In silico Selection and Experimental Validation of FDA-Approved Drugs as Anti-quorum Sensing Agents.
Mellini M1, Di Muzio E1, D'Angelo F1, Baldelli V1, Ferrillo S1, Visca P1, Leoni L1, Polticelli F1,2, Rampioni G1.
Author information
1
Department of Science, University Roma Tre, Rome, Italy.
2
National Institute of Nuclear Physics, Roma Tre Section, Rome, Italy.
Abstract
The emergence of antibiotic resistant bacterial pathogens is increasing at an unprecedented pace, calling for the development of new therapeutic options. Small molecules interfering with virulence processes rather than growth hold promise as an alternative to conventional antibiotics. Anti-virulence agents are expected to decrease bacterial virulence and to pose reduced selective pressure for the emergence of resistance. In the opportunistic pathogen Pseudomonas aeruginosa the expression of key virulence traits is controlled by quorum sensing (QS), an intercellular communication process that coordinates gene expression at the population level. Hence, QS inhibitors represent promising anti-virulence agents against P. aeruginosa. Virtual screenings allow fast and cost-effective selection of target ligands among vast libraries of molecules, thus accelerating the time and limiting the cost of conventional drug-discovery processes, while the drug-repurposing approach is based on the identification of off-target activity of FDA-approved drugs, likely endowed with low cytotoxicity and favorable pharmacological properties. This study aims at combining the advantages of virtual screening and drug-repurposing approaches to identify new QS inhibitors targeting the pqs QS system of P. aeruginosa. An in silico library of 1,467 FDA-approved drugs has been screened by molecular docking, and 5 hits showing the highest predicted binding affinity for the pqs QS receptor PqsR (also known as MvfR) have been selected. In vitro experiments have been performed by engineering ad hoc biosensor strains, which were used to verify the ability of hit compounds to decrease PqsR activity in P. aeruginosa. Phenotypic analyses confirmed the impact of the most promising hit, the antipsychotic drug pimozide, on the expression of P. aeruginosa PqsR-controlled virulence traits. Overall, this study highlights the potential of virtual screening campaigns of FDA-approved drugs to rapidly select new inhibitors of important bacterial functions.

Copyright © 2019 Mellini, Di Muzio, D’Angelo, Baldelli, Ferrillo, Visca, Leoni, Polticelli and Rampioni.

KEYWORDS:
PqsR; Pseudomonas aeruginosa; anti-virulence strategy; in silico screening; molecular docking; new therapeutics; pimozide; quorum sensing inhibition

PMID: 31649658 PMCID: PMC6796623 DOI: 10.3389/fmicb.2019.02355
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2.
Front Microbiol. 2019 Oct 9;10:2336. doi: 10.3389/fmicb.2019.02336. eCollection 2019.
Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii.
Wang Z1,2, Jiang Y1,2, Wu H1, Xie X1, Huang B1.
Author information
1
Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.
2
School of Plant Protection, Anhui Agricultural University, Hefei, China.
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in stress responses. To date, only a few studies have reported the role of lncRNAs in insect-pathogenic fungi. Here, we report a genome-wide transcriptional analysis of lncRNAs produced in response to heat stress in Metarhizium robertsii, a model insect-pathogenic fungus, using strand-specific RNA sequencing. A total of 1655 lncRNAs with 1742 isoforms were identified, of which 1081 differentially expressed (DE) lncRNAs were characterized as being heat responsive. By characterizing their genomic structures and expression patterns, we found that the lncRNAs possessed shorter transcripts, fewer exons, and lower expression levels than the protein-coding genes in M. robertsii. Furthermore, target prediction analysis of the lncRNAs revealed thousands of potential DE lncRNA-messenger RNA (mRNA) pairs, among which 5381 pairs function in the cis-regulatory mode. Further pathway enrichment analysis of the corresponding cis-regulated target genes showed that the targets were significantly enriched in the following biological pathways: the Hippo signaling pathway and cell cycle. This finding suggested that these DE lncRNAs control the expression of their corresponding neighboring genes primarily through environmental information processing and cellular processes. Moreover, only 26 trans-regulated lncRNA-mRNA pairs were determined. In addition, among the targets of heat-responsive lncRNAs, two classic genes that may be involved in the response to heat stress were also identified, including hsp70 (XM_007821830 and XM_007825705). These findings expand our knowledge of lncRNAs as important regulators of the response to heat stress in filamentous fungi, including M. robertsii.

Copyright © 2019 Wang, Jiang, Wu, Xie and Huang.

KEYWORDS:
Metarhizium robertsii; RNA-seq; heat stress; long non-coding RNAs; transcriptional profiling

PMID: 31649657 PMCID: PMC6794563 DOI: 10.3389/fmicb.2019.02336
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3.
Front Microbiol. 2019 Oct 10;10:2330. doi: 10.3389/fmicb.2019.02330. eCollection 2019.
Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition.
Epp Schmidt DJ1, Kotze DJ2, Hornung E3, Setälä H2, Yesilonis I4, Szlavecz K5, Dombos M6, Pouyat R7, Cilliers S8, Tóth Z3, Yarwood S1.
Author information
1
Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States.
2
Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland.
3
Department of Ecology, University of Veterinary Science, Budapest, Hungary.
4
Baltimore Ecosystem Study, USDA Forest Service, Baltimore, MD, United States.
5
Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, United States.
6
Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
7
Northern Research Station, University of Delaware, Newark, DE, United States.
8
Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
Abstract
Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.

