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)

Low cost adsorbents for the removal of organic pollutants from wastewater.

Wastewater treatment high rate algal ponds for biofuel production.

Campylobacter jejuni infection is one of the most widespread infectious diseases of the last century. The incidence and prevalence of campylobacteriosis have increased in both developed and developing countries over the last 10 years. The dramatic increase in North America, Europe, and Australia is alarming, and data from parts of Africa, Asia, and the Middle East indicate that campylobacteriosis is endemic in these areas, especially in children. In addition to C. jejuni, there is increasing recognition of the clinical importance of emerging Campylobacter species, including Campylobacter concisus and Campylobacter ureolyticus. Poultry is a major reservoir and source of transmission of campylobacteriosis to humans. Other risk factors include consumption of animal products and water, contact with animals, and international travel. Strategic implementation of multifaceted biocontrol measures to reduce the transmission of this group of pathogens is paramount for public health. Overall, campylobacteriosis is still one of the most important infectious diseases that is likely to challenge global health in the years to come. This review provides a comprehensive overview of the global epidemiology, transmission, and clinical relevance of Campylobacter infection.

Global Epidemiology of Campylobacter Infection

Cryptosporidium is increasingly recognized as one of the major causes of moderate to severe diarrhoea in developing countries. With treatment options limited, control relies on knowledge of the biology and transmission of the members of the genus responsible for disease. Currently, 26 species are recognized as valid on the basis of morphological, biological and molecular data. Of the nearly 20 Cryptosporidium species and genotypes that have been reported in humans, Cryptosporidium hominis and Cryptosporidium parvum are responsible for the majority of infections. Livestock, particularly cattle, are one of the most important reservoirs of zoonotic infections. Domesticated and wild animals can each be infected with several Cryptosporidium species or genotypes that have only a narrow host range and therefore have no major public health significance. Recent advances in next-generation sequencing techniques will significantly improve our understanding of the taxonomy and transmission of Cryptosporidium species, and the investigation of outbreaks and monitoring of emerging and virulent subtypes. Important research gaps remain including a lack of subtyping tools for many Cryptosporidium species of public and veterinary health importance, and poor understanding of the genetic determinants of host specificity of Cryptosporidium species and impact of climate change on the transmission of Cryptosporidium.

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Cryptosporidium species in humans and animals: current understanding and research needs

The fifth conference of the European Pond Conservation Network (Luxembourg, June 2012) brought together researchers, environmental managers, and other stakeholders with the aim to share state-of-the-art knowledge on the ecology, management, and conservation of ponds in the context of the many challenges facing the wider water environment. Although well-known ecological patterns apply to most ponds in Europe and elsewhere, recent data highlight that part of the environmental variables governing pond biodiversity remain specific to climatic/biogeographic regions and to elevation ranges, suggesting that, in addition to common practice, management plans should include range-specific measures. Beyond the contribution of individual ponds to the aquatic and terrestrial life, connected networks of ponds are vital in the provision of new climate space as a response to global climate change, by allowing the observed northward and/or upward movements of species. In terms of services, ponds offer sustainable solutions to key issues of water management and climate change such as nutrient retention, rainfall interception, or carbon sequestration. While the ecological role of ponds is now well-established, authoritative research-based advice remains needed to inform future direction in the conservation of small water bodies and to further bridge the gap between science and practice.

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The ecological role of ponds in a changing world

Chitin is widely distributed in nature and its annual production is thought to be huge. However, the chitin production has been rarely estimated in aquatic ecosystems, despite the growing economic interest in this polymer. Arthropods are one of the main chitin producers in the hydrosphere and a correct evaluation of the chitin production by these organisms in the different marine and freshwater ecosystems is of prime interest to understand their importance in the biogeochemical cycles of carbon and nitrogen. Such evaluation is also worth considering to achieve a rational exploitation of crustaceans which are currently the major source of chitin for the industry. Annual chitin production of crustaceans and insects in aquatic ecosystems was estimated on the basis of annual tissue production estimates and body chitin content measurements. About 800 annual tissue production estimates were collected from the literature. Estimates mainly concerned continental fresh waters and neritic ecosystems. Data were almost inexistent for athalassohaline and oceanic ecosystems. On the whole, 60% of the production estimates fell between 0.1 and 10.0 g dry weight m−2 yr−1. Published chitin levels in crustaceans and insects ranged from 3 to 16% of the whole body dry weight. Data were, however, lacking for some major groups such as trichopterans or amphipods. Aquatic insects and crustaceans were therefore collected and assayed for chitin using a highly specific enzymatic method. The chitin content of the collected insects (Coleoptera, Diptera, Ephemeroptera, Odonata, Plecoptera, Trichoptera) varied from 3 to 10% of the whole body dry weight; that of the collected crustaceans (Amphipoda, Branchiopoda, Copepoda) from 2.5 to 8.5% of the whole body dry weight. Total annual chitin production by arthropods had been estimated to 28 × 106 T chitin yr−1 for the freshwater ecosystems, to 6 × 106 T chitin yr−1 for athalassohaline ecosystems and to 1328 × 106 T chitin yr−1 for marine ecosystems. The importance of the chitin production corresponding to the formation of exuviae and peritrophic membranes in arthropods and the chitin production by non-arthropod organisms in the chitin budget of aquatic ecosystems was highlighted and discussed.

