scholarly journals Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage

2013 ◽  
Vol 79 (12) ◽  
pp. 3716-3723 ◽  
Author(s):  
Christopher A. Gulvik ◽  
Alison Buchan
Keyword(s):  
Salt Marshes ◽  
Aromatic Compounds ◽  
Soil Bacteria ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Content Type ◽  
Coastal Salt Marshes ◽  
Metabolic Versatility ◽  
Organic Carbon Pool ◽  
Ruegeria Pomeroyi

ABSTRACTPlant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, includingSagittula stellataE-37, utilize aromatic compounds as primary growth substrates. The genome sequence ofS. stellatacontains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists inS. stellatawhen the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them,p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated thatS. stellatasimultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed whenS. stellatawas provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,Ruegeria pomeroyiDSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.

scholarly journals Outer Cell Surface Components Essential for Fe(III) Oxide Reduction by Geobacter metallireducens

2012 ◽  
Vol 79 (3) ◽  
pp. 901-907 ◽  
Author(s):  
Jessica A. Smith ◽  
Derek R. Lovley ◽  
Pier-Luc Tremblay
Keyword(s):  
Outer Surface ◽  
Surface Protein ◽  
Transcript Abundance ◽  
Geobacter Sulfurreducens ◽  
Extracellular Electron Transfer ◽  
Outer Cell ◽  
Gene Transcript ◽  
Oxide Reduction ◽  
Geobacter Metallireducens ◽  
Content Type

ABSTRACTGeobacterspecies are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail inGeobacter sulfurreducens, but a number of the most thoroughly studied outer surface components ofG. sulfurreducens, particularlyc-type cytochromes, are not well conserved amongGeobacterspecies. In order to identify cellular components potentially important for Fe(III) oxide reduction inGeobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes forc-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified sixc-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of thec-type cytochromes which were essential for Fe(III) oxide reduction inG. metallireducenshave homologs inG. sulfurreducensthat are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer betweenG. metallireducensandG. sulfurreducensbut the outer-surfacec-type cytochromes involved in Fe(III) oxide reduction are different.

scholarly journals Nitrogen Utilization and Metabolism in Ruminococcus albus 8

2014 ◽  
Vol 80 (10) ◽  
pp. 3095-3102 ◽  
Author(s):  
Jong Nam Kim ◽  
Emily DeCrescenzo Henriksen ◽  
Isaac K. O. Cann ◽  
Roderick I. Mackie
Keyword(s):  
Growth Rate ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Enzyme Activities ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Sole Nitrogen Source ◽  
Ruminococcus Albus ◽  
Content Type ◽  
Maximum Cell

ABSTRACTThe model rumenFirmicutesorganismRuminococcus albus8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth ofR. albus8 on ammonia and urea showed the same growth rate (0.08 h−1) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD600] was 1.01; and for urea, the OD600was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h−1) and a lower maximum cell density (OD600= 0.58). To identify differences in gene expression and enzyme activities, the transcript abundances of 10 different genes involved in nitrogen metabolism and specific enzyme activities were analyzed by harvesting mRNA and crude protein from cells at the mid- and late exponential phases of growth on the different N sources. Transcript abundances and enzyme activities varied according to nitrogen source, ammonia concentration, and growth phase. Growth ofR. albus8 on ammonia and urea was similar, with the only observed difference being an increase in urease transcript abundance and enzyme activity in urea-grown cultures. Growth ofR. albus8 on peptides showed a different nitrogen metabolism pattern, with higher gene transcript abundance levels ofgdhA,glnA,gltB,amtB,glnK, andureC, as well as higher activities of glutamate dehydrogenase and urease. These results demonstrate that ammonia, urea, and peptides can all serve as nitrogen sources forR. albusand that nitrogen metabolism genes and enzyme activities ofR. albus8 are regulated by nitrogen source and the level of ammonia in the growth medium.

scholarly journals Molecular Analysis of the Metabolic Rates of Discrete Subsurface Populations of Sulfate Reducers

2011 ◽  
Vol 77 (18) ◽  
pp. 6502-6509 ◽  
Author(s):  
M. Miletto ◽  
K. H. Williams ◽  
A. L. N'Guessan ◽  
D. R. Lovley
Keyword(s):  
Transcript Abundance ◽  
Sulfite Reductase ◽  
Gene Transcript ◽  
Content Type ◽  
Sulfate Reducers ◽  
Sulfate Reducing ◽  
Sedimentary Environments ◽  
Predominant Component ◽  
Reducing Activity ◽  
The Individual

ABSTRACTElucidating thein situmetabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis ofdsrABsequences prior to the addition of acetate indicated thatDesulfobacteraceae,Desulfobulbaceae, andSyntrophaceae-related sulfate reducers were the most abundant. QuantifyingdsrBtranscripts of the individual populations suggested thatDesulfobacteraceaeinitially had higherdsrBtranscripts per cell thanDesulfobulbaceaeorSyntrophaceaepopulations and that the activity ofDesulfobacteraceaeincreased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast,dsrBtranscript abundance inDesulfobulbaceaeandSyntrophaceaeremained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in theDesulfobacteraceaewas consistent with the finding thatDesulfobacteraceaebecame the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline indsrBtranscript abundance in theDesulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.

