps driven by ABC transporters like HlyBD-TolC of Escherichia coli. The all5304 mutant shows less resistance against low pH, even though the expression of the gene is independent from the pH of the medium. We compared the exoproteome of the wild type and mutant cultures and identified three proteins-candidate substrates of the putative transporter. Including the in silico analysis of All5304, our results suggest that All5304 functions as part of an efflux pump, secreting of a protein necessary for acid tolerance in Anabaena sp. [ABSTRACT FROM AUTHOR]

Viruses, especially bacteriophages, are thought to have important functions in the deep-sea ecosystem, but little is known about the induction mechanism of benthic phages in response to environmental change. Our prior work characterized a cold-active filamentous phage SW1 that infects the deep-sea bacterium Shewanella piezotolerans WP3; however, the underlying mechanism of the putative thermo-regulated genetic switch of SW1 is still unclear. In this study, the DNA copy number and mRNA abundance of the deep-sea phage SW1 were quantified in the whole life cycle of its host S. piezotolerans WP3 at different temperatures. Our results demonstrated that the induction of SW1 is dependent on a threshold temperature (4°C), but this dependency is not proportional to temperature gradient. RNA-Seq analyses revealed two highly transcribed regions at 4°C and verified the presence of a long 3′ untranslated region (UTR) in the SW1 genome. Interestingly, recruitment analysis showed that SW1-like inoviruses prevail in deep sea (depth >1000 m) and photic epipelagic and mesopelagic zones (depth <1000 m), which suggested that the thermo-regulated genetic switch revealed in SW1 may be widely distributed in the ocean. [ABSTRACT FROM AUTHOR]

Cell differentiation is one of the marks of multicellular organisms. Terminally specialised nitrogen-fixing cells, termed heterocysts, evolved in filamentous cyanobacteria more than 2 Gya. The development of their spacing pattern has been thoroughly investigated in model organisms such as Anabaena sp. PCC 7120. This paper focuses on the more complex, branching cyanobacterium Mastigocladus laminosus (Stigonematales). Contrary to what has been previously published, a heterocyst spacing pattern is present in M. laminosus but it varies with the age of the culture and the morphology of the cells. Heterocysts in young, narrow trichomes were more widely spaced (~14.8 cells) than those in old, wide trichomes (~9.4 cells). Biochemical and transgenic experiments reveal that the heterocyst spacing pattern is affected by the heterocyst inhibitor PatS. Addition of the pentapeptide RGSGR (PatS-5) to the growth medium and overexpression of patS from Anabaena sp. PCC 7120 in M. laminosus resulted in the loss of heterocyst differentiation under nitrogen deprivation. Bioinformatics investigations indicated that putative PatS sequences within cyanobacteria are highly diverse, and fall into two main clades. Both are present in most branching cyanobacteria. Despite its more complex, branching phenotype, M. laminosus appears to use a PatS-based pathway for heterocyst differentiation, a property shared by Anabaena/Nostoc. [ABSTRACT FROM AUTHOR]

If the in situ growth rate of filamentous bacteria in activated sludge can be quantified, researchers can more accurately assess the effect of operating conditions on the growth of filaments and improve the mathematical modeling of filamentous bulking. We developed a method to quantify the in situ specific growth rate of Sphaerotilus natans (a model filament) in activated sludge using the species-specific 16S rRNA:rDNA ratio. Primers targeting the 16S rRNA of S. natans were designed, and real-time PCR and RT-PCR were used to quantify DNA and RNA levels of S. natans, respectively. A positive linear relationship was found between the rRNA:rDNA ratio (from 440 to 4500) and the specific growth rate of S. natans (from 0.036 to 0.172 h-1) using chemostat experiments. The in situ growth rates of S. natans in activated sludge samples from three water reclamation facilities were quantified, illustrating how the approach can be applied in a complex environment such as activated sludge. [ABSTRACT FROM AUTHOR]

Filamentous sulfur bacteria of the genus Thiothrix are able to respire nitrate (NO3 -> NO2 ) under anaerobic growth. Here, Thiothrix caldifontis (G1T, G3), Thiothrix unzii (A1T, TN) and Thiothrix lacustris AS were shown to be capable of further reduction of nitrite and/or nitrous oxides (denitrification). In particular, in the genomes of these strains, excluding T. unzii TN, the nirS gene encoding periplasmic respiratory nitrite reductase was detected, and for T. lacustris AS the nirS expression was confirmed during anaerobic growth. The nirK gene, coding for an alternative nitrite reductase, and the nrfA gene, encoding nitrite reduction to ammonia, were not found in any investigated strains. All Thiothrix species capable of denitrification possess the cnorB gene encoding cytochrome c-dependent NO reductase but not the qnorB gene coding for quinol-dependent NO reductase. Denitrifying capacity (‘full’ or ‘truncated’) can vary between strains belonging to the same species and correlates with physical-chemical parameters of the environment such as nitrate, hydrogen sulfide and oxygen concentrations. Phylogenetic analysis revealed the absence of recent horizontal transfer events for narG and nirS; however, cnorB was subjected to gene transfer before the separation of modern species from a last common ancestor of the Thiothrix species. [ABSTRACT FROM AUTHOR]

