A large number of descriptive surveys have shown that microbial communities experience successional changes over time and that ecological dominance is common in the microbial world. However, direct ...evidence for the ecological processes mediating succession or causing ecological dominance remains rare. Different dispersal abilities among species may be a key mechanism. We surveyed fungal diversity within a metacommunity of pitchers of the model carnivorous plant
and discovered that the yeast
was ecologically dominant. Its frequency in the metacommunity increased during the growing season, and it was not replaced by other taxa. We next measured its competitive ability in a manipulative laboratory experiment and tracked its dispersal over time in nature. Despite its dominance,
is not a superior competitor. Instead, it is a superior disperser: it arrives in pitchers earlier, and disperses into more pitchers, than other fungi. Differential dispersal across the spatially structured metacommunity of individual pitchers emerges as a key driver of the continuous dominance of
during succession.
Microbial communities are ubiquitous and occupy nearly every imaginable habitat and resource, including human-influenced habitats (e.g., fermenting food and hospital surfaces) and habitats with little human influence (e.g., aquatic communities living in carnivorous plant pitchers). We studied yeast communities living in pitchers of the carnivorous purple pitcher plant to understand how and why microbial communities change over time. We found that dispersal ability is not only important for fungal communities early in their existence, it can also determine which species is dominant (here, the yeast
) long after the species and its competitors have arrived. These results contrast with observations from many human-influenced habitats, in which a good competitor eventually outcompetes good dispersers, since humans often design these habitats to favor a specific competitor. This study will help microbiologists understand the qualities of microbial species that enable takeover of new habitats in both natural and human-influenced environments.
A key unmet need in metabolomics is the ability to efficiently quantify a large number of known cellular metabolites. Here we present a liquid chromatography (LC)–electrospray ionization tandem mass ...spectrometry (ESI-MS/MS) method for reliable measurement of 141 metabolites, including components of central carbon, amino acid, and nucleotide metabolism. The selected LC approach, hydrophilic interaction chromatography with an amino column, effectively separates highly water soluble metabolites that fail to retain using standard reversed-phase chromatography. MS/MS detection is achieved by scanning through numerous selected reaction monitoring events on a triple quadrupole instrument. When applied to extracts of
Escherichia coli grown in
12C- versus
13Cglucose, the method reveals appropriate
12C- and
13C-peaks for 79 different metabolites.
Many key regulatory proteins in bacteria are present in too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such proteins can ...contribute greatly to phenotypic heterogeneity. Here we develop a microfluidics-based platform that enables single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion within the cytoplasm of live Escherichia coli (E. coli) cells. Our technique also allows for automated microscopy at high throughput with minimal perturbation to native physiology, as well as viable enrichment/retrieval. We illustrate the method by analysing the control of the master regulator of the E. coli stress response, RpoS, by its adapter protein, SprE (RssB). Quantification of SprE numbers shows that though SprE is necessary for RpoS degradation, it is expressed at levels as low as 3-4 molecules per average cell cycle, and fluctuations in SprE are approximately Poisson distributed during exponential phase with no sign of bursting.
Bacterial Diversity across Individual Lichens MUSHEGIAN, Alexandra A; PETERSON, Celeste N; BAKER, Christopher C. M ...
Applied and Environmental Microbiology,
06/2011, Volume:
77, Issue:
12
Journal Article
The master regulator of stationary phase in Escherichia coli, RpoS, responds to carbon availability through changes in stability, but the individual steps in the pathway are unknown. Here we ...systematically block key steps of glycolysis and the citric acid cycle and monitor the effect on RpoS degradation in vivo. Nutrient upshifts trigger RpoS degradation independently of protein synthesis by activating metabolic pathways that generate small energy molecules. Using metabolic mutants and inhibitors, we show that ATP, but not GTP or NADH, is necessary for RpoS degradation. In vitro reconstitution assays directly demonstrate that ClpXP fails to degrade RpoS, but not other proteins, at low ATP hydrolysis rates. These data suggest that cellular ATP levels directly control RpoS stability.
Biology and biochemistry students must learn to visualize and comprehend the complex three‐dimensional (3D) structures of macromolecules such as proteins or DNA. However, most tools available for ...teaching biomolecular structures typically operate in two dimensions. Here, we present protocols and pedagogical approaches for using immersive augmented reality (AR) visors, specifically the Microsoft HoloLens, to reinforce learning with large scale 3D holographic structures. We developed a novel workflow to render vividly colored custom biomolecules in AR visors. In addition, we developed AR exercises to review concepts relevant to protein or DNA structure and then implemented the exercises in four different biology and biochemistry courses. Surveys showed that students reported greater interest in biomolecular structures after the exercise. We also highlight some of the advantages and disadvantages of the software and hardware of this upcoming technology.
The implementation of Course‐Based Undergraduate Research Experiences (CUREs) has made it possible to expose large undergraduate populations to research experiences. For these research experiences to ...be authentic, they should reflect the increasing collaborative nature of research. While some CUREs have expanded with multiple schools across the nation, it is still unclear how a structured extramural collaboration between students and faculty from an outside institution affects student outcomes. In this study, we established three cohorts of students: 1) no‐CURE 2) single institution CURE (CURE) and 3) external collaborative CURE (ec‐CURE) and assessed academic and attitudinal outcomes. The ec‐CURE differs from a regular CURE in that students work with faculty member from an external institution to refine their hypothesis and discuss their data. The sharing of ideas, data and materials with an external faculty allowed students to experience a level of collaboration not typically found in an undergraduate setting. Students in the ec‐CURE had the greatest gains in experimental design, self‐reported course benefits, scientific skills and STEM importance. Importantly this study occurred in a diverse community of STEM disciplinary faculty from 2‐ and 4‐year institutions illustrating that exposing students to structured external collaboration is both feasible and beneficial to student learning.
Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating ...pollution. This study aimed to determine individual cultures' and a strain mixture's ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The
ICP1 and
ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants.
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