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)

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Antibacterial activity of zinc oxide nanoparticles (ZnO-NPs) has received significant interest worldwide particularly by the implementation of nanotechnology to synthesize particles in the nanometer region. Many microorganisms exist in the range from hundreds of nanometers to tens of micrometers. ZnO-NPs exhibit attractive antibacterial properties due to increased specific surface area as the reduced particle size leading to enhanced particle surface reactivity. ZnO is a bio-safe material that possesses photo-oxidizing and photocatalysis impacts on chemical and biological species. This review covered ZnO-NPs antibacterial activity including testing methods, impact of UV illumination, ZnO particle properties (size, concentration, morphology, and defects), particle surface modification, and minimum inhibitory concentration. Particular emphasize was given to bactericidal and bacteriostatic mechanisms with focus on generation of reactive oxygen species (ROS) including hydrogen peroxide (H2O2), OH− (hydroxyl radicals), and O2 −2 (peroxide). ROS has been a major factor for several mechanisms including cell wall damage due to ZnO-localized interaction, enhanced membrane permeability, internalization of NPs due to loss of proton motive force and uptake of toxic dissolved zinc ions. These have led to mitochondria weakness, intracellular outflow, and release in gene expression of oxidative stress which caused eventual cell growth inhibition and cell death. In some cases, enhanced antibacterial activity can be attributed to surface defects on ZnO abrasive surface texture. One functional application of the ZnO antibacterial bioactivity was discussed in food packaging industry where ZnO-NPs are used as an antibacterial agent toward foodborne diseases. Proper incorporation of ZnO-NPs into packaging materials can cause interaction with foodborne pathogens, thereby releasing NPs onto food surface where they come in contact with bad bacteria and cause the bacterial death and/or inhibition.

/pdf/review-on-zinc-oxide-nanoparticles-antibacterial-activity-2smaigi8sc.pdf

Review on Zinc Oxide Nanoparticles: Antibacterial Activity and Toxicity Mechanism.

The recent advances in nanotechnology and the corresponding increase in the use of nanomaterials in products in every sector of society have resulted in uncertainties regarding environmental impacts. The objectives of this review are to introduce the key aspects pertaining to nanomaterials in the environment and to discuss what is known concerning their fate, behavior, disposition, and toxicity, with a particular focus on those that make up manufactured nanomaterials. This review critiques existing nanomaterial research in freshwater, marine, and soil environments. It illustrates the paucity of existing research and demonstrates the need for additional research. Environmental scientists are encouraged to base this research on existing studies on colloidal behavior and toxicology. The need for standard reference and testing materials as well as methodology for suspension preparation and testing is also discussed.

Nanomaterials in the environment: Behavior, fate, bioavailability, and effects

The search for understanding the interactions of nanosized materials with living organisms is leading to the rapid development of key applications, including improved drug delivery by targeting nanoparticles, and resolution of the potential threat of nanotechnological devices to organisms and the environment. Unless they are specifically designed to avoid it, nanoparticles in contact with biological fluids are rapidly covered by a selected group of biomolecules to form a corona that interacts with biological systems. Here we review the basic concept of the nanoparticle corona and its structure and composition, and highlight how the properties of the corona may be linked to its biological impacts. We conclude with a critical assessment of the key problems that need to be resolved in the near future.

/pdf/biomolecular-coronas-provide-the-biological-identity-of-3m15njjzti.pdf

Biomolecular coronas provide the biological identity of nanosized materials

The β-D-galactosidase activity of viable but non-culturable (vnc) Escherichia coli cells in seawater was investigated using a rapid fluorimetric enzyme assay. Results from microcosm studies showed that loss of culturability did not necessarily result in loss of the ability to produce the galactosidase enzyme. Even when no culturable cells were detected, a positive enzyme assay response was observed and the activity of the inducible enzyme over time more closely reflected the number of vnc cells present.

β-D-galactosidase activity of viable, non-culturable coliform bacteria in marine waters

Examination of the range of copper complexing ligands in natural waters using a combination of cathodic stripping voltammetry and computer simulation

