Methane Monooxygenase Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3b.
In this study, pure cultures of a model Type II methanotroph Methylosinus trichosporium OB3b were grown in hollow-fiber membrane bioreactors (HFMBR) under different steady state methane oxidation conditions. Methanotroph biomass (DNA based) and methane oxidation biomarker mRNA transcript amounts were determined using qPCR and RT-qPCR, respectively. Under both copper-present and copper-limited conditions, per cell pmoA mRNA transcript levels positively correlated with measured per cell methane oxidation rates across three orders of magnitude. These correlations, if maintained across different methanotrophs, could prove valu...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Tentori EF, Richardson RE Tags: Appl Environ Microbiol Source Type: research

Competence-stimulating peptide-dependent localized cell death and extracellular DNA production in Streptococcus mutans biofilms.
Abstract Extracellular DNA (eDNA) is a biofilm component that contributes to the formation and structural stability of biofilms. Streptococcus mutans, a major cariogenic bacterium, induces eDNA-dependent biofilm formation under specific conditions. Since cell death can result in the release and accumulation of DNA, the dead cells in biofilms are a source of eDNA. However, it remains unknown how eDNA is released from dead cells and is localized within S. mutans biofilms. We focused on cell death induced by the extracellular signaling peptide, competence-stimulating peptide (CSP). We demonstrate that nucleic acid re...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Nagasawa R, Yamamoto T, Utada AS, Nomura N, Obana N Tags: Appl Environ Microbiol Source Type: research

High-throughput generation of product profiles for arabinoxylan-active enzymes from metagenomes.
Abstract Metagenomics is an exciting alternative to seek for carbohydrate-active enzymes from a range of sources. Typically, metagenomics reveals dozens of putative catalysts that require functional characterization for further application in industrial processes. High-throughput screening methods compatible with adequate natural substrates are crucial for an accurate functional elucidation of substrate preferences. Based on DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) analysis of enzymatic reaction products, we generated product profiles to consequently infer substrate cleavage...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Fonseca MJMD, Armstrong Z, Withers SG, Briers Y Tags: Appl Environ Microbiol Source Type: research

Genome-centric metagenomic insights into the impact of alkaline/acid and thermal sludge pre-treatment on digestion sludge microbiome.
In this study, genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different feeding sludge: APAD, WAS pre-treated with 0.25 mol/L alkaline/acid; HS-APAD, WAS pre-treated with 0.8 mol/L alkaline/acid; Thermal-AD, thermal pre-treated WAS; Control-AD, fresh WAS. We retrieved 254 metagenomic-assembled genomes (MAGs) to identify the key functional populations involved in methanogenic digestion process. These MAGs span 28 phyla with 69 of them as yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated wi...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Liang Z, Shi J, Wang C, Li J, Liang D, Yong EL, He Z, Wang S Tags: Appl Environ Microbiol Source Type: research

Deciphering the impact of diet and host physiology on the mammalian gut microbiome by multi-omics approaches.
Abstract In recent years various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were primarily focused on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe co-evolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics wa...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Milani C, Alessandri G, Mancabelli L, Mangifesta M, Lugli GA, Viappiani A, Longhi G, Anzalone R, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M Tags: Appl Environ Microbiol Source Type: research

Formate-dependent acetogenic utilization of glucose by the fecal acetogen Clostridium bovifaecis.
This study gave an insight into a unique metabolic feature for the fecal acetogens. As the requirement of formate for the acetogenic growth of certain acetogens, the ecological impact of acetogens could be more complex and important in the formate-rich environment due to their trophic interactions with other microbes. PMID: 32948524 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Yao Y, Fu B, Han D, Zhang Y, Liu H Tags: Appl Environ Microbiol Source Type: research

Detection of Cyclospora cayetanensis in Agricultural Water Using Dead-End Ultrafiltration (DEUF) and DNA-based Methods.
In this study, a method to detect C. cayetanensis in water by combining dead-end ultrafiltration (DEUF) with sensitive and specific molecular detection was developed and evaluated. Triplicates of 10-L agricultural water samples were seeded with 200, 100, 25, 12, and 6 C. cayetanensis oocysts. Surface water samples were also collected in the Mid-Atlantic region. All water samples were processed by DEUF and backflushed from the ultrafilters. DNA was extracted from concentrated samples and analyzed by a qPCR targeting the C. cayetanensis 18S rRNA gene. All water samples seeded with 12, 25, 100 and 200 oocysts were positive an...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: Durigan M, Murphy HR, da Silva AJ Tags: Appl Environ Microbiol Source Type: research

