211 research outputs found
Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations
Enclosure experiments are frequently used to investigate the impact of
changing environmental conditions on microbial assemblages. Yet, how the incuba-
tion itself challenges complex bacterial communities is thus far unknown. In this
study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were com-
bined to evaluate bacterial communities derived from marine, mesohaline, and oli-
gohaline conditions after long-term batch incubations. Early in the experiment, the
three bacterial communities were highly diverse and differed significantly in their
compositions. Manipulation of the enclosures with terrigenous dissolved organic car-
bon resulted in notable differences compared to the control enclosures at this early
phase of the experiment. However, after 55 days, bacterial communities in the ma-
nipulated and the control enclosures under marine and mesohaline conditions were
all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclo-
sures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late
phase of the incubation. Metaproteome analyses suggested that the ability to use
outer membrane-based internal energy stores, in addition to the previously de-
scribed grazing resistance, may enable the gammaproteobacterium Spongiibacter to
prevail in long-time incubations. Under oligohaline conditions, the utilization of ex-
ternal recalcitrant carbon appeared to be more important (hgc-I). Enclosure experi-
ments with complex natural microbial communities are important tools to investi-
gate the effects of manipulations. However, species-specific properties, such as
individual carbon storage strategies, can cause manipulation-independent effects
and need to be considered when interpreting results from enclosures.This study was financially supported by the SAW-funded ATKiM project, which provided funds to D. P. R. Herlemann, C. Meeske, K. Jürgens, S. Markert, and T. Schweder. D. P. R. Herlemann was also supported by the European Regional Develop- ment Fund/Estonian Research Council funded Mobilitas Plus Top Researcher grant MOBTT24. We thank the crew and captain of the RV Meteor (M86, M87) for support during the research cruise. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Centre for High Performance Computing (PDC-HPC) and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). We thank Jana Matulla for excellent technical assis- tance and Stephan Fuchs for his help and advice in MS database construction. We also thank Stefan E. Heiden for valuable help with the CDD BLAST analyses.This study was financially supported by the SAW-funded ATKiM project, which
provided funds to D. P. R. Herlemann, C. Meeske, K. Jürgens, S. Markert, and T.
Schweder. D. P. R. Herlemann was also supported by the European Regional Develop-
ment Fund/Estonian Research Council funded Mobilitas Plus Top Researcher grant
MOBTT24.
We thank the crew and captain of the RV Meteor (M86, M87) for support during the
research cruise. The computations were performed on resources provided by the
Swedish National Infrastructure for Computing (SNIC) at the PDC Centre for High
Performance Computing (PDC-HPC) and Uppsala Multidisciplinary Center for Advanced
Computational Science (UPPMAX). We thank Jana Matulla for excellent technical assis-
tance and Stephan Fuchs for his help and advice in MS database construction. We also
thank Stefan E. Heiden for valuable help with the CDD BLAST analyses
Genome Majority Vote Improves Gene Predictions
Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps
Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes
The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world
Bioinformatics challenges and potentialities in studying extreme environments
Cold environments are populated by organisms able to contravene deleterious effects of low temperature by diverse adaptive strategies, including the production of ice binding proteins (IBPs) that inhibit the growth of ice crystals inside and outside cells. We describe the properties of such a protein (EfcIBP) identified in the metagenome of an Antarctic biological consortium composed of the ciliate Euplotes focardii and psychrophilic non-cultured bacteria. Recombinant EfcIBP can resist freezing without any conformational damage and is moderately heat stable, with a midpoint temperature of 66.4 degrees C. Tested for its effects on ice, EfcIBP shows an unusual combination of properties not reported in other bacterial IBPs. First, it is one of the best-performing IBPs described to date in the inhibition of ice recrystallization, with effective concentrations in the nanomolar range. Moreover, EfcIBP has thermal hysteresis activity (0.53 degrees C at 50 mu M) and it can stop a crystal from growing when held at a constant temperature within the thermal hysteresis gap. EfcIBP protects purified proteins and bacterial cells from freezing damage when exposed to challenging temperatures. EfcIBP also possesses a potential N-terminal signal sequence for protein transport and a DUF3494 domain that is common to secreted IBPs. These features lead us to hypothesize that the protein is either anchored at the outer cell surface or concentrated around cells to provide survival advantage to the whole cell consortium
Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages
Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs),
such as eicosapentaenoic acid (EPA, 20:5n-3) and
docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow
subset of marine γ-proteobacteria. The genes responsible for de
novo bacterial PUFA biosynthesis, designated
pfaEABCD, encode large, multi-domain protein complexes akin
to type I iterative fatty acid and polyketide synthases, herein referred to as
“Pfa synthases”. In addition to the archetypal Pfa synthase gene
products from marine bacteria, we have identified homologous type I FAS/PKS gene
clusters in diverse microbial lineages spanning 45 genera representing 10 phyla,
presumed to be involved in long-chain fatty acid biosynthesis. In total, 20
distinct types of gene clusters were identified. Collectively, we propose the
designation of “secondary lipids” to describe these
biosynthetic pathways and products, a proposition consistent with the
“secondary metabolite” vernacular. Phylogenomic analysis reveals a
high degree of functional conservation within distinct biosynthetic pathways.
Incongruence between secondary lipid synthase functional clades and taxonomic
group membership combined with the lack of orthologous gene clusters in closely
related strains suggests horizontal gene transfer has contributed to the
dissemination of specialized lipid biosynthetic activities across disparate
microbial lineages
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria
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
Nevrological manifestations in patiens with West Nile fever
Гарячка Західного Нілу (ГЗН) є найпоширенішим зооантропонозним трансмісивним «комариним» захворюванням у групі природно осередкових інфекцій. Вірус ГЗН належить до роду Flavivirus родини Flaviviridae, поширений на усіх континентах за винятком Антарктиди. В Європі основним видом комарів, які передають вірус ГЗН людям, є Culex pipiens. Інфікування описане також при вертикальній передачі від матері до дитини та парентеральним шляхом. За філогенетичними властивостями вірусу розрізняють кілька генетичних груп – генотипів, деякі з яких містять підгрупи, що обумовлює нерівномірний територіальний розподіл та тяжкість клінічної маніфестації ГЗН
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