Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen ...effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.
Microbial phototrophs, key primary producers on Earth, use H
O, H
, H
S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic ...photosynthesis to anaerobic respiration that we call 'syntrophic anaerobic photosynthesis'. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii does not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. This process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities.
The influence of feed supplements on behavior and memory has been recently studied in livestock. The objectives of the study were to evaluate the effects of a synbiotic on: an episodic-like (SOR: ...Spontaneous Object Recognition), a working (BARR: Fence barrier task), a long-term (TMAZE: Spatial T-maze task) memory test and on gut microbiota composition. Eighteen female piglets were supplemented from 1 to 28 days of age with a synbiotic (SYN), while 17 served as control (CTL). Feces were collected on days 16, 33 and 41 for 16S rRNA gene composition analyses. In the SOR, SYN piglets interacted more quickly with the novel object than CTL piglets. In the BARR, SYN piglets had shorter distances to finish the test in trial 3. In the TMAZE, SYN piglets were quicker to succeed on specific days and tended to try the new rewarded arm earlier during the reversal stage. Difference of microbiota composition between treatments was nonexistent on D16, a tendency on D33 and significant on D41. The synbiotic supplement may confer memory advantages in different cognitive tasks, regardless of the nature of the reward and the memory request. Difference in memory abilities can potentially be explained by differences in microbiota composition.
We present, implement, and analyze a spectrum of closely-related planners, designed to gain insight into the relationship between classical grid search and probabilistic roadmaps (PRMs). Building on ...the quasi-Monte Carlo sampling literature, we have developed deterministic variants of the PRM that use low-discrepancy and low-dispersion samples, including lattices. Classical grid search is extended using subsampling for collision detection and also the dispersion-optimal Sukharev grid, which can be considered as a kind of lattice-based roadmap to complete the spectrum. Our experimental results show that the deterministic variants of the PRM offer performance advantages in comparison to the original, multiple-query PRM and the single-query, lazy PRM. Surprisingly, even some forms of grid search yield performance that is comparable to the original PRM. Our theoretical analysis shows that all of our deterministic PRM variants are resolution complete and achieve the best possible asymptotic convergence rate, which is shown to be superior to that obtained by random sampling. Thus, in surprising contrast to recent trends, there is both experimental and theoretical evidence that the randomization used in the original PRM is not advantageous.
Differences in the chemical and physical properties of dietary fibers are increasingly known to exert effects on their fermentation by gut microbiota. Here, we demonstrate that maize bran particle ...size fractions show metabolic output and microbial community differences similar to those we previously observed for wheat brans. As for wheat brans, maize bran particles varied in starch and protein content and in sugar composition with respect to size. We fermented maize bran particles varying in size
in vitro
with human fecal microbiota as inocula, measuring their metabolic fate i.e., short-chain fatty acids (SCFAs) and resulting community structure (via 16S rRNA gene amplicon sequencing). Metabolically, acetate, propionate and butyrate productions were size-dependent. 16S rRNA sequencing revealed that the size-dependent SCFA production was linked to divergent microbial community structures, which exerted effects at fine taxonomic resolution (the genus and species level). These results further suggest that the physical properties of bran particles, such as size, are important variables governing microbial community compositional and metabolic responses.
Intrinsic photodegradation of organic solar cells, theoretically attributed to CH bond rearrangement/breaking, remains a key commercialization barrier. This work presents, via dark electron ...paramagnetic resonance (EPR), the first experimental evidence for metastable C dangling bonds (DBs) formed by blue/UV irradiation of polymer:fullerene blend films in nitrogen. The DB density increases with irradiation and decreases ≈4‐fold after 2 weeks in the dark. The dark EPR also shows increased densities of other spin‐active sites in photodegraded polymer, fullerene, and polymer:fullerene blend films, consistent with broad electronic measurements of fundamental properties, including defect/gap state densities. The EPR and electronic measurements enable identification of defect states, whether in the polymer, fullerene, or at the donor/acceptor (D/A) interface. Importantly, the EPR results indicate that the DBs are at the D/A interface, as they were present only in the blend films. The role of polarons in interface DB formation is also discussed.
For the first time, strong electron paramagnetic resonance evidence is provided that irradiation of bulk heterojunction polymer:fullerene solar cells by blue and shorter wavelength photons (<495 nm), likely assisted by highly energized (“hot”) polarons, generates C dangling bonds at the polymer:fullerene interfaces. This photodegradation process may be one of the key obstacles to commercialization of such cells.
Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the ...disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.
To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. ...Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.
Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. ...We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
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