Cross-Feeding between Members of Thauera spp. and Rhodococcus spp. Drives Quinoline-Denitrifying Degradation in a Hypoxic Bioreactor

ABSTRACT The complex bacterial community in a quinoline-degrading denitrifying bioreactor is predominated by several taxa, such as Thauera and Rhodococcus. However, it remains unclear how the interactions between the different bacteria mediate quinoline metabolism under denitrifying conditions. In this study, we designed a sequence-specific amplification strategy to isolate the most predominant bacteria and obtained four strains of Thauera aminoaromatica, a representative of a key member in the bioreactor. Tests on these isolates demonstrated that all were unable to degrade quinoline but efficiently degraded 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing conditions. However, another isolate, Rhodococcus sp. YF3, corresponding to the second most abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 largely varied according to the quantity of available oxygen. Specifically, quinoline could be converted only to 2-hydroxyquinoline without further transformation under insufficient oxygen conditions, e.g., less than 0.5% initial oxygen in the vials. However, resting YF3 cells aerobically precultured in medium with quinoline could anaerobically convert quinoline to 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated efficient denitrifying degradation of quinoline. Thus, we experimentally verified that the metabolic interaction based on 2-hydroxyquinoline cross-feeding between two predominant bacteria constitutes the main quinoline degradation mechanism. This work uncovers the mechanism of quinoline removal by two cooperative bacterial species existing in denitrifying bioreactors. IMPORTANCE We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

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Cross-feeding between Thauera aminoaromatica and Rhodococcus pyridinivorans drove quinoline biodegradation in a denitrifying bioreactor

10.1101/2020.01.31.929745 ◽

2020 ◽

Author(s):

Xinxin Wu ◽

Xiaogang Wu ◽

Ji Li ◽

Qiaoyu Wu ◽

Yiming Ma ◽

...

Keyword(s):

Heterocyclic Compounds ◽

Removal Rate ◽

Resting Cells ◽

Intermediate Metabolites ◽

End Products ◽

Initial Oxygen ◽

Significant Step ◽

Abundant Taxon ◽

Specific Amplification ◽

Microbial Mechanism

AbstractThe complex bacterial community is predominated by several taxa, such as Thauera and Rhodococcus, in a quinoline-degrading denitrifying bioreactor. Yet it remains unclear about how the interactions between the different bacteria mediate the quinoline metabolism in denitrifying condition. In this study, we designed a sequence-specific amplification to guide the isolation of the most predominant bacteria and obtained four strains of Thauera aminoaromatica, the representative of one key member in the bioreactor. Test on these isolates demonstrated that all of them were unable to strive on quinoline but could efficiently degrade 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing condition. However, another isolate, Rhodococcus pyridinivorans YF3, corresponding to the second abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 were largely varied with the quantity of available oxygen. Specifically, quinoline could only be converted into 2-hydroxyquinoline without further transformation under the condition with insufficient oxygen, e.g. less than 0.5% initial oxygen in the vials. However, if were aerobically pre-cultured in the medium with quinoline the resting cells of YF3 could anaerobically convert quinoline into 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated an efficient denitrifying degradation of quinoline. Thus, we experimentally proved that the metabolism interaction based on the 2-hydroxyquinoline cross-feeding between two predominant bacteria constituted the mainstream of quinoline degradation. This work sheds light on the understanding of mechanism of quinoline removal in the denitrifying bioreactor.ImportanceWe experimentally verified the most predominant Thauera sp. was indeed active degrader for the intermediate metabolites and the second abundant taxon Rhodococcus exerted, however, key function for opening the food box for a complex quinoline-degrading community. An ecological guild composed of two isolates was assembled, revealing the different roles of keystone organisms in the microbial community. This study, to our best knowledge, is the first report on the cross feeding between the initial attacker with unprofitable catalysis of reluctant heterocyclic compounds and the second bacterium which then completely degrade the compound transformed by the first bacterium. These results could be a significant step forward towards elucidation of microbial mechanism for quinoline denitrifying degradation.