Copyright © 2019 Epp Schmidt, Kotze, Hornung, Setälä, Yesilonis, Szlavecz, Dombos, Pouyat, Cilliers, Tóth and Yarwood.

KEYWORDS:
DNRA; Ni-Fe hydrogenase; ammonia oxidation; methanogenesis; microbiology; nitrification; soil metagenomics; urban

PMID: 31649656 PMCID: PMC6795690 DOI: 10.3389/fmicb.2019.02330
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4.
Front Microbiol. 2019 Oct 9;10:2329. doi: 10.3389/fmicb.2019.02329. eCollection 2019.
Chlamydial Infection From Outside to Inside.
Gitsels A1, Sanders N2, Vanrompay D1.
Author information
1
Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
2
Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
Abstract
Chlamydia are obligate intracellular bacteria, characterized by a unique biphasic developmental cycle. Specific interactions with the host cell are crucial for the bacteria's survival and amplification because of the reduced chlamydial genome. At the start of infection, pathogen-host interactions are set in place in order for Chlamydia to enter the host cell and reach the nutrient-rich peri-Golgi region. Once intracellular localization is established, interactions with organelles and pathways of the host cell enable the necessary hijacking of host-derived nutrients. Detailed information on the aforementioned processes will increase our understanding on the intracellular pathogenesis of chlamydiae and hence might lead to new strategies to battle chlamydial infection. This review summarizes how chlamydiae generate their intracellular niche in the host cell, acquire host-derived nutrients in order to enable their growth and finally exit the host cell in order to infect new cells. Moreover, the evolution in the development of molecular genetic tools, necessary for studying the chlamydial infection biology in more depth, is discussed in great detail.

Copyright © 2019 Gitsels, Sanders and Vanrompay.

KEYWORDS:
Chlamydia; inclusion membrane proteins; internalization; non-vesicular pathways; pathogen–host cell interactions; vesicular pathways

PMID: 31649655 PMCID: PMC6795091 DOI: 10.3389/fmicb.2019.02329
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5.
Front Microbiol. 2019 Oct 10;10:2323. doi: 10.3389/fmicb.2019.02323. eCollection 2019.
Alteration of Methanogenic Archaeon by Ethanol Contribute to the Enhancement of Biogenic Methane Production of Lignite.
Yang X1, Liang Q1, Chen Y1, Wang B2,3.
Author information
1
Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China.
2
State Key Laboratory of Coal and CBM Co-Mining, Jincheng, China.
3
Yi'an Lanyan Coal and Coalbed Methane Simultaneous Extraction Technology Co., Ltd., Jincheng, China.
Abstract
Bioconverting coal to methane is a green and environmental friendly method to reuse waste coal. In this study, heterologous bacteria were used for the gas-producing fermentation of lignite under laboratory conditions, simultaneously, different concentrations of ethanol added into the culture to investigate the effect of ethanol on gas production and microbial flora structure. Results show that when the ethanol concentration was 1%, the best methanogenesis was achieved at 44.86 mL/g, which was twice the gas production of 0% ethanol. Before and after gas fermentation, the composition and structure of the coal changed, the volatile matter and fixed carbon increased, and the ash decreased. The absorbance value at characteristic peaks of all functional groups decreased, new peaks were generated at 2,300/cm, and the peak value disappeared at 3,375/cm. Thus, microorganisms interacted with coal, consumed it, and produced new materials. The microbial flora changes during gas production were tracked in real time. 0.5 and 1% ethanol did not obviously change the bacterial communities but strongly influenced the archaeon communities, thereby changed the methane production pathway. In the absence of ethanol, Methanosarcina was continuously increasing with the extension of fermentation time, this pathway was the nutrient type of acetic acid. When ethanol was added, Methanobacterium gradually increased, the pathway was mainly hydrotropic type. In summary, adding ethanol can increase the coalbed methane production, change the structure and composition of coal, and facilitate the interaction of microbe with coal. Therefore, the methanogenic archaeon changes could help improve the methane-producing ability of lignite in the presence of ethanol.

Copyright © 2019 Yang, Liang, Chen and Wang.

KEYWORDS:
coalbed methane (CBM); enhanced biogenic methane; ethanol; microbial community; physicochemical property