Segmented filamentous bacteria (SFB) are inhabitants of the small intestine of various animals, where they can be detected microscopically due to their specific morphology and intimate association with the intestinal epithelium. SFB colonize the distal part of the small intestine in a host-specific manner and affects important functions of the immune system, such as the induction of secretory IgA production and regulation of T-cell maturation. Considering the influences SFB have on immune functions, they could be regarded as a key species in host-microbial interactions of the gastrointestinal tract. Although these influences might be executed by other microorganisms, a human-adapted variant of SFB is not unlikely. In this study, ileostomy samples from 10 human subjects were screened with PCR, using primers derived from sequences of SFB from rat and mouse. PCR products were obtained from samples taken from one individual at two time points. Sequencing revealed the presence of a 16S r RNA gene with high similarity (98%) to the corresponding genes from SFB of mouse and rat origin, thus indicating the presence of a human variant of SFB. The findings presented in this study will hopefully encourage research to elucidate whether this intriguing organism is a persistent member of the normal human microbiota. [ABSTRACT FROM AUTHOR]

The complete genome sequence of Lysinibacillus varians GY32 was determined to be 4 662 822 base pairs in a single circular chromosome. Genes in cell division, cell cycle, surface layer and cell wall synthesis are foundation of its unique cell morphology. The genome contains multiple clusters of transcriptional regulator, two-component system and sigma factors, providing the organism with the ability to regulate a filament-to-rod cell cycle progression. L. varians GY32 was, to our knowledge, the first bacterium with a filament-to-rod cell cycle to be sequenced and its annotated genome might provide new insights into our understanding of bacterial cell cycle regulation. [ABSTRACT FROM AUTHOR]

All well-established cell size homeostasis paradigms are based on the researches of rod bacteria like B. subtilis and E. coli , suggesting a constant division time (timer model), division size (sizer model) or added size (adder model) before division. However, Lysinibacillus varians , a new species with regular filament-to-rod cell cycle, is inconsistent with existing models. In this study, the cell size parameters of the type strain GY32, were investigated by combing multiple microscopy techniques and single-cell approach. Our results showed that the filaments of strain GY32 were unicellular cells with multiple nucleoids. The division time of GY32 cells was variable and their daughter cells produced by asymmetric binary fission had different birth sizes, which were proportional to their elongation rates, resulting in high heterogeneity among the sister cells. Furthermore, the added size from birth to division was significantly shorter than birth size (p  < 0.01) and decreased along generations. The results above revealed that the asymmetric division site and varied cell size parameters resulted in filament-to-rod cell cycle of L. varians and cell size homeostasis could be a more complex and dynamic process than previously assumed. These findings would be helpful in elucidating the open questions in cell division and cell size heterogeneity. [ABSTRACT FROM AUTHOR]

The filamentous cyanobacterium Nostoc punctiforme has several oxidative stress-managing systems, including Dps proteins. Dps proteins belong to the ferritin superfamily and are involved in abiotic stress management in prokaryotes. Previously, we found that one of the five Dps proteins in N. punctiforme, NpDps2, was critical for H2O2 tolerance. Stress induced by high light intensities is aggravated in N. punctiforme strains deficient of either NpDps2, or the bacterioferritin-like NpDps5. Here, we have investigated the capacity of NpDps2 and NpDps5 to enhance stress tolerance by homologous overexpression of these two proteins in N. punctiforme. Both overexpression strains were found to tolerate twice as high concentrations of added H2O2 as the control strain, indicating that overexpression of either NpDps2 or NpDps5 will enhance the capacity for H2O2 tolerance. Under high light intensities, the overexpression of the two NpDps did not enhance the tolerance against general light-induced stress. However, overexpression of the heterocyst-specific NpDps5 in all cells of the filament led to a higher amount of chlorophyll-binding proteins per cell during diazotrophic growth. The OENpDps5 strain also showed an increased tolerance to ammonium-induced oxidative stress. Our results provide information of how Dps proteins may be utilised for engineering of cyanobacteria with enhanced stress tolerance. [ABSTRACT FROM AUTHOR]

The complete genome sequence of Lysinibacillus varians GY32 was determined to be 4,662,822 base pairs in a single circular chromosome. Genes in cell division, cell cycle, surface layer and cell wall synthesis are foundation of its unique cell morphology. The genome contains multiple clusters of transcriptional regulator, two-component system and sigma factors, providing the organism with the ability to regulate a filament-to-rod cell cycle progression. L. varians GY32 was, to our knowledge, the first bacterium with a filament-to-rod cell cycle to be sequenced and its annotated genome might provide new insights into our understanding of bacterial cell cycle regulation., (© FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)