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Parameters for Measuring the Activity and Viability of Activated Sludge

Water Quality Research Journal ◽

10.2166/wqrj.1974.022 ◽

1974 ◽

Vol 9 (1) ◽

pp. 235-249 ◽

Cited By ~ 1

Author(s):

S.G. Nutt ◽

K.L. Murphy

Keyword(s):

Organic Carbon ◽

Activated Sludge ◽

Biological System ◽

Analytical Methods ◽

Heterogeneous System ◽

Removal Rate ◽

Bacterial Species ◽

Atp Content ◽

Culture Studies ◽

Activated Sludge System

Abstract Conventional wastewater parameters are accepted as inadequate estimates of the condition of activated sludge but numerous other indices have been suggested as specific measurements of the activity and viability of the biomass. Literature in the related fields of microbiology and biochemistry were reviewed in order to select the most appropriate activity parameters for application to a heterogeneous biological material. Modified analytical methods were applied to a well-controlled biological system containing a single predominant bacterial species to evaluate the relative merit of each as an indicator of viability and activity. The potential of each parameter in a complex heterogeneous system was determined by monitoring each index in a bench activated sludge system. The predominant culture studies indicated that the ATP content of the biomass and the dehydrogenase activity were potential indicators of cell viability in a simple system. However, in the complex activated sludge system, only the ATP content showed significant correlation to the organic carbon removal rate.

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Biodegradation rates of aromatic contaminants in biofilm reactors

Water Science & Technology ◽

10.2166/wst.1995.0027 ◽

1995 ◽

Vol 31 (1) ◽

pp. 117-128 ◽

Cited By ~ 8

Author(s):

Jean-Pierre Arcangeli ◽

Erik Arvin

Keyword(s):

Aromatic Hydrocarbons ◽

Competitive Inhibition ◽

Removal Rate ◽

First Order ◽

Biofilm Reactors ◽

First Order Kinetics ◽

Reducing Conditions ◽

Low Concentrations ◽

Degradation Rates ◽

Order Surface

This study has shown that microorganisms can adapt to degrade mixtures of aromatic pollutants at relatively high rates in the μg/l concentration range. The biodegradation rates of the following compounds were investigated in biofilm systems: aromatic hydrocarbons, phenol, methylphenols, chlorophenols, nitrophenol, chlorobenzenes and aromatic nitrogen-, sulphur- or oxygen-containing heterocyclic compounds (NSO-compounds). Furthermore, a comparison with degradation rates observed for easily degradable organics is also presented. At concentrations below 20-100 μg/l the degradation of the aromatic compounds was typically controlled by first order kinetics. The first-order surface removal rate constants were surprisingly similar, ranging from 2 to 4 m/d. It appears that NSO-compounds inhibit the degradation of aromatic hydrocarbons, even at very low concentrations of NSO-compounds. Under nitrate-reducing conditions, toluene was easily biodegraded. The xylenes and ethylbenzene were degraded cometabolically if toluene was used as a primary carbon source; their removal was influenced by competitive inhibition with toluene. These interaction phenomena are discussed in this paper and a kinetic model taking into account cometabolism and competitive inhibition is proposed.

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Pyrometallurgical Lithium-Ion-Battery Recycling: Approach to Limiting Lithium Slagging with the InduRed Reactor Concept

Processes ◽

10.3390/pr9010084 ◽

2021 ◽

Vol 9 (1) ◽

pp. 84

Author(s):

Stefan Windisch-Kern ◽

Alexandra Holzer ◽

Christoph Ponak ◽

Harald Raupenstrauch

Keyword(s):

Removal Rate ◽

Oxygen Affinity ◽

Lithium Ion ◽

Transfer Coefficients ◽

Scanning Calorimetry ◽

Recycling Industry ◽

Reducing Conditions ◽

Novel Approach ◽

Input Material ◽

High Oxygen Affinity

The complexity of the waste stream of spent lithium-ion batteries poses numerous challenges on the recycling industry. Pyrometallurgical recycling processes have a lot of benefits but are not able to recover lithium from the black matter since lithium is slagged due to its high oxygen affinity. The presented InduRed reactor concept might be a promising novel approach, since it does not have this disadvantage and is very flexible concerning the chemical composition of the input material. To prove its basic suitability for black matter processing, heating microscope experiments, thermogravimetric analysis and differential scanning calorimetry have been conducted to characterize the behavior of nickel rich cathode materials (LiNi0.8Co0.15Al0.05O2 and LiNi0.33Mn0.33Co0.33O2) as well as black matter from a pretreatment process under reducing conditions. Another experimental series in a lab scale InduRed reactor was further used to investigate achievable transfer coefficients for the metals of interest. The promising results show technically feasible reaction temperatures of 800 ∘C to 1000 ∘C and high recovery potentials for nickel, cobalt and manganese. Furthermore, the slagging of lithium was largely prevented and a lithium removal rate of up to 90% of its initial mass was achieved.