scholarly journals Transcriptomic and Genetic Analysis of Direct Interspecies Electron Transfer

2013 ◽  
Vol 79 (7) ◽  
pp. 2397-2404 ◽  
Author(s):  
Pravin Malla Shrestha ◽  
Amelia-Elena Rotaru ◽  
Zarath M. Summers ◽  
Minita Shrestha ◽  
Fanghua Liu ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Expression Patterns ◽  
Transcript Abundance ◽  
Geobacter Sulfurreducens ◽  
Acetate Metabolism ◽  
Gene Transcript ◽  
Content Type ◽  
Direct Interspecies Electron Transfer ◽  
Interspecies Electron Transfer ◽  
Pilin Gene

ABSTRACTThe possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in whichGeobacter sulfurreducenswas the electron-accepting partner for eitherGeobacter metallireducens, which performs DIET, orPelobacter carbinolicus, which relies on HIT. Transcript abundance forG. sulfurreducensuptake hydrogenase genes was 7-fold lower in cocultures withG. metallireducensthan in cocultures withP. carbinolicus, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures withG. metallireducensthan in cocultures withP. carbinolicus. The pilin genepilAwas moderately expressed despite a mutation that might be expected to represspilAexpression. Lower transcript abundance forG. sulfurreducensgenes associated with acetate metabolism in the cocultures withP. carbinolicuswas consistent with the repression of these genes by H2during HIT. Genes for the biogenesis of pili and flagella and severalc-type cytochrome genes were among the most highly expressed inG. metallireducens. Mutant strains that lacked the ability to produce pili, flagella, or the outer surfacec-type cytochrome encoded by Gmet_2896 were not able to form cocultures withG. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.

scholarly journals Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Annette Summers Engel ◽  
Chang Liu ◽  
Audrey T. Paterson ◽  
Laurie C. Anderson ◽  
R. Eugene Turner ◽  
...  
Keyword(s):  
Oil Spill ◽  
Salt Marshes ◽  
Bacterial Communities ◽  
Deepwater Horizon ◽  
Environmental Stressors ◽  
Marine Phytoplankton ◽  
Rrna Gene ◽  
Content Type ◽  
Coastal Salt Marshes

ABSTRACT Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria (Rhizobiales), Chloroflexi (Dehalococcoidia), and Planctomycetes. Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts. IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The Deepwater Horizon oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to in situ environmental changes, aside from oil exposure.

scholarly journals Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuhua Zhan ◽  
Cortland Griswold ◽  
Lewis Lukens
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Reference Genome ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Rna Seq ◽  
Individual Genome ◽  
Abundance Estimates ◽  
Mapping Bias ◽  
Quantify Gene Expression

Abstract Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species.

Coastal Salt Marshes

2020 ◽  
pp. 1-39
Author(s):  
Maria Sarika ◽  
Andreas Zikos
Keyword(s):  
Salt Marshes ◽  
Coastal Salt Marshes

scholarly journals Interplay of Nitric Oxide Synthase (NOS) and SrrAB in Modulation ofStaphylococcus aureusMetabolism and Virulence

2018 ◽  
Vol 87 (2) ◽  
Author(s):  
Kimberly L. James ◽  
Austin B. Mogen ◽  
Jessica N. Brandwein ◽  
Silvia S. Orsini ◽  
Miranda J. Ridder ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitric Oxide Synthase ◽  
Double Mutant ◽  
Nitrate Assimilation ◽  
Arginine Deiminase ◽  
Growth Defect ◽  
Content Type ◽  
Metabolic Versatility ◽  
Oxide Synthase

ABSTRACTStaphylococcus aureusnitric oxide synthase (saNOS) is a major contributor to virulence, stress resistance, and physiology, yet the specific mechanism(s) by which saNOS intersects with other known regulatory circuits is largely unknown. The SrrAB two-component system, which modulates gene expression in response to the reduced state of respiratory menaquinones, is a positive regulator ofnosexpression. Several SrrAB-regulated genes were also previously shown to be induced in an aerobically respiringnosmutant, suggesting a potential interplay between saNOS and SrrAB. Therefore, a combination of genetic, molecular, and physiological approaches was employed to characterize anos srrABmutant, which had significant reductions in the maximum specific growth rate and oxygen consumption when cultured under conditions promoting aerobic respiration. Thenos srrABmutant secreted elevated lactate levels, correlating with the increased transcription of lactate dehydrogenases. Expression of nitrate and nitrite reductase genes was also significantly enhanced in thenos srrABdouble mutant, and its aerobic growth defect could be partially rescued with supplementation with nitrate, nitrite, or ammonia. Furthermore, elevated ornithine and citrulline levels and highly upregulated expression of arginine deiminase genes were observed in the double mutant. These data suggest that a dual deficiency in saNOS and SrrAB limitsS. aureusto fermentative metabolism, with a reliance on nitrate assimilation and the urea cycle to help fuel energy production. Thenos,srrAB, andnos srrABmutants showed comparable defects in endothelial intracellular survival, whereas thesrrABandnos srrABmutants were highly attenuated during murine sepsis, suggesting that SrrAB-mediated metabolic versatility is dominantin vivo.

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