Biology subjects

McMahon, K.

Publications and source records attributed to McMahon, K..

6 recordsLinked to original sources

bioRxiv2018

acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively-synthesized Retinal

Freshwater lakes harbor complex microbial communities, but these ecosystems are often dominated by acI Actinobacteria from three clades (acI-A, acI-B, acI-C). Members of this cosmopolitan lineage are proposed to bolster heterotrophic growth using phototrophy because their genomes encode actino-opsins (actR). This model has been difficult to experimentally validate because acI are not consistently culturable. In this study, using genomes from single cells and metagenomes, we provide a detailed biosynthetic route for many acI-A and -B members to synthesize retinal and its carotenoid precursors. Accordingly, these acI should be able to natively assemble light-driven actinorhodopsins (holo-ActR) to pump protons, in contrast to acI-C members and other bacteria that encode opsins but lack retinal-production machinery. Moreover, we show that all acI clades contain genes for a complex carotenoid pathway that starts with retinal precursors. Transcription analysis of acI in a eutrophic lake shows that all retinal and carotenoid pathway operons are transcribed and that actR is among the most highly-transcribed of all acI genes. Furthermore, heterologous expression of retinal pathway genes shows that lycopene, retinal, and ActR can be made. Model cells producing ActR and the key acI retinal-producing {beta}-carotene oxygenase formed acI-holo-ActR and acidified solution during illumination. Our results prove that acI containing both ActR and retinal-production enzymes have the capacity to natively synthesize a green light-dependent outward proton-pumping rhodopsin.\n\nIMPORTANCEMicrobes play critical roles in determining the quality of freshwater ecosystems that are vital to human civilization. Because acI Actinobacteria are ubiquitous and abundant in freshwater lakes, clarifying their ecophysiology is a major step in determining the contributions that they make to nitrogen and carbon cycling. Without accurate knowledge of these cycles, freshwater systems cannot be incorporated into climate change models, ecosystem imbalances cannot be predicted, and policy for service disruption cannot be planned. Our work fills major gaps in microbial light utilization, secondary metabolite production, and energy cycling in freshwater habitats.

microbiology↗

bioRxiv2017

Cyanobacterial Growth on Municipal Wastewater Requires Low Temperatures

Side-streams in wastewater treatment plants can serve as concentrated sources of nutrients (i.e. nitrogen and phosphorus) to support the growth of photosynthetic organisms that ultimately serve as feedstock for production of fuels and chemicals. However, other chemical characteristics of these streams may inhibit growth in unanticipated ways. Here, we evaluated the use of liquid recovered from municipal anaerobic digesters via gravity belt filtration as a nutrient source for growing the cyanobacterium Synechococcus sp. strain PCC 7002. The gravity belt filtrate (GBF) contained high levels of complex dissolved organic matter (DOM), which seemed to negatively influence cells. We investigated the impact of GBF on physiological parameters such as growth rate, membrane integrity, membrane composition, photosystem composition, and oxygen evolution from photosystem II. At 37{degrees}C, we observed an inverse correlation between GBF concentration and membrane integrity. Radical production was also detected upon exposure to GBF at 37{degrees}C. However, at 27{degrees}C the dose dependent relationship between GBF concentration and lack of membrane integrity was abolished. Immediate resuspension of strains in high doses of GBF showed markedly reduced oxygen evolution rates relative to the control. Together, this suggests that one mechanism responsible for GBF toxicity to Synechococcus is the interruption of photosynthetic electron flow and subsequent phenomena. We hypothesize this is likely due to the presence of phenolic compounds within the DOM.\n\nIMPORTANCECyanobacteria are viewed as promising platforms to produce fuels and/or high-value chemicals as part of so-called \"bio-refineries\". Their integration into wastewater treatment systems is particularly interesting because removal of the nitrogen and phosphorus in many wastewater streams is an expensive but necessary part of wastewater treatment. In this study, we evaluated strategies for cultivating Synechococcus strain PCC 7002 on media comprised of two wastewater streams; treated secondary effluent supplemented with the liquid fraction extracted from sludge following anaerobic digestion. This strain is commonly used for metabolic engineering to produce a variety of valuable chemical products and product precursors (e.g. lactate). However, initial attempts to grow PCC 7002 under otherwise standard conditions of light and temperature failed. We thus systematically evaluated alternative cultivation conditions and then used multiple methods to dissect the apparent toxicity of the media under standard cultivation conditions.