PMID: 31649654 PMCID: PMC6796574 DOI: 10.3389/fmicb.2019.02323
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6.
Front Microbiol. 2019 Oct 9;10:2322. doi: 10.3389/fmicb.2019.02322. eCollection 2019.
Seeding Public Goods Is Essential for Maintaining Cooperation in Pseudomonas aeruginosa.
Loarca D1, Díaz D1, Quezada H2, Guzmán-Ortiz AL2, Rebollar-Ruiz A3, Presas AMF1, Ramírez-Peris J1,4, Franco-Cendejas R5, Maeda T6, Wood TK7, García-Contreras R1.
Author information
1
Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
2
Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.
3
Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico.
4
Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Mexico City, Mexico.
5
División de Infectología, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, Mexico.
6
Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan.
7
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States.
Abstract
Quorum sensing in Pseudomonas aeruginosa controls the production of costly public goods such as exoproteases. This cooperative behavior is susceptible to social cheating by mutants that do not invest in the exoprotease production but assimilate the amino acids and peptides derived by the hydrolysis of proteins in the extracellular media. In sequential cultures with protein as the sole carbon source, these social cheaters are readily selected and often reach equilibrium with the exoprotease producers. Nevertheless, an excess of cheaters causes the collapse of population growth. In this work, using the reference strain PA14 and a clinical isolate from a burn patient, we demonstrate that the initial amount of public goods (exoprotease) that comes with the inoculum in each sequential culture is essential for maintaining population growth and that eliminating the exoprotease in the inoculum leads to rapid population collapse. Therefore, our results suggest that sequential washes should be combined with public good inhibitors to more effectively combat P. aeruginosa infections.

Copyright © 2019 Loarca, Díaz, Quezada, Guzmán-Ortiz, Rebollar-Ruiz, Presas, Ramírez-Peris, Franco-Cendejas, Maeda, Wood and García-Contreras.

KEYWORDS:
Pseudomonas aeruginosa; public goods; quorum sensing; social cheating; tragedy of the commons

PMID: 31649653 PMCID: PMC6794470 DOI: 10.3389/fmicb.2019.02322
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7.
Front Microbiol. 2019 Oct 9;10:2321. doi: 10.3389/fmicb.2019.02321. eCollection 2019.
Variants of the Bacillus subtilis LysR-Type Regulator GltC With Altered Activator and Repressor Function.
Dormeyer M1, Lentes S1, Richts B1, Heermann R2, Ischebeck T3, Commichau FM1.
Author information
1
Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany.
2
Institut für Molekulare Physiologie, Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, Mainz, Germany.
3
Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany.
Abstract
The Gram-positive soil bacterium Bacillus subtilis relies on the glutamine synthetase and the glutamate synthase for glutamate biosynthesis from ammonium and 2-oxoglutarate. During growth with the carbon source glucose, the LysR-type transcriptional regulator GltC activates the expression of the gltAB glutamate synthase genes. With excess of intracellular glutamate, the gltAB genes are not transcribed because the glutamate-degrading glutamate dehydrogenases (GDHs) inhibit GltC. Previous in vitro studies revealed that 2-oxoglutarate and glutamate stimulate the activator and repressor function, respectively, of GltC. Here, we have isolated GltC variants with enhanced activator or repressor function. The majority of the GltC variants with enhanced activator function differentially responded to the GDHs and to glutamate. The GltC variants with enhanced repressor function were still capable of activating the P gltA promoter in the absence of a GDH. Using P gltA promoter variants (P gltA ∗ ) that are active independent of GltC, we show that the wild type GltC and the GltC variants with enhanced repressor function inactivate P gltA ∗ promoters in the presence of the native GDHs. These findings suggest that GltC may also act as a repressor of the gltAB genes in vivo. We discuss a model combining previous models that were derived from in vivo and in vitro experiments.

Copyright © 2019 Dormeyer, Lentes, Richts, Heermann, Ischebeck and Commichau.

KEYWORDS:
glutamate biosynthesis; glutamate dehydrogenase; mutational analysis; promoter; trigger enzyme

PMID: 31649652 PMCID: PMC6794564 DOI: 10.3389/fmicb.2019.02321
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8.
Front Microbiol. 2019 Oct 9;10:2313. doi: 10.3389/fmicb.2019.02313. eCollection 2019.
MYH9 Aggregation Induced by Direct Interaction With PRRSV GP5 Ectodomain Facilitates Viral Internalization by Permissive Cells.
Xue B1, Hou G1, Zhang G1, Huang J1, Li L1, Nan Y1, Mu Y1, Wang L1, Zhang L1, Han X1, Ren X1, Zhao Q1, Wu C1, Wang J2, Zhou EM1.
Author information
1
College of Veterinary Medicine, Northwest A&F University, Xianyang, China.
2
State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
Abstract
Prevention and control of infection by porcine reproductive and respiratory syndrome virus (PRRSV) remains a challenge, due to our limited understanding of the PRRSV invasion mechanism. Our previous study has shown that PRRSV glycoprotein GP5 interacts with MYH9 C-terminal domain protein (PRA). Here we defined that the first ectodomain of GP5 (GP5-ecto-1) directly interacted with PRA and this interaction triggered PRA and endogenous MYH9 to form filament assembly. More importantly, MYH9 filament assembly was also formed in GP5-ecto-1-transfected MARC-145 cells. Notably, PRRSV infection of MARC-145 cells and porcine alveolar macrophages also induced endogenous MYH9 aggregation and polymerization that were required for subsequent PRRSV internalization. Moreover, overexpression of S100A4, a MYH9-specific disassembly inducer, in MARC-145 cells significantly resulted in diminished MYH9 aggregation and marked inhibition of subsequent virion internalization and infection by both PRRSV-1 and PRRSV-2 isolates. The collective results of this work reveal a novel molecular mechanism employed by MYH9 that helps PRRSV gain entry into permissive cells.

Copyright © 2019 Xue, Hou, Zhang, Huang, Li, Nan, Mu, Wang, Zhang, Han, Ren, Zhao, Wu, Wang and Zhou.

KEYWORDS:
GP5; MYH9; PRRSV; protein–protein interaction; virus internalization

PMID: 31649651 PMCID: PMC6794372 DOI: 10.3389/fmicb.2019.02313
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9.
Front Microbiol. 2019 Oct 9;10:2311. doi: 10.3389/fmicb.2019.02311. eCollection 2019.
Pseudomonas aeruginosa-Derived Volatile Sulfur Compounds Promote Distal Aspergillus fumigatus Growth and a Synergistic Pathogen-Pathogen Interaction That Increases Pathogenicity in Co-infection.
Scott J1, Sueiro-Olivares M1, Ahmed W2,3, Heddergott C4, Zhao C1, Thomas R1, Bromley M1, Latgé JP4, Krappmann S5, Fowler S2,6, Bignell E1, Amich J1.
Author information
1
Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.
2
Respiratory and Allergy Research Group, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom.
3
Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.
4
Unité des Aspergillus, Institut Pasteur, Paris, France.
5
Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
6
NIHR Manchester Biomedical Research Centre - Manchester Academic Health Science Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.
Abstract
Pathogen-pathogen interactions in polymicrobial infections are known to directly impact, often to worsen, disease outcomes. For example, co-infection with Pseudomonas aeruginosa and Aspergillus fumigatus, respectively the most common bacterial and fungal pathogens isolated from cystic fibrosis (CF) airways, leads to a worsened prognosis. Recent studies of in vitro microbial cross-talk demonstrated that P. aeruginosa-derived volatile sulfur compounds (VSCs) can promote A. fumigatus growth in vitro. However, the mechanistic basis of such cross-talk and its physiological relevance during co-infection remains unknown. In this study we combine genetic approaches and GC-MS-mediated volatile analysis to show that A. fumigatus assimilates VSCs via cysteine (CysB)- or homocysteine (CysD)-synthase. This process is essential for utilization of VSCs as sulfur sources, since P. aeruginosa-derived VSCs trigger growth of A. fumigatus wild-type, but not of a ΔcysBΔcysD mutant, on sulfur-limiting media. P. aeruginosa produces VSCs when infecting Galleria mellonella and co-infection with A. fumigatus in this model results in a synergistic increase in mortality and of fungal and bacterial burdens. Interestingly, the increment in mortality is much greater with the A. fumigatus wild-type than with the ΔcysBΔcysD mutant. Therefore, A. fumigatus' ability to assimilate P. aeruginosa derived VSCs significantly triggers a synergistic association that increases the pathobiology of infection. Finally, we show that P. aeruginosa can promote fungal growth when growing on substrates that resemble the lung environment, which suggests that this volatile based synergism is likely to occur during co-infection of the human respiratory airways.

Copyright © 2019 Scott, Sueiro-Olivares, Ahmed, Heddergott, Zhao, Thomas, Bromley, Latgé, Krappmann, Fowler, Bignell and Amich.

KEYWORDS:
P. aeruginosa – A. fumigatus interaction; co-infection; interkingdom interaction; polymicrobial infection; volatile interaction; volatile sulfur compounds

PMID: 31649650 PMCID: PMC6794476 DOI: 10.3389/fmicb.2019.02311
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10.
Front Microbiol. 2019 Oct 9;10:2310. doi: 10.3389/fmicb.2019.02310. eCollection 2019.
Development of Potential Yeast Protein Extracts for Red Wine Clarification and Stabilization.
Gaspar LM1, Machado A1, Coutinho R1, Sousa S1, Santos R1, Xavier A2, Figueiredo M2, Teixeira MF2, Centeno F2, Simões J1.
Author information
1
Genomics Unit, Biocant, Cantanhede, Portugal.
2
PROENOL - Indústria Biotecnológica, Lda., Canelas, Portugal.
Abstract
Recently, new technologies have been combined to improve quality and sensorial diversity of wine. Several fining agents were developed to induce flocculation and sedimentation of particulate matter in wine, enhancing its clarification, and stabilization. The fining agents most commonly used are animal proteins, such as milk casein or egg albumin. However, its use is being related to food intolerance. To overcome this issue, alternative sources should be explored for use in industrial processes. In previous studies performed by our consortium, the potential of yeast protein extracts (YPE) in white wine clarification, stabilization, and curative processes was identified. Thus, the main objective of the present work is to select YPE with the potential to develop fining agents for red wine, without health risk to consumers. Therefore, five yeast strains were selected from a diversified collection of oenological yeasts, in order to produce protein extracts. Along with the fining trials, a vinification assay was performed to evaluate the maceration effect of the obtained YPE. The previously selected yeast strains were also screened for the production of the usual enzymatic activities found in commercial maceration preparations, namely polygalacturonase, cellulase, protease, and ß-glucosidase activities, in order to evaluate its potential effect on wine. Our results indicate that YPE, particularly BCVII 1, BCVII 2, and BCVII 5 were able to promote a significant brilliance increase, along with a turbidity reduction and final color improvement. In the vinification assay, BCVII 2 stands out with better results for color intensity and phenolic compounds content improvement. In what refers to enzymatic activities, BCVII 2 shows advantage over the other YPEs, due to its protease and β-glucosidase activity. We demonstrate that the selected YPEs, with emphasis on BCVII 2, may represent an efficient alternative to the commonly used fining products.

Copyright © 2019 Gaspar, Machado, Coutinho, Sousa, Santos, Xavier, Figueiredo, Teixeira, Centeno and Simões.

KEYWORDS:
color; fining agents; turbidity; vinification; wine

PMID: 31649649 PMCID: PMC6794431 DOI: 10.3389/fmicb.2019.02310
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11.
Front Microbiol. 2019 Oct 9;10:2308. doi: 10.3389/fmicb.2019.02308. eCollection 2019.
Two Phenotype-Differentiated Acinetobacter baumannii Mutants That Survived in a Meropenem Selection Display Large Differences in Their Transcription Profiles.
Gao Q1, Meng X2,3, Gu H2,3, Chen X2,3, Yang H1, Qiao Y1, Guo X2,3,4.
Author information
1
Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
2
Meizhou People's Hospital, Meizhou, China.
3
Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translation Research of Hakka Population, Meizhou, China.
4
Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.
Abstract
37662RM1 and 37662RM2 are two phenotypically different, carbapenem-resistant mutants of Acinetobacter baumannii 37662 isolate following selection with meropenem (MEM) at sub-inhibitory concentrations. 37662RM2 lacks capsule synthesis and shows dramatically increased biofilm formation, while 37662RM1 shows merely impaired capsule synthesis. Here we report that 37662RM1 and RM2 have transcription profiles that are different from those of their starting strain, 37662WT. There were far more differentially expressed genes in 37662RM2 than in 37662RM1. The capsule polysaccharide (CPS) synthesis-required genes (itrA2, gtr5, psaA, psaB, psaC, psaD, psaE, psaF, kpsS2, wzx, wzy, wza, wzb, and wzc) showed reduced transcription levels in 37662RM2, which may at least partially explain the loss of capsule synthesis. The csu operon genes responsible for pili assembly and their regulator genes bfmR-bfmS were over-expressed in 37662RM2. This result together with the established critical roles of these genes in biofilm formation provide solid evidence that up-regulation of csu and bfmR-bfmS should be considered responsible for the enhanced biofilm formation in 37662RM2. ISAba1 was found to insert into the intergenic region between the csu operon and the acrR gene and should be responsible for the significant up-regulation of acrR, which was proposed to be associated with biofilm formation. Genome sequencing revealed that the ISAba1 upstream bla OXA- 508 (a new member of bla OXA- 51-like) and acrR were duplicated, suggesting a replicative transposition event. Altogether, the phenotype divergence driven by MEM selection mainly occurs at the RNA level and the transposition of ISAba1 plays an important role in modulating gene expression to adapt to the environment.

Copyright © 2019 Gao, Meng, Gu, Chen, Yang, Qiao and Guo.

KEYWORDS:
Acinetobacter baumannii; biofilm formation; capsule synthesis; carbapenem resistance; transcription profile

PMID: 31649648 PMCID: PMC6794425 DOI: 10.3389/fmicb.2019.02308
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12.
Front Microbiol. 2019 Oct 9;10:2307. doi: 10.3389/fmicb.2019.02307. eCollection 2019.
Editorial: Engineering the Microbial Platform for the Production of Biologics and Small-Molecule Medicines.
Dhakal D1, Kim ES2, Koffas M3.
Author information
1
Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea.
2
Department of Biological Engineering, Inha University, Incheon, South Korea.
3
Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States.
KEYWORDS:
biologics and small molecule medicines; heterologous production; metabolic engineering; microbial cell factories; synthetic biology

PMID: 31649647 PMCID: PMC6794555 DOI: 10.3389/fmicb.2019.02307
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13.
Front Microbiol. 2019 Oct 9;10:2305. doi: 10.3389/fmicb.2019.02305. eCollection 2019.
Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors.
Engevik MA1,2, Morra CN1,3, Röth D4, Engevik K5, Spinler JK1,2, Devaraj S1,2, Crawford SE5, Estes MK5,6, Kalkum M4,7, Versalovic J1,2.
Author information
1
Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States.
2
Department of Pathology, Texas Children's Hospital, Houston, TX, United States.
3
Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States.
4
Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, United States.
5
Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States.
6
Department of Medicine - Gastroenterology, Hepatology and Infectious Diseases, Baylor College of Medicine, Houston, TX, United States.
7
Mass Spectrometry and Proteomics Core, Beckman Research Institute of the City of Hope, Duarte, CA, United States.
Abstract
Microbial metabolites, including B complex vitamins contribute to diverse aspects of human health. Folate, or vitamin B9, refers to a broad category of biomolecules that include pterin, para-aminobenzoic acid (pABA), and glutamate subunits. Folates are required for DNA synthesis and epigenetic regulation. In addition to dietary nutrients, the gut microbiota has been recognized as a source of B complex vitamins, including folate. This study evaluated the predicted folate synthesis capabilities in the genomes of human commensal microbes identified in the Human Microbiome Project and folate production by representative strains of six human intestinal bacterial phyla. Bacterial folate synthesis genes were ubiquitous across 512 gastrointestinal reference genomes with 13% of the genomes containing all genes required for complete de novo folate synthesis. An additional 39% of the genomes had the genetic capacity to synthesize folates in the presence of pABA, an upstream intermediate that can be obtained through diet or from other intestinal microbes. Bacterial folate synthesis was assessed during exponential and stationary phase growth through the evaluation of expression of select folate synthesis genes, quantification of total folate production, and analysis of folate polyglutamylation. Increased expression of key folate synthesis genes was apparent in exponential phase, and increased folate polyglutamylation occurred during late stationary phase. Of the folate producers, we focused on the commensal Lactobacillus reuteri to examine host-microbe interactions in relation to folate and examined folate receptors in the physiologically relevant human enteroid model. RNAseq data revealed segment-specific folate receptor distribution. Treatment of human colonoid monolayers with conditioned media (CM) from wild-type L. reuteri did not influence the expression of key folate transporters proton-coupled folate transporter (PCFT) or reduced folate carrier (RFC). However, CM from L. reuteri containing a site-specific inactivation of the folC gene, which prevents the bacteria from synthesizing a polyglutamate tail on folate, significantly upregulated RFC expression. No effects were observed using L. reuteri with a site inactivation of folC2, which results in no folate production. This work sheds light on the contributions of microbial folate to overall folate status and mammalian host metabolism.

Copyright © 2019 Engevik, Morra, Röth, Engevik, Spinler, Devaraj, Crawford, Estes, Kalkum and Versalovic.

KEYWORDS:
B vitamin; Lactobacilli; Lactobacillus reuteri; enteroids; folate transporters; folylpolyglutamate; microbiome

PMID: 31649646 PMCID: PMC6795088 DOI: 10.3389/fmicb.2019.02305
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14.
Front Microbiol. 2019 Oct 10;10:2304. doi: 10.3389/fmicb.2019.02304. eCollection 2019.
Francisella tularensis subsp. holarctica Releases Differentially Loaded Outer Membrane Vesicles Under Various Stress Conditions.
Klimentova J1, Pavkova I1, Horcickova L1, Bavlovic J1, Kofronova O2, Benada O2,3, Stulik J1.
Author information
1
Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czechia.
2
Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.
3
Faculty of Science, Jan Evangelista Purkyně University, Ústí nad Labem, Czechia.
Abstract
Francisella tularensis is a Gram-negative, facultative intracellular bacterium, causing a severe disease called tularemia. It secretes unusually shaped nanotubular outer membrane vesicles (OMV) loaded with a number of virulence factors and immunoreactive proteins. In the present study, the vesicles were purified from a clinical isolate of subsp. holarctica strain FSC200. We here provide a comprehensive proteomic characterization of OMV using a novel approach in which a comparison of OMV and membrane fraction is performed in order to find proteins selectively enriched in OMV vs. membrane. Only these proteins were further considered to be really involved in the OMV function and/or their exceptional structure. OMV were also isolated from bacteria cultured under various cultivation conditions simulating the diverse environments of F. tularensis life cycle. These included conditions mimicking the milieu inside the mammalian host during inflammation: oxidative stress, low pH, and high temperature (42°C); and in contrast, low temperature (25°C). We observed several-fold increase in vesiculation rate and significant protein cargo changes for high temperature and low pH. Further proteomic characterization of stress-derived OMV gave us an insight how the bacterium responds to the hostile environment of a mammalian host through the release of differentially loaded OMV. Among the proteins preferentially and selectively packed into OMV during stressful cultivations, the previously described virulence factors connected to the unique intracellular trafficking of Francisella were detected. Considerable changes were also observed in a number of proteins involved in the biosynthesis and metabolism of the bacterial envelope components like O-antigen, lipid A, phospholipids, and fatty acids. Data are available via ProteomeXchange with identifier PXD013074.

Copyright © 2019 Klimentova, Pavkova, Horcickova, Bavlovic, Kofronova, Benada and Stulik.

KEYWORDS:
FSC200; Francisella tularensis; host–pathogen interaction; outer membrane vesicles; stress response; virulence factor

PMID: 31649645 PMCID: PMC6795709 DOI: 10.3389/fmicb.2019.02304
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15.
Front Microbiol. 2019 Oct 10;10:2303. doi: 10.3389/fmicb.2019.02303. eCollection 2019.
Caecal Microbiota of Experimentally Campylobacter jejuni-Infected Chickens at Different Ages.
Hankel J1, Jung K2, Kuder H1, Keller B1, Keller C3, Galvez E4, Strowig T4, Visscher C1.
Author information
1
Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Hanover, Germany.
2
Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hanover, Germany.
3
Boehringer Ingelheim Veterinary Research Center GmbH & Co. KG, Hanover, Germany.
4
Helmholtz Center for Infection Research, Braunschweig, Germany.
Abstract
Campylobacter jejuni is the most common bacterial cause of foodborne zoonosis in the European Union. Infections are often linked to the consumption and handling of poultry meat. The aim of the present study was to investigate the caecal microbiota of birds infected with C. jejuni at different ages. Therefore, a total of 180 birds of the laying hybrid Lohmann Brown-Classic were housed in 12 subgroups of 15 animals each in three performed repetitions. Three birds per subgroup were experimentally infected with C. jejuni at an age of about 21 days and about 78 days (4.46 ± 0.35 log10 CFU/bird). Twenty-one days after experimental infection, microbiome studies were performed on 72 caecal samples of dissected birds (three primary infected and three further birds/subgroup). Amplification within the hypervariable region V 4 of the 16S rRNA gene was performed and sequenced with the Illumina MiSeq platform. Statistical analyses were performed using SAS® Enterprise Guide® (version 7.1) and R (version 3.5.2). Both factors, the experimental replication (p < 0.001) and the chickens' age at infection (p < 0.001) contributed significantly to the differences in microbial composition of the caecal samples. The factor experimental replication explained 24% of the sample's variability, whereas the factor age at infection explained 14% thereof. Twelve of 32 families showed a significantly different count profile between the two age groups, whereby strongest differences were seen for seven families, among them the family Campylobacteraceae (adjusted p = 0.003). The strongest difference between age groups was seen for a bacterial species that is assigned to the genus Turicibacter which in turn belongs to the family Erysipelotrichaceae (adjusted p < 0.0001). Correlation analyses revealed a common relationship in both chicken ages at infection between the absolute abundance of Campylobacteraceae and Alcaligenaceae, which consists of the genus Parasutterella. In general, concentrations of particular volatile fatty acids (VFA) demonstrated a negative correlation to absolute abundance of Campylobacteraceae, whereby the strongest link was seen for n-butyrate (-0.51141; p < 0.0001). Despite performing consecutive repetitions, the factor experimental replication contributed more to the differences of microbial composition in comparison to the factor age at infection.

Copyright © 2019 Hankel, Jung, Kuder, Keller, Keller, Galvez, Strowig and Visscher.

KEYWORDS:
16S rRNA; Campylobacter jejuni; foodborne pathogen; gut microbiota; volatile fatty acids

PMID: 31649644 PMCID: PMC6796544 DOI: 10.3389/fmicb.2019.02303
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16.
Front Microbiol. 2019 Oct 9;10:2302. doi: 10.3389/fmicb.2019.02302. eCollection 2019.
Exploring the Link Between the Geographical Origin of European Fermented Foods and the Diversity of Their Bacterial Communities: The Case of Fermented Meats.
Van Reckem E1, Geeraerts W1, Charmpi C1, Van der Veken D1, De Vuyst L1, Leroy F1.
Author information
1
Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
Abstract
European fermented meat products are prepared according to a wide variety of different recipes and processing conditions, which can influence their fermentative microbiota. However, due to the diverse processing conditions applied across Europe, it remained unclear to which degree bacterial heterogeneity can be encountered in commercially available fermented meat products and whether this is linked to their geographical origin. Therefore, the bacterial species diversity of 80 fermented meat products available in the Belgian retail, coming from five different countries, was investigated. It was also assessed how this related to the country of origin and the key processing parameters pH and salt concentration. The samples originated from Belgium, France, Germany, Italy, and Spain. In general, Southern European fermented meat products commonly had a higher pH, with their lactic acid bacteria (LAB) communities being represented by Lactobacillus sakei and with mostly Staphylococcus xylosus and Staphylococcus equorum governing over the coagulase-negative staphylococci (CNS) communities. Among these products, the Spanish variants showed a higher prevalence of S. equorum, whereas S. xylosus was the prevailing CNS species in most French and Italian fermented meat products. In contrast, Northern European fermented meat products were generally more acidified and showed a higher prevalence of Pediococcus pentosaceus in their LAB communities, whereas Staphylococcus carnosus represented the CNS communities. Non-parametric statistical tests indicated the impact of the geographical origin on the prevalence of the LAB and CNS species. The latter was likely due to the combination of differences in process technology as well as starter culture use.

Copyright © 2019 Van Reckem, Geeraerts, Charmpi, Van der Veken, De Vuyst and Leroy.

KEYWORDS:
European fermented meat products; geographical origin; meat fermentation; meat microbiota; starter cultures

PMID: 31649643 PMCID: PMC6794416 DOI: 10.3389/fmicb.2019.02302
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17.
Front Microbiol. 2019 Oct 9;10:2301. doi: 10.3389/fmicb.2019.02301. eCollection 2019.
Bactericidal and Anti-biofilm Activity of the Retinoid Compound CD437 Against Enterococcus faecalis.
Tan F1, She P1, Zhou L1, Liu Y1, Chen L1, Luo Z1, Wu Y1.
Author information
1
Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China.
Abstract
Enterococcus faecalis (E. faecalis), a biofilm-forming pathogen, causes nosocomial infections. In recent years, drug resistance by enterococci has become increasingly severe due to widespread antibiotic abuse. Therefore, novel antibacterial agents are urgently needed. In this study, the synthetic retinoid compound CD437 was found to have potent bactericidal effect on E. faecalis. In addition, CD437 exhibited synergistic effects when administered in combination with gentamicin and additive effects when combined with ceftriaxone sodium. CD437 also inhibited biofilm formation by E. faecalis and exerted bactericidal effect on mature biofilm. Moreover, CD437 exhibited antibacterial and anti-biofilm effects against Staphylococcus. No bactericidal action of CD437 was observed against the gram-negative bacillus, but Pseudomonas aeruginosa biofilm extracellular polymeric substances (EPS) matrix formation was reduced. Overall, these findings indicate that CD437 has the potential to be developed as a novel antibacterial drug.

Copyright © 2019 Tan, She, Zhou, Liu, Chen, Luo and Wu.

KEYWORDS:
Enterococcus faecalis; antibacterial; biofilm; resistance; retinoid; synergism

PMID: 31649642 PMCID: PMC6794434 DOI: 10.3389/fmicb.2019.02301
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18.
Front Microbiol. 2019 Oct 9;10:2300. doi: 10.3389/fmicb.2019.02300. eCollection 2019.
Use of Wine and Dairy Yeasts as Single Starter Cultures for Flavor Compound Modification in Fish Sauce Fermentation.
Gao P1,2, Xia W1, Li X2, Liu S2,3.
Author information
1
State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.
2
Department of Food Science and Technology, National University of Singapore, Singapore, Singapore.
3
Laboratory of Advanced Food Technology & 3D Printing, National University of Singapore (Suzhou) Research Institute, Suzhou, China.
Abstract
Effects of wine and dairy yeast fermentation on chemical constituents of tilapia fish head hydrolysate supplemented with glucose in an unsalted and acidic environment were investigated. Three wine yeasts (Torulaspora delbrueckii Biodiva, Saccharomyces cerevisiae Lalvin EC-1118 and Pichia kluyveri Frootzen) and one dairy yeast (Kluyveromyces marxianus NCYC1425) were employed as single starter cultures, respectively, and were compared with one soy sauce yeast (Candida versatilis NCYC1433). Each yeast showed different growth kinetics and fermentation performance. Compared with C. versatilis NCYC1433, other yeasts presented a significant higher rate of glucose consumption (P < 0.05). Besides, K. marxianus NCYC1425 and P. kluyveri Frootzen produced more citric acid and succinic acid, respectively, while S. cerevisiae Lalvin EC-1118 exhibited higher pyruvic acid production. Significant lower levels of total free amino acids were observed in samples inoculated with wine yeasts relative to other yeasts (P < 0.05). Non-soy sauce yeasts produced increased various levels of esters and alcohols without traditional fish sauce unpleasant odorants, especially K. marxianus NCYC1425 and P. kluyveri Frootzen. The results confirmed that non-soy sauce yeasts are suitable for fish sauce flavor compound modification and to develop a fast fermentation process for saltless fish sauce from fish head, which could increase the acceptability of fish sauce and improve the utilization of fish by-products.

Copyright © 2019 Gao, Xia, Li and Liu.

KEYWORDS:
fish sauce; flavor; hydrolysate; tilapia; yeasts

PMID: 31649641 PMCID: PMC6794352 DOI: 10.3389/fmicb.2019.02300
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19.
Front Microbiol. 2019 Oct 9;10:2299. doi: 10.3389/fmicb.2019.02299. eCollection 2019.
Editorial: Characterizing Modern Microbialites and the Geobiological Processes Underlying Their Formation.
Foster JS1, Reid RP2, Visscher PT3, Dupraz C4.
Author information
1
Department of Microbiology and Cell Science, Space Life Science Laboratory, University of Florida, Merritt Island, FL, United States.
2
Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States.
3
Department of Geosciences, University of Connecticut, Groton, CT, United States.
4
Department of Geological Sciences, Stockholm University, Stockholm, Sweden.
KEYWORDS:
geobiology; meta-omics approaches; microbialites; microbiology; microbiome

PMID: 31649640 PMCID: PMC6794560 DOI: 10.3389/fmicb.2019.02299
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20.
Front Microbiol. 2019 Oct 9;10:2296. doi: 10.3389/fmicb.2019.02296. eCollection 2019.
Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments.
Böhnke S1, Sass K1, Gonnella G2, Diehl A3, Kleint C4, Bach W3, Zitoun R5, Koschinsky A4, Indenbirken D6, Sander SG5, Kurtz S2, Perner M1.
Author information
1
Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
2
Center for Bioinformatics (ZBH), Universität Hamburg, Hamburg, Germany.
3
Department of Geosciences, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
4
Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
5
Department of Chemistry, University of Otago, Dunedin, New Zealand.
6
Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
Abstract
The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO2 fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO2 fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO2 fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO2 fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas' dominance in the Brothers natural hydrothermal fluids.

Copyright © 2019 Böhnke, Sass, Gonnella, Diehl, Kleint, Bach, Zitoun, Koschinsky, Indenbirken, Sander, Kurtz and Perner.

KEYWORDS:
16S rRNA genes; MiSeq; autotrophic CO2 fixation; microbial hydrogen oxidation; microbial hydrothermal vent communities; microbial iron oxidation; microbial sulfide oxidation

PMID: 31649639 PMCID: PMC6794353 DOI: 10.3389/fmicb.2019.02296
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