Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies

Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia

Microzooplankton community associated with phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)

The spatial and temporal community composition of microzooplankton (dinoflagellates and ciliates) was assessed in the Kerguelen area (Southern Ocean) during the KEOPS2 cruise in early spring (October-November) 2011. This naturally iron-fertilized region was characterized by a complex mesoscale circulation resulting in a patchy distribution of phytoplankton blooms. Collectively, 97 morphospecies of dinoflagellates and ciliates belonging to 41 genera were identified by microscopy, and 202 Alveolata-related OTUs (operational taxonomical units) were retrieved with tag-pyrosequencing. Microscopy and pyrosequencing data were in accordance, in that diatom-consuming dinoflagellates were the most enhanced taxa in the blooms. Dinoflagellates also showed significant positive relationships with phytoplankton pigments, while no major differences were found in the ciliate abundances inside and outside the blooms. Cluster analysis showed clear differences in the phytoplankton and microzooplankton community structures between the iron-fertilized and HNLC (high nutrient low chlorophyll) waters, and between the blooms, concerning their location and the fertilization mechanisms. These results were combined with the rates of primary production and mesozooplankton consumption determined for the study area. The potential role of dinoflagellates and ciliates as phytoplankton consumers and as prey for mesozooplankton was then evaluated. Overall, heterotrophic dinoflagellates were probably the most important group of phytoplankton grazers, and a potential food source for copepods

Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations

The aim of this study was to analyze planktonic protistan assemblages under different environmental pressures at 2 adjacent coastal stations (inshore and offshore; similar to 6.4 km apart) in the eastern English Channel (EEC). Samples were collected between March 2012 and June 2013, and analyzed using bioinformatic analysis and tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. In addition to the taxonomic composition of the protistan communities, the detected operational taxonomic units (OTUs) were sorted into 6 major functional groups based on their trophic roles in marine systems. Comparisons of 13 environmental factors, including physical and chemical variables, indicated significant differences between the 2 stations. However, the only significant relationship between environmental pressures and protistan community structure was detected when the trophic role of the OTUs was considered at the inshore station. In order to interpret differences in community structure, the effect of biotic inter actions was investigated through the examination of the co-occurrence networks of the protistan communities at both stations. In terms of the number of edges and connectivity of nodes, the analysis showed that the inshore station had more complex associations between OTUs than the offshore station. This strongly suggests that due to the higher and more variable environmental pressures the inshore station comparatively receives, its protistan community has developed a greater complexity of biotic connections. This in turn reflects the rapid responses of trophic interactions within the entire microbial community

Seasonal variations of marine protist community structure based on taxon-specific traits using the eastern English Channel as a model coastal system

Previous microscopy-based studies in the eastern English Channel have revealed it to be a productive meso-eutrophic coastal ecosystem, characterized by strong repeating patterns in microplankton succession. The present study examines the seasonal structure of the entire protistan community from March 2011 to July 2013, using tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. A total of 1242 OTUs and 28 high-level taxonomic groups, which included previously undetected taxa in the area, were identified. The detected OTUs were considered according to taxon-specific traits, which included their trophic role, abundance and specialization level. Taxa differentiation based on specialization level rather than abundance was more informative in describing community organization. While generalists were always abundant, numerous specialists that were either rare or absent in most samples, increased in abundance for short periods, appearing to be overall abundant. Statistical and network analyses showed that the protistan seasonal organization was influenced by environmental parameters. It also highlighted that in addition to grazers, fungi and parasites played potentially significant roles during phytoplankton blooms. Overall, while the protistan succession was mainly shaped by environmental variations, biotic interactions among co-occurring taxa were the main structural drivers of the temporal assemblages

Microplanktonic Community Structure in a Coastal System Relative to a Phaeocystis Bloom Inferred from Morphological and Tag Pyrosequencing Methods

Background: Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC), have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. Methodology and Principal Findings: The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates) was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. Conclusions: Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa) along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the challenge of modelling and predicting ecological change requires the use of different complementary approaches, to link taxonomic data with the functional roles of microbes in biogeochemical cycles

Bioaccumulation of trace metal elements and biomarker responses in caged juvenile flounder at a polluted site: Effects of fish density and time exposure

International audienceThis study investigates the effect of fish density and exposure duration on trace metal elements (TME) bioaccumulation and several biomarkers response. Juvenile flounders were caged at low, medium and high densities and exposed during 15 or 30 days in the Seine estuary. The concentrations of the TME measured in the muscle of the caged fish were all in agreement with their bioavailability percentage in the sediments. Higher concentrations of TME were found in flounders' muscle exposed for 15 days compared with those caged for 30 days. For the same exposure time, the density of fish had no effect on the accumulation of the TME in the flounders' muscle. Biomarkers responses varied according to density and duration of exposure. Special care should be taken in their interpretation. We underline that for an optimal assessment of TME pollution in the field, 15 days with low densities of fish per cage are sufficient

Tobacco use vs. helminths in Congo basin hunter-gatherers: self-medication in humans?

We tested a novel hypothesis that recreational use of neurotoxic plants helps defend against parasites. Spec ifically, we investigated the relationship between smoking and helminthiasis among the Aka, a remote population of Central African foragers who are avid tobacco smokers, suffer high rates of helminthiasis, and have little-to-no access to commercial anthelmintics. Two hundred and six healthy Aka men provided saliva and stool samples. Saliva samples were assayed for cotinine, a nicotine metabolite; a subsample was genotyped for the CYP2A6 enzyme, which metabolizes nicotine. Stool samples were assayed for intestinal helminth eggs as an index of worm burden. After 1 year, a subsample of participants was located and provided additional saliva and stool samples. We found (1) an exceptionally high prevalence of tobacco use, (2) a significant negative correlation between cotinine (a nicotine metabolite) and worm burden, (3) that treating helminths with albendazole, a commercial anthelmintic, reduced cotinine concentration two weeks later, compared to placebo controls, (4) among treated participants, higher cotinine concentrations in year 1 predicted less reinfection by year 2, and (5) younger and older participants with slow nicotine-metabolizing CYP2A6 alleles had lower worm burdens compared to those with extensive metabolizing alleles. These results provide the first evidence of a link between helminthiasis and smoking. They also suggest that, in populations where intestinal helminths are endemic, tobacco use might protect against helminth infection and reduce worm burden among infected individuals, and that individuals modulate nicotine exposure in response to infection. The results thus support the hypothesis that substance use helps defend against parasites