Manuela Filippini

Infection paradox: high abundance but low impact of freshwater benthic viruses.

ABSTRACT The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of ∼15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of ∼5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments.

Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008.

A Gram-staining-negative, pink bacterium, designated strain BUZ 2(T), was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany). Cells were rod-shaped and able to form multicellular filaments. Growth after 7 days was observed at 10-40 °C, at pH 6-8 and with 0-0.5 % NaCl. The phylogenetic tree based on 16S rRNA gene sequences indicated that strain BUZ 2(T) is a member of the family Cytophagaceae, its closest neighbours being Rudanella lutea 5715S-11(T), Spirosoma linguale LMG 10896(T) and Spirosoma panaciterrae Gsoil 1519(T) (87.8, 86.4 and 86.1 % sequence similarity, respectively). The major fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 1)ω5c and iso-C(15 : 0). The predominant respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine and several unidentified aminophospholipids. The DNA G+C content was 56.5 mol%. On the basis of this polyphasic study, we propose that strain BUZ 2(T) represents a novel genus and species, for which the name Fibrella aestuarina gen. nov., sp. nov. is proposed. The type strain of Fibrella aestuarina is BUZ 2(T) (=DSM 22563(T) =CCUG 58136(T)). An emended description of the genus Rudanella is also proposed.

Emergent multicellular life cycles in filamentous bacteria owing to density-dependent population dynamics

Filamentous bacteria are the oldest and simplest known multicellular life forms. By using computer simulations and experiments that address cell division in a filamentous context, we investigate some of the ecological factors that can lead to the emergence of a multicellular life cycle in filamentous life forms. The model predicts that if cell division and death rates are dependent on the density of cells in a population, a predictable cycle between short and long filament lengths is produced. During exponential growth, there will be a predominance of multicellular filaments, while at carrying capacity, the population converges to a predominance of short filaments and single cells. Model predictions are experimentally tested and confirmed in cultures of heterotrophic and phototrophic bacterial species. Furthermore, by developing a formulation of generation time in bacterial populations, it is shown that changes in generation time can alter length distributions. The theory predicts that given the same population growth curve and fitness, species with longer generation times have longer filaments during comparable population growth phases. Characterization of the environmental dependence of morphological properties such as length, and the number of cells per filament, helps in understanding the pre-existing conditions for the evolution of developmental cycles in simple multicellular organisms. Moreover, the theoretical prediction that strains with the same fitness can exhibit different lengths at comparable growth phases has important implications. It demonstrates that differences in fitness attributed to morphology are not the sole explanation for the evolution of life cycles dominated by multicellularity.

Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats.

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3(T)) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 1)ω5c and iso-C(17 : 0) 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3(T) represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3(T) ( = DSM 22564(T)  = CCUG 58137(T)).

Interspecies variation in survival and growth of filamentous heterotrophic bacteria in response to UVC radiation

Ultraviolet radiation is an important environmental constraint on the evolution of life. In addition to its harmful effects, ultraviolet radiation plays an important role in generating genetic polymorphisms and acting as a selective agent. Understanding how prokaryotes cope with high radiation can give insights on the evolution of life on Earth. Four representative filamentous bacteria from the family Cytophagaceae with different pigmentation were selected and exposed to different doses of UVC radiation (15-32,400Jm(-2)). The effect of UVC radiation on bacterial survival, growth and morphology were investigated. Results showed high survival in response to UVC for Rudanella lutea and Fibrisoma limi, whereas low survival was observed for Fibrella aestuarina and Spirosoma linguale. S. linguale showed slow growth recovery after ultraviolet exposure, R. lutea and F. limi showed intermediate growth recovery, while F. aestuarina had the fastest recovery among the four tested bacteria. In terms of survival, S. linguale was the most sensitive bacterium whereas R. lutea and F. limi were better at coping with UVC stress. The latter two resumed growth even after 2h exposure (∼10,800Jm(-2)). Additionally, the ability to form multicellular filaments after exposure was tested using two bacteria: one representative of the high (R. lutea) and one of the low (F. aestuarina) survival rates. The ability to elongate filaments due to cell division was preserved but modified. In R. lutea 10min exposure reduced the average filament length. The opposite was observed in F. aestuarina, where the 5 and 10min exposures increased the average filament length. R. lutea and F. limi are potential candidates for further research into survival and resistance to ultraviolet radiation stress.

Genome Sequence of Fibrella aestuarina BUZ 2T, a Filamentous Marine Bacterium

Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella. Here we report the draft genome sequence of this strain, which consists of a single scaffold representing the chromosome (with 11 gaps) and a 161-kb circular plasmid.

Genome Sequence of the Filamentous Bacterium Fibrisoma limi BUZ 3T

Fibrisoma limi strain BUZ 3(T), a Gram-negative bacterium, was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany) and characterized using a polyphasic approach in 2011. The genome consists of a chromosome of about 7.5 Mb and three plasmids.

Low virus to prokaryote ratios in the cold: benthic viruses and prokaryotes in a subpolar marine ecosystem (Hornsund, Svalbard).

The density and spatial distribution of benthic viruses and prokaryotes in relation to biotic and abiotic factors were investigated in sediment cores collected in Hornsund, a permanently cold fjord on the West coast of Svalbard, Norway. The cores were obtained from the mouth of the fjord to the central basin, along a longitudinal transect. The results of our analyses showed lower densities of viruses (0.2 x 10(8) to 5.4 x 10(8) virus-like particles/g) and lower virus-to-prokaryote ratios (0.2-0.6, with the exception of the uppermost layer in the central basin, where the ratio was about 1.2) at the study site than generally found in the temperate areas, despite the relatively high organic matter content in subpolar sediments. Variations in benthic viral and prokaryote abundances along gradients of particle sedimentation rates, phytopigment concentrations, and macrobenthic species composition together suggested the influence of particle sedimentation and macrobenthic bioturbation on the abundance and spatial distribution ofprokaryotes and viruses in cold habitats.

Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier

An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera Pseudomonas and Serratia, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone.