Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (BLAST) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96 %) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra-and interspecies relationships at around 95-96 % ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65 % 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0 %) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea. INTRODUCTIONDNA-DNA hybridization (DDH) is a category of experimental methods which indirectly measure the overall similarity between two genome sequences (McCarthy & Bolton, 1963;Schildkraut et al., 1961). Over the last 50 years, DDH has been the 'gold standard' for bacterial species demarcation as it provides a clear and objective numerical threshold for a species boundary, for which 70 % DDH was suggested and is widely used (Tindall et al., 2010;Wayne et al., 1987). However, due to the labour-intensive and error-prone nature of DDH experiments, there has been a continuous demand for an alternative genotype-based standard (Gevers et al., 2005;Stackebrandt et al., 2002).The genome sequence of a microbial strain is the ultimate information for microbial taxonomy. As whole-genome sequencing has become more widely accessible due to the introduction of cost-effective high-throughput DNA sequencing technology, it is evident that genome sequence similarities have the potential to be a routine taxonomic parameter as a replacement for DDH. Much effort has been put into correlating DDH values with digital DDH-like similarity indices based on computational comparisons of two genome sequences. These include average nucleotide identity (ANI) (Konstantinidis et al., 2006), genome BLAST distance phylogeny (GBDP) (Henz et al., 2005) and the maximal unique matches index (MUMi) (Deloger et al., 2009). Of these, ANI has been most widely used as a possible next-generation gold standard for species delineation (Chan et al., 2012;Goris et a...

Little is known about the factors affecting the relative influences of stochastic and deterministic processes that govern the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soil datasets distributed across different regions. Different relationships between pH and successional age across these datasets allowed us to separate the influences of successional age (i.e., time) from soil pH. We found that extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.

MoS2 is considered a promising two-dimensional active channel material for future nanoelectronics. However, the development of a facile, reliable, and controllable doping methodology is still critical for extending the applicability of MoS2. Here, we report surface charge transfer doping via thiol-based binding chemistry for modulating the electrical properties of vacancy-containing MoS2 (v-MoS2). Although vacancies present in 2D materials are generally regarded as undesirable components, we show that the electrical properties of MoS2 can be systematically engineered by exploiting the tight binding between the thiol group and sulfur vacancies and by choosing different functional groups. For example, we demonstrate that NH2-containing thiol molecules with lone electron pairs can serve as an n-dopant and achieve a substantial increase of electron density (Δn = 3.7 × 10(12) cm(-2)). On the other hand, fluorine-rich molecules can provide a p-doping effect (Δn = -7.0 × 10(11) cm(-2)) due to its high electronegativity. Moreover, the n- and p-doping effects were systematically evaluated by photoluminescence (PL), X-ray photoelectron spectroscopy (XPS), and electrical measurement results. The excellent binding stability of thiol molecules and recovery properties by thermal annealing will enable broader applicability of ultrathin MoS2 to various devices.

Einer koreanischen Studie zufolge bringt die Teilresektion des Innenmeniskus nach Einreißen keine Vorteile gegenüber einer konservativen Behandlung. Von 102 Pati-enten mit Knieschmerz und degenerativ bedingtem horizontalem Riss im Hinter-horn des Innenmeniskus unterzogen sich 50 einer arthroskopischen Meniskusteil-resektion, 52 machten nur kräftigende Übungen. Hinsichtlich der Funktionsfähigkeit unter-schieden sich operierte Patienten nicht von konservativ behandelten (Durchschnitts-wert im VAS-Score 1,8 vs. 1,7). Nach zwei Jahren waren 68% der Operierten und 67% der konservativ Behandelten komplett schmerzfrei, und die Kniefunktion hatte sich in gleichem Maß verbessert. Die Be-funde sind umso wichtiger, als nach Me-niskektomie das Arthroserisiko steigt und oft Revisionsoperationen nötig sind.