No abstract

One of the fundamental methods for cultivating bacterial strains is conventional plating on solid media, but this method does not reveal the true diversity of the bacterial community. In this study, we develop a new technique and introduce a new device we term, I-tip. The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment. The new method was used to cultivate microorganisms from Baikalian sponges, and the results were compared with conventional plating as well as a pyrosequencing-based molecular survey. The I-tip method produced cultures of 34 species from five major phyla, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, and Gammaproteobacteria, 'missing' only two major phyla detected by pyrosequencing. Meanwhile, standard cultivation produced a smaller collection of 16 species from three major phyla, Betaproteobacteria, Firmicutes, and Gammaproteobacteria, failing to detect over half of the major phyla registered by pyrosequencing. We conclude that the I-tip method can narrow the gap between cultivated and uncultivated species, at least for some of the more challenging microbial communities such as those associated with animal hosts.

Background Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. Results Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. Conclusions The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.

N eurosurgical vascular cases often require complex microvascular bypass techniques, such as those used in operative corrections for moyamoya disease, 7,26,32 cerebral aneurysms, 9,13,14,19 and intracranial tumors. 30,31 Therefore, simple and accessible models for microvascular anastomosis training are increasingly essential for providing a means for refining and preserving skills. Several models, including chicken wings, 12,17 turkey wings, 1 rats, 15 human cadavers, 24,29 and plastic tubing, 22 have been proposed. However, these models are still less than ideal for various reasons, such as vessel diameter diversity, cost-effectiveness, artifacts due to storage (e.g., Low-flow and high-flow neurosurgical bypass and anastomosis training models using human and bovine placental vessels: a histological analysis and validation study obJective Microvascular anastomosis is a basic neurosurgical technique that should be mastered in the laboratory. Human and bovine placentas have been proposed as convenient surgical practice models; however, the histologic characteristics of these tissues have not been compared with human cerebral vessels, and the models have not been validated as simulation training models. In this study, the authors assessed the construct, face, and content validities of microvascular bypass simulation models that used human and bovine placental vessels. methods The characteristics of vessel segments from 30 human and 10 bovine placentas were assessed anatomically and histologically. Microvascular bypasses were performed on the placenta models according to a delineated training module by "trained" participants (10 practicing neurosurgeons and 7 residents with microsurgical experience) and "untrained" participants (10 medical students and 3 residents without experience). Anastomosis performance and impressions of the model were assessed using the Northwestern Objective Microanastomosis Assessment Tool (NOMAT) scale and a posttraining survey. results Human placental arteries were found to approximate the M 2 -M 4 cerebral and superficial temporal arteries, and bovine placental veins were found to approximate the internal carotid and radial arteries. The mean NOMAT performance score was 37.2 ± 7.0 in the untrained group versus 62.7 ± 6.1 in the trained group (p < 0.01; construct validity). A 50% probability of allocation to either group corresponded to 50 NOMAT points. In the posttraining survey, 16 of 17 of the trained participants (94%) scored the model's replication of real bypass surgery as high, and 16 of 17 (94%) scored the difficulty as "the same" (face validity). All participants, 30 of 30 (100%), answered positively to questions regarding the ability of the model to improve microsurgical technique (content validity). coNclusioNs Human placental arteries and bovine placental veins are convenient, anatomically relevant, and beneficial models for microneurosurgical training. Microanastomosis simulation using these models has high face, content, and construct validities. A NOMAT score of more than 5...

RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet’s carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.

No abstract

The autotrophic picoplankton of Lake Baikal was discovered more than 30 years ago; the productivity of the endemic member of the group, Synechocystis limnetica, is of particular interest. In the course of long-term investigations, the abundance of this species was established using the sedimentation technique. Maximum abundance was reached at 104 cells per ml in summer. In addition to estimating the distribution of this species throughout a defined lake area during the spring-summer period, the character of interrelations with large phytoplankton was revealed. Baikalian autotrophic picoplankton was studied from 1997 to 2000 using epifluorecsence and scanning electron microscopy. The study of seasonal and annual dynamics of picoplankton abundance was conducted monthly at the monitoring station in southern Baikal. The spatial distribution of autotrophic picoplankton was observed in the period when Lake Baikal was free of ice; the lake area was defined by 50 stations. Microscopic examination of planktonic samples revealed that the phycoerythrin-rich cyanobacteria of genus Synechococcus generated the largest biomass of autotrophic picoplankton in Lake Baikal. Morphotype diversity of the representatives of genus Synechecoccus was revealed in the study: Synechococcus spp. of coccoid and ellipsoid forms were dominant by abundance. The coccoid and ellipsoid forms had diameters of 0.9 and 0.7 to 1.3 μm, respectively. The portion of picoplanktonic algae in the Baikalian picoplankton community is not high and does not exceed 10% in the summer time when growth is highest. The autotrophic picoplankton abundance throughout the year in the 0–50 m layer varies by more than one hundred times. Maximal concentration of picocyanobacteria occurs in late July–August at 10 to 25 m depths where it reached 106 cells ml−1. The minimal concentration (103 cells ml−1) was observed in December at the same depths. A small peak of the picoplankton growth occurred in April of each year when the total numbers of picocyanobacteria increased 2 to 4 times after winter. In 1999 the peak rose to 105 cells ml−1 . During the investigation period the highest indices of autotrophic picoplankton numbers were observed in 1999 and the lowest in 1997. The spatial distribution of this group in the whole Baikal aquatorium was characteristically heterogeneous; its abundance varied by 2 to 10 times in different parts of the lake. The largest fluctuation occurred in August and the least in September. The maximum picoplankton abundance was observed in the epilimnion during the periods of thermal stratification. In the course of homothermy a comparably homogeneous distribution of picocyanobacteria was revealed up to 300 m depth, but the highest numbers were found in the upper 30 m layer.

This study describes two viral communities from the world’s oldest lake, Lake Baikal. For the analysis, we chose under-ice and late spring periods of the year as the most productive for Lake Baikal. These periods show the maximum seasonal biomass of phytoplankton and bacterioplankton, which are targets for viruses, including bacteriophages. At that time, the main group of viruses were tailed bacteriophages of the order Caudovirales that belong to the families Myoviridae, Siphoviridae and Podoviridae. Annotation of functional genes revealed that during the under-ice period, the “Phages, Prophages, Transposable Elements and Plasmids” (27.4%) category represented the bulk of the virome. In the late spring period, it comprised 9.6% of the virome. We assembled contigs by two methods: Separately assembled in each virome or cross-assembled. A comparative analysis of the Baikal viromes with other aquatic environments indicated a distribution pattern by soil, marine and freshwater groups. Viromes of lakes Baikal, Michigan, Erie and Ontario form the joint World’s Largest Lakes clade.