The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

I. the origin of species by means of natural selection

The Aquatic Species Program was a relatively small research effort intended to look at the use of aquatic plants as sources of energy. Its history dates back to 1978, but much of the research from 1978 to 1982 focused on using algae to produce hydrogen. The program switched emphasis to other transportation fuels, particularly biodiesel, beginning in the early 1980's. This report summarizes the research activities carried out from 1980 to 1996, with an emphasis on algae for biodiesel production.

/pdf/look-back-at-the-u-s-department-of-energy-s-aquatic-species-3j2xsi0wk0.pdf

Look Back at the U.S. Department of Energy's Aquatic Species Program: Biodiesel from Algae; Close-Out Report

Multiple regression analyses were performed on a worldwide 236—site data set compiled from studies that compared species composition, aboveground net primary production (ANPP), root biomass, and soil nutrients of grazed vs. protected, ungrazed sites. The objective was to quantitatively assess factors relating to differential sensitivities of ecosystems to grazing by large herbivores. A key question in this assessment was: Do empirically based, broad—scale relationships correspond to ecological theories of plant—animal interactions and conceptual frameworks for management of the world's grazing lands? Changes in species composition with grazing were primarily a function of ANPP and the evolutionary history of grazing of the site, with level of consumption third in importance. Changes in species composition increased with increasing productivity and with longer, more intense evolutionary histories of grazing. These three variables explained >50% of the variance in the species response of grasslands or grasslands—plus—shrublands to grazing, even though methods of measurement and grazing systems varied among studies. Years of protection from grazing was a significant variable only in the model for shrublands. Similar variables entered models of change in the dominant species with grazing. As with species composition, sensitivities of change in dominant species were greater to varying ecosystem—environmental variables than to varying grazing variables, from low to high values. Increase of the dominant species under grazing were predicted under some conditions, and decreases were more likely among bunch grasses than other life—forms and more likely among perennials than annuals. The response of shrublands was different from that of grasslands, both in terms of species composition and the dominant species. Our analyses support the perception of grazing as a factor in the conversion of grasslands to less desirable shrublands, but also suggest that we may be inadvertently grazing shrublands more intensively than grasslands. Percentage differences in ANPP between grazed and ungrazed sites decreased with increasingly long evolutionary histories of grazing and increased with increasing ANPP, levels of consumption, or years of treatment. Although most effects of grazing on ANPP were negative, some were not, and the statistical models predicted increases in ANPP with grazing under conditions of long evolutionary history, low consumption, few years of treatment, and low ANPP for grasslands—plus—shrublands. The data and the models support the controversial hypothesis that grazing can increase ANPP in some situations. Similar to species variables, percentage differences in ANPP between grazed and ungrazed treatments were more sensitive to varying ecosystem—environmental variables than to varying grazing variables. Within levels not considered to be abusive "overgrazing," the geographical location where grazing occurs may be more important than how many animals are grazed or how intensively an area is grazed. Counter to the commonly held view that grazing negatively impacts root systems, there was no relationship between difference in ANPP with grazing and difference in root mass; as many positive as negative differences occurred, even though most ANPP differences were negative. Further, there was a weak relationship between change in species composition and change in ANPP, and no relationship with root mass, soil organic matter, or soil nitrogen. All three belowground variables displayed both positive and negative values in response to grazing. Current management of much of the world's grazing lands based on species composition criteria may lead to erroneous conclusions concerning the long—term ability of a system to sustain productivity.

Quantitative effects of grazing on vegetation and soils over a global range of environments

Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring 'extremophiles'. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe.

/pdf/life-in-extreme-environments-qdlikt0yc0.pdf

Life in Extreme Environments

The whole classification of cyanobacteria (species, genera, families, orders) has undergone extensive restructuring and revision in recent years with the advent of phylogenetic analyses based on molecular sequence data. Several recent revisionary and monographic works initiated a revision and it is anticipated there will be further changes in the future. However, with the completion of the monographic series on the Cyanobacteria in Süsswasserflora von Mitteleuropa, and the recent flurry of taxonomic papers describing new genera, it seems expedient that a summary of the modern taxonomic system for cyanobacteria should be published. In this review, we present the status of all currently used families of cyanobacteria, review the results of molecular taxonomic studies, descriptions and characteristics of new orders and new families and the elevation of a few subfamilies to family level. All recently defined cyanobacterial genera (some still invalid) are listed in the family to which they are likely to belong and an indication is given of their taxonomic validity and level of polyphasic characterization of each genus.

Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) 2014, using a polyphasic approach

Microbiotic crusts are biological soil crusts composed of lichens, cyanobacteria, algae, mosses, and fungi. The biodiversity of these crusts is poorly understood; several cosmopolitan species dominate in most areas, but many species are confined to one or a few sites. Nitrogen fixation by organisms within the crust can be the dominant source of nitrogen input into many ecosystems, although rates of nitrogen input are limited by water availability, temperature, and nitrogen loss from the crust. Photosynthetic rates of the microbiotic crust can be 50% of those observed for higher plants, but the contribution of crusts to carbon cycling is not known. The microbiotic crust binds soil particles together, and this significantly increases soil surface stability and resistance to erosion. Greenhouse studies have found that crusts can enhance seed germination, seedling survivorship, and plant nutrient status, but further experiments are needed under field conditions. Crusts are extremely susceptible to surface dis...

Microbiotic Crusts and Ecosystem Processes

We amplified, TA-cloned, and sequenced the 16S-23S internal transcribed spacer (ITS) regions from single isolates of several cyanobacterial species, Calothrix parietina, Scytonema hyalinum, Coelodesmium wrangelii, Tolypothrix distorta, and a putative new genus (isolates SRS6 and SRS70), to investigate the potential of this DNA sequence for phylogenetic and population genetic studies. All isolates carried ITS regions containing the sequences coding for two tRNA molecules (tRNA and tRNA). We retrieved additional sequences without tRNA features from both C. parietina and S. hyalinum. Furthermore, in S. hyalinum, we found two of these non-tRNA-encoding regions to be identical in length but different in sequence. This is the first report of ITS regions from a single cyanobacterial isolate not only different in configuration, but also, within one configuration, different in sequence. The potential of the ITS region as a tool for studying molecular systematics and population genetics is significant, but the presence of multiple nonidentical rRNA operons poses problems. Multiple nonidentical rRNA operons may impact both studies that depend on comparisons of phylogenetically homologous sequences and those that employ restriction enzyme digests of PCR products. We review current knowledge of the numbers and kinds of 16S-23S ITS regions present across bacterial groups and plastids, and we discuss broad patterns congruent with higher-level systematics of prokaryotes.

/pdf/is-the-16s-23s-rrna-internal-transcribed-spacer-region-a-5dk3jqi10y.pdf

Is the 16S–23S rRNA Internal Transcribed Spacer Region a Good Tool for Use in Molecular Systematics and Population Genetics? A Case Study in Cyanobacteria

Cryptogamic crusts of semiarid and arid lands of north america

An approximately 1400-bp region of the 16S rRNA gene was sequenced for 10 polar or near-polar strains putatively placed in the Oscillatorialean genera Oscillatoria, Phormidium, and Lyngbya obtained from the University of Toronto Culture Collection to assess phylogenetic relationships The strains were also examined for thylakoid structure and cell division type with TEM as well as traditional morphology with LM Phylogenetic trees constructed using parsimony, distance, and maximum likelihood methods were similar in topology If the original epithets applied to the sequenced strains (both polar and those from GenBank) were used, it was clear that taxa were not monophyletic However, using the revised taxonomic system of Anagnostidis and Komarek, we were able to reassign these strains to their current correct taxa (species, genus, and family) When these assignments were made, it was determined that the molecular sequence data analyses were congruent with morphology and ultrastructure Nine of the polar strains were found to be new species, and eight were described as such: Arthronema gygaxiana Casamatta et Johansen sp nov, Pseudanabaena tremula Johansen et Casamatta sp nov, Leptolyngbya angustata Casamatta et Johansen sp nov, Phormidium lumbricale Johansen et Casamatta sp nov, Microcoleus glaciei Johansen et Casamatta sp nov, Microcoleus rushforthii Johansen et Casamatta sp nov, Microcoleus antarcticus Casamatta et Johansen sp nov, Microcoleus acremannii Casamatta et Johansen sp nov Some genera (Leptolyngbya and Microcoleus) were clearly not monophyletic and require future revision

Jeffrey R. Johansen

Papers

Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) 2014, using a polyphasic approach

Microbiotic Crusts and Ecosystem Processes

Is the 16S–23S rRNA Internal Transcribed Spacer Region a Good Tool for Use in Molecular Systematics and Population Genetics? A Case Study in Cyanobacteria

Cryptogamic crusts of semiarid and arid lands of north america

Molecular and morphological characterization of ten polar and near‐polar strains within the oscillatoriales (cyanobacteria)