Chitin production by arthropods in the hydrosphere

Biofilms colonizing surfaces inside drinking water distribution networks may provide a habitat and shelter to pathogenic viruses and parasites. If released from biofilms, these pathogens may disseminate in the water distribution system and cause waterborne diseases. Our study aimed to investigate the interactions of protozoan parasites (Cryptosporidium parvum and Giardia lamblia [oo]cysts) and viruses (vaccinal poliovirus type 1, phiX174, and MS2) with two contrasting biofilms. First, attachment, persistence, and detachment of the protozoan parasites and the viruses were assessed with a drinking water biofilm. This biofilm was allowed to develop inside a rotating annular reactor fed with tap water for 7 months prior to the inoculation. Our results show that viable parasites and infectious viruses attached to the drinking water biofilm within 1 h and persisted within the biofilm. Indeed, infectious viruses were detected in the drinking water biofilm up to 6 days after the inoculation, while viral genome and viable parasites were still detected at day 34, corresponding to the last day of the monitoring period. Since viral genome was detected much longer than infectious particles, our results raise the question of the significance of detecting viral genomes in biofilms. A transfer of viable parasites and viruses from the biofilm to the water phase was observed after the flow velocity was increased but also with a constant laminar flow rate. Similar results regarding parasite and virus attachment and detachment were obtained using a treated wastewater biofilm, suggesting that our observations might be extrapolated to a wide range of environmental biofilms and confirming that biofilms can be considered a potential secondary source of contamination.

Interactions of Cryptosporidium parvum, Giardia lamblia, vaccinal poliovirus type 1, and bacteriophages ΦX174 and MS2 with a drinking water biofilm and a wastewater biofilm

The aim of this study was to determine the influence of environmental variables on the structure of benthic diatom assemblages, and to propose type assemblages of diatoms characterizing unpolluted headwater streams of Luxembourg. A total of 289 diatom samples were collected in the headwater streams of Luxembourg. At each sampling site, physical and chemical variables were also measured. The relationships between environmental variables and the distribution of the taxa were estimated using univariate and multivariate statistical analyses. On the basis of geology and stream water chemistry, Luxembourg could be separated in two regions. The streams in the schistose northern part of Luxembourg presented a low carbonate hardness (median 3.5° F); the streams in the southern part of Luxembourg presented a high carbonate hardness (median 21.8° F) notably connected to the presence of sandstone and limestone substrata. A Twinspan classification carried out on diatom assemblages defined two groups of samples corresponding to these two regions. The carbonate hardness that is related to the nature of the geological substratum appeared to be the major structuring variable for the assemblage composition. Anthropogenic pollution was a secondary structuring variable for diatom assemblages since each group could be subdivided in subgroups presenting statistically different nutrient and organic matter concentrations. The diatom assemblages of these subgroups were characterised by differences of saprobic and trophic preferences. On the basis of these results, two type assemblages of diatoms are proposed for the unpolluted headwater streams in the two regions of Luxembourg. The presence of these different type assemblages in Luxembourg shows the necessity to adapt diatom bioindication to the different regions of the country.

Henry-Michel Cauchie

Papers

The ecological role of ponds in a changing world

Chitin production by arthropods in the hydrosphere

Interactions of Cryptosporidium parvum, Giardia lamblia, vaccinal poliovirus type 1, and bacteriophages ΦX174 and MS2 with a drinking water biofilm and a wastewater biofilm

Regional distribution of diatom assemblages in the headwater streams of Luxembourg

Occurrence and persistence of enteroviruses, noroviruses and F-specific RNA phages in natural wastewater biofilms