microbiology↗

bioRxiv2017

Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics

Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions, and greatly expand the known genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide-degraders in freshwater, uncovered interesting genomic features for this life style, and suggested their adaptation to nutrient availabilities in their environments. Between the two lakes, Verrucomicrobia populations differ significantly in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially-derived allochthonous carbon sources of the two ecosystems respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humic-rich environment. Notably, most epilimnion genomes have large numbers of so-called \"Planctomycete-specific\" cytochrome c-containing genes, which exhibited nearly opposite distribution patterns with glycoside hydrolase genes, probably associated with the different environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes are a major step towards understanding the role, ecophysiology and distribution of Verrucomicrobia in freshwater.\n\nIMPORTANCEFreshwater Verrucomicrobia are cosmopolitan in lakes and rivers, yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia are restricted to one subdivision of this phylum. Here, we greatly expand the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia as potential (poly)saccharide-degraders, and suggested their adaptation to carbon source of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called \"Planctomycete-specific\" cytochrome c-containing genes, and found their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

microbiology↗

bioRxiv2017

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multi-year time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. Multiple sites and sampling events were necessary to begin to fully describe the bacterial communities. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each site. The community present in each year and site was also unique. Despite high interannual variability in community composition, we detected a core community of ubiquitous freshwater taxa. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term observations, as analyzing only a single year of data would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here.\n\nImportanceLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community dynamics operate on multi-year timescales, a finding which likely applies to other ecosystems, with implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities, and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource to anyone seeking to answer their own microbial ecology questions using a multi-year time series.

microbiology↗

bioRxiv2017

Cohesion: A method for quantifying the connectivity of microbial communities

The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a communitys complexity might improve predictive power in microbial models. Here, we present a new metric, called community \"cohesion,\" that quantifies the degree of connectivity of a microbial community. We validate our approach using long-term (10+ year) phytoplankton datasets, where absolute abundance counts are available. As a case study of our metrics utility, we show that community cohesion is a strong predictor of Bray-Curtis dissimilarity (R2 = 0.47) between phytoplankton communities in Lake Mendota, WI, USA. Our cohesion metrics outperform a model built using all available environmental data collected during a long-term sampling program. The result that cohesion corresponds strongly to Bray-Curtis dissimilarity is consistent across the five lakes analyzed here. Our cohesion metrics can be used as a predictor for many community-level properties, such as phylogenetic diversity, nutrient fluxes, or ecosystem services. We explain here the calculation of our cohesion metrics and their potential uses in microbial ecology.\n\nConflict of InterestThe authors declare no conflict of interest.

microbiology↗

bioRxiv2017

Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans

AbstractSusceptibility genes for psychiatric and neurological disorders - including APOE, BDNF, CLU,CNTNAP2, COMT, DISC1, DTNBP1, ErbB4, HFE, NRG1, NTKR3, and ZNF804A - have been reported to affect white matter (WM) microstructure in the healthy human brain, as assessed through diffusion tensor imaging (DTI). However, effects of single nucleotide polymorphisms (SNPs) in these genes explain only a small fraction of the overall variance and are challenging to detect reliably in single cohort studies. To date, few studies have evaluated the reproducibility of these results. As part of the ENIGMA-DTI consortium, we pooled regional fractional anisotropy (FA) measures for 6,165 subjects (CEU ancestry N=4,458) from 11 cohorts worldwide to evaluate effects of 15 candidate SNPs by examining their associations with WM microstructure. Additive association tests were conducted for each SNP. We used several meta-analytic and mega-analytic designs, and we evaluated regions of interest at multiple granularity levels. The ENIGMA-DTI protocol was able to detect single-cohort findings as originally reported. Even so, in this very large sample, no significant associations remained after multiple-testing correction for the 15 SNPs investigated. Suggestive associations (1.3x10-4 < p < 0.05, uncorrected) were found for BDNF, COMT, and ZNF804A in specific tracts. Meta-and mega-analyses revealed similar findings. Regardless of the approach, the previously reported candidate SNPs did not show significant associations with WM microstructure in this largest genetic study of DTI to date; the negative findings are likely not due to insufficient power. Genome-wide studies, involving large-scale meta-analyses, may help to discover SNPs robustly influencing WM microstructure.

neuroscience↗