Environmental Context. The pathways by which arsenic is accumulated, biotransformed and transferred in aquatic ecosystems are relatively unknown. Examination of whole marine ecosystems rather than individual organisms provides greater insights into the biogeochemical cycling of arsenic. Rocky intertidal zones, which have a high abundance of organisms but low ecological diversity, are an important marine habitat. This study examines the cycling of arsenic within intertidal ecosystems to further understand its distribution and transfer. Abstract. The present study reports total arsenic and arsenic species in a short rocky intertidal marine food chain in NSW, Australia. Total mean arsenic concentrations increased up the food chain in the following order: 4 ± 2 µg g–1 in attached rock microalgae, 31 ± 14 µg g–1 in Bembicium nanum Lamarck, 45 ± 14 µg g–1 in Cellana tramoserica Sowerby, 58 ± 14 µg g–1 in Nerita atramentosa Reeve, 75 ± 15 µg g–1 in Austrocochlea constrica Lamarck (a herbivore) and 476 ± 285 µg g–1 in the carnivore Morula marginalba Blainville. Significant differences in arsenic concentrations of B. nanum, N. atramentosa and M. marginalba were found among locations and may be related to food availability, spawning or differences in age and/or size classes of individuals. Significant differences in arsenic concentrations were also found within locations among species, and increased in the order: rock microalgae < B. nanum < C. tramoserica < N. atramentosa < A. constricta < M. marginalba. Although small differences in total arsenic concentrations were found among locations for some gastropod species, arsenic species proportions were very consistent within gastropod species across locations. The majority of arsenic in Homosira banksii (macroalgae) was oxo-arsenoribosides, with thio-arsenoribosides making up ~10% of the total methanol–water extractable arsenic. The rock microalgae contained arsenobetaine (AB) (59 ± 5%) and arsenoribosides (36 ± 15%). The AB content of the herbivores B. nanum, N. atramentosa and A. constricta ranged from 71 to 95%, and that of the carnivore M. marginalba was 98%. Most gastropods contained thio-arsenosugars (up to 13 ± 3% of total extractable arsenic), with C. tramoserica containing higher proportions of thio-phosphate arsenoriboside (7 ± 2%) and lower proportions of AB (69 ± 4%). Glycerol trimethylarsonioribosides (1.4 ± 0.1%) were also found in most of the herbivorous gastropods. Oxo-dimethylarsinoylethanol (oxo-DMAE) was found in N. atramentosa (<1%).

Arsenic Species in a Rocky Intertidal Marine Food Chain in NSW, Australia, revisited

Environmental context Aluminium may be released into coastal waters in dissolved and particulate forms from urban runoff, industrial discharges and acid sulfate soils. Aquatic organisms may experience toxic effects from exposure to dissolved and particulate aluminium. Therefore, the current study reports the geochemical controls such as speciation, precipitation and adsorption that influence the exposure to these aluminium forms in the field and the laboratory. Abstract A combination of field and laboratory investigations was conducted in order to gain an understanding of aluminium dynamics in coastal seawater environments. Filterable ( 0.025 to <0.45µm) aluminium species were generally minimal, apart from one field sample collected close to a river mouth where aluminium was associated with iron-containing colloids. In seawater (pH 8.15, 22°C) spiked with small increments of aluminium so as not to attain supersaturation, the solubility limit was ~500µgL–1. However, at higher total aluminium concentrations the solution chemistry became highly dynamic. In the presence of aluminium precipitate it was not possible to measure a solubility limit over the 28-day duration of the experiment because the dissolved aluminium concentration varied with both reaction time and precipitate concentration. For instance, when seawater solutions were spiked with 10000µgL–1 of total aluminium, a pulse of dissolved aluminium up to 1250µgL–1 was sustained for several days before decreasing to below 100µgL–1 after 28 days. The initial precipitate appeared to be solely aluminium hydroxide and transformed over time to contain increasing magnesium, consistent with the formation of hydrotalcite (Mg6Al2CO3(OH)16·4H2O), reaching 21% of the precipitate mass after 28 days. Adsorption studies showed that at anticipated suspended particulate concentrations for coastal waters, natural particulate material has a fairly low affinity for dissolved aluminium. The results of the current study highlight the complex chemistry of aluminium in marine waters and the role of precipitation reactions.

Geochemical controls on aluminium concentrations in coastal waters

About the Cover: Nanomaterials are highly reactive and dynamic in the environment and can undergo a range of physical, chemical, and biological transformations. Some examples of transformations include heteroaggregation, adsorption of biomacromolecules, biodegradation, and sulfidation. These transformations will affect the nanomaterial properties and environmental behaviors and impacts. Professor David Hannah, University of Birmingham, UK, is acknowledged for providing the original photograph from which the background cover art is taken. See Lowry and co‐workers, p 6893. View the article. Table of

https://pubs.acs.org/doi/pdf/10.1021/es3022039

Simon C. Apte

Papers

β-D-galactosidase activity of viable, non-culturable coliform bacteria in marine waters

Examination of the range of copper complexing ligands in natural waters using a combination of cathodic stripping voltammetry and computer simulation

Arsenic Species in a Rocky Intertidal Marine Food Chain in NSW, Australia, revisited

Geochemical controls on aluminium concentrations in coastal waters

Guest Comment: Transformations of Nanomaterials in the Environment Focus Issue