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Overcoming the capital investment hurdle in worker-controlled firms

Journal of Participation and Employee Ownership ◽

10.1108/jpeo-01-2019-0001 ◽

2019 ◽

Vol 2 (2) ◽

pp. 133-150

Author(s):

Guy Major ◽

Jonathan Preminger

Keyword(s):

Capital Investment ◽

Value Added ◽

Employee Ownership ◽

Workplace Democracy ◽

Equity Investment ◽

Content Type ◽

Academic Literature ◽

Worker Ownership ◽

Significant Step ◽

Average Worker

Purpose Both the academic literature and practitioners have long noted the need for an equity investment mechanism for worker-controlled firms that alleviates investor anxieties without undermining internal workplace democracy. The purpose of this paper is to outline one such possible mechanism. Design/methodology/approach The proposal locks together the interests of workers and external investors, via non-voting shares with dividends set by a pre-agreed value-added sharing formula. Each worker is paid a base wage, with the average across the firm being a pre-defined multiple of the national minimum wage. Any additional surplus is split into a number of equal “slices”, with each share receiving one slice as its dividend, and the average worker receiving a pre-agreed number of slices as a bonus. Findings Workers have an incentive to maximise their own incomes, and in so doing, will also automatically maximise the dividends received by investors, obviating the need for the shares to have normal voting rights. Working on this principle of aligned interests, the authors also discuss reinvestment, worker ownership of non-voting shares and possibilities for a secondary share market. The authors show how this proposal will be a significant step in aligning the interests of investors with owner-workers in a democratic, negotiated way that shares both risk and returns, thus making worker-controlled firms more attractive to equity investment. Originality/value In light of the recognised problem of underinvestment in worker-controlled firms and the risk of their degeneration, this paper will interest both academics and practitioners in employee ownership, co-operatives and various forms of workplace democracy.

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Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate

Applied and Environmental Microbiology ◽

10.1128/aem.02920-14 ◽

2014 ◽

Vol 81 (1) ◽

pp. 130-138 ◽

Cited By ~ 30

Author(s):

James Kirby ◽

Minobu Nishimoto ◽

Ruthie W. N. Chow ◽

Edward E. K. Baidoo ◽

George Wang ◽

...

Keyword(s):

Bacterial Species ◽

Xylose Reductase ◽

Pentose Phosphate ◽

Terpene Biosynthesis ◽

Content Type ◽

E Coli ◽

Pathway Expression ◽

Terpene Synthesis ◽

Selection For

ABSTRACTTerpene synthesis in the majority of bacterial species, together with plant plastids, takes place via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. The first step of this pathway involves the condensation of pyruvate and glyceraldehyde 3-phosphate by DXP synthase (Dxs), with one-sixth of the carbon lost as CO2. A hypothetical novel route from a pentose phosphate to DXP (nDXP) could enable a more direct pathway from C5sugars to terpenes and also circumvent regulatory mechanisms that control Dxs, but there is no enzyme known that can convert a sugar into its 1-deoxy equivalent. Employing a selection for complementation of adxsdeletion inEscherichia coligrown on xylose as the sole carbon source, we uncovered two candidate nDXP genes. Complementation was achieved either via overexpression of the wild-typeE. coliyajOgene, annotated as a putative xylose reductase, or via various mutations in the nativeribBgene.In vitroanalysis performed with purified YajO and mutant RibB proteins revealed that DXP was synthesized in both cases from ribulose 5-phosphate (Ru5P). We demonstrate the utility of these genes for microbial terpene biosynthesis by engineering the DXP pathway inE. colifor production of the sesquiterpene bisabolene, a candidate biodiesel. To further improve flux into the pathway from Ru5P, nDXP enzymes were expressed as fusions to DXP reductase (Dxr), the second enzyme in the DXP pathway. Expression of a Dxr-RibB(G108S) fusion improved bisabolene titers more than 4-fold and alleviated accumulation of intracellular DXP.

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hfqPlays Important Roles in Virulence and Stress Adaptation in Cronobacter sakazakii ATCC 29544

Infection and Immunity ◽

10.1128/iai.03161-14 ◽

2015 ◽

Vol 83 (5) ◽

pp. 2089-2098 ◽

Cited By ~ 21

Author(s):

Seongok Kim ◽

Hyelyeon Hwang ◽

Kwang-Pyo Kim ◽

Hyunjin Yoon ◽

Dong-Hyun Kang ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Bacterial Species ◽

Soft Agar ◽

Host Cells ◽

Neonatal Meningitis ◽

Animal Cells ◽

Content Type ◽

Flagellar Biosynthesis

Cronobacterspp. are opportunistic pathogens that cause neonatal meningitis and sepsis with high mortality in neonates. Despite the peril associated withCronobacterinfection, the mechanisms of pathogenesis are still being unraveled. Hfq, which is known as an RNA chaperone, participates in the interaction with bacterial small RNAs (sRNAs) to regulate posttranscriptionally the expression of various genes. Recent studies have demonstrated that Hfq contributes to the pathogenesis of numerous species of bacteria, and its roles are varied between bacterial species. Here, we tried to elucidate the role of Hfq inC. sakazakiivirulence. In the absence ofhfq,C. sakazakiiwas highly attenuated in disseminationin vivo, showed defects in invasion (3-fold) into animal cells and survival (103-fold) within host cells, and exhibited low resistance to hydrogen peroxide (102-fold). Remarkably, the loss ofhfqled to hypermotility on soft agar, which is contrary to what has been observed in other pathogenic bacteria. The hyperflagellated bacteria were likely to be attributable to the increased transcription of genes associated with flagellar biosynthesis in a strain lackinghfq. Together, these data strongly suggest thathfqplays important roles in the virulence ofC. sakazakiiby participating in the regulation of multiple genes.

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An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽

10.1128/mbio.00309-12 ◽

2012 ◽

Vol 3 (5) ◽

Cited By ~ 52

Author(s):

Peter Jorth ◽

Marvin Whiteley

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Bacterial Diversity ◽

Natural Transformation ◽

Bacterial Species ◽

Comparative Genomic ◽

Content Type ◽

Immune Systems ◽

Adaptive Immune ◽

Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

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The Putative Eukaryote-LikeO-GlcNAc Transferase of the Cyanobacterium Synechococcus elongatus PCC 7942 Hydrolyzes UDP-GlcNAc and Is Involved in Multiple Cellular Processes

Journal of Bacteriology ◽

10.1128/jb.01948-14 ◽

2014 ◽

Vol 197 (2) ◽

pp. 354-361 ◽

Cited By ~ 5

Author(s):

Kerry A. Sokol ◽

Neil E. Olszewski

Keyword(s):

Deletion Mutant ◽

Bacterial Species ◽

Synechococcus Elongatus ◽

Single Amino Acid ◽

Content Type ◽

Cellular Processes ◽

Mutant Phenotypes ◽

Glcnac Transferase ◽

Pcc 7942 ◽

Mutant Cells

The posttranslational addition of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine or threonine residues regulates numerous metazoan cellular processes. The enzyme responsible for this modification,O-GlcNAc transferase (OGT), is conserved among a wide variety of organisms and is critical for the viability of many eukaryotes. Although OGTs with domain structures similar to those of eukaryotic OGTs are predicted for many bacterial species, the cellular roles of these OGTs are unknown. We have identified a putative OGT in the cyanobacteriumSynechococcus elongatusPCC 7942 that shows active-site homology and similar domain structure to eukaryotic OGTs. An OGT deletion mutant was created and found to exhibit several phenotypes. Without agitation, mutant cells aggregate and settle out of the medium. The mutant cells have higher free inorganic phosphate levels, wider thylakoid lumen, and differential accumulation of electron-dense inclusion bodies. These phenotypes are rescued by reintroduction of the wild-type OGT but are not fully rescued by OGTs with single amino acid substitutions corresponding to mutations that reduce eukaryotic OGT activity.S. elongatusOGT purified fromEscherichia colihydrolyzed the sugar donor, UDP-GlcNAc, while the mutant OGTs that did not fully rescue the deletion mutant phenotypes had reduced or no activity. These results suggest that bacterial eukaryote-like OGTs, like their eukaryotic counterparts, influence multiple processes.

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Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

Applied and Environmental Microbiology ◽

10.1128/aem.03001-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 177-183 ◽

Cited By ~ 10

Author(s):

Lavane Kim ◽

Eulyn Pagaling ◽

Yi Y. Zuo ◽

Tao Yan

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Bacterial Species ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Content Type ◽

Property Change ◽

And Control ◽

Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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