Genomic characterization of Enterotoxigenic E. coli F4 and F18 positive strains from post-weaning diarrhea in pigs.
This study aimed to characterize in silico Enterotoxigenic E. coli F4- and F18-positive-isolates (n=90) causing swine post-weaning diarrhea, including pathogenic potential, phylogenetic relationship, antimicrobial and biocide resistance (R), prophage content and metal tolerance rates. F4-strains belonged mostly to the O149 and O6 serogroups and ST100 and ST48 MLST-types. F18-strains were mainly assigned to the O8 and O147 serogroups and ST10, ST23 and ST42. The highest rates of antimicrobial-R were found against streptomycin, sulfamethoxazole, tetracycline, trimethoprim and ampicillin. No resistance was found towards cipro...
Source: Applied and Environmental Microbiology - September 18, 2020 Category: Microbiology Authors: García V, Gambino M, Pedersen K, Haugegaard S, Olsen JE, Herrero-Fresno A Tags: Appl Environ Microbiol Source Type: research

Correction for Theofel et al., "Microorganisms Move a Short Distance into an Almond Orchard from an Adjacent Upwind Poultry Operation".
Correction for Theofel et al., "Microorganisms Move a Short Distance into an Almond Orchard from an Adjacent Upwind Poultry Operation". Appl Environ Microbiol. 2020 Sep 17;86(19): Authors: Theofel CG, Williams TR, Gutierrez E, Davidson GR, Jay-Russell M, Harris LJ PMID: 32943394 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 17, 2020 Category: Microbiology Authors: Theofel CG, Williams TR, Gutierrez E, Davidson GR, Jay-Russell M, Harris LJ Tags: Appl Environ Microbiol Source Type: research

Mining and statistical modeling of natural and variant class IIa bacteriocins elucidates activity and selectivity profiles across species.
Abstract Class IIa bacteriocin antimicrobial peptides (AMPs) are a compelling alternative to current antimicrobials because of potential specific activity towards antibiotic-resistant bacteria, including vancomycin-resistant enterococci. Engineering of these molecules would be enhanced by a better understanding of AMP sequence-activity relationships to improve efficacy in vivo and limit effects of off-target activity. Towards this goal, we experimentally evaluated 210 natural and variant class IIa bacteriocins for antimicrobial activity against six strains of enterococci. Inhibitory activity was ridge regressed to...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Tresnak DT, Hackel BJ Tags: Appl Environ Microbiol Source Type: research

Bacillus subtilis modulates its usage of biofilm-bound iron in response to environmental iron availability.
We report that this B. subtilis strain can accumulate a large quantity of Fe in the biofilm, largely exceeding Fe associated with cells. We also report that only a fraction of biofilm-bound Fe is available for uptake in the absence of other sources of Fe in the vicinity of the biofilm. We observed that availability of environmental Fe modulates the usage of this pool of biofilm-bound Fe. Finally, our data suggest that consumption of biofilm-bound Fe relates to the efficacy of B. subtilis to transport Fe from the environment to the biofilm, possibly through siderophores.Importance Recent evidences suggest that Fe bound to t...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Rizzi A, Leroux J, Charron-Lamoureux V, Roy S, Beauregard PB, Bellenger JP Tags: Appl Environ Microbiol Source Type: research

Expanded diversity and metabolic versatility of marine nitrite-oxidizing bacteria revealed by cultivation- and genomics-based approaches.
In conclusion, this study provides more insights into the ecological roles of NOB in marine environments. PMID: 32917751 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Park SJ, Andrei AŞ, Bulzu PA, Kavagutti VS, Ghai R, Mosier AC Tags: Appl Environ Microbiol Source Type: research

The heterotrophic bacterium Cupriavidus pinatubonensis JMP134 oxidizes sulfide to sulfate with thiosulfate as a key intermediate.
n L Abstract Heterotrophic bacteria actively participate in the biogeochemical cycle of sulfur on Earth. The heterotrophic bacterium Cupriavidus pinatubonensis JMP134 contains several enzymes involved in sulfur oxidation, but how these enzymes work together to oxidize sulfide in the bacterium has not been studied. Using gene-deletion and whole cell assays, we determined that the bacterium uses sulfide:quinone oxidoreductase to oxidize sulfide to polysulfide, which is further oxidized to sulfite by persulfide dioxygenase. Sulfite spontaneously reacts with polysulfide to produce thiosulfate. The Sox system oxidizes ...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Xin Y, Gao R, Cui F, Lü C, Liu H, Liu H, Xia Y, Xun L Tags: Appl Environ Microbiol Source Type: research

Oxidation of cytochrome 605 is the rate limiting step when Ferrimicrobium acidiphilum respires aerobically on soluble iron.
Abstract Proteins that oxidize extracellular substrates in Gram-positive bacteria are poorly understood. Ferrimicrobium acidiphilum is an actinobacterium that respires aerobically on extracellular ferrous ions at pH 1.5. In situ absorbance measurements were conducted on turbid suspensions of intact Fm. acidiphilum using an integrating cavity absorption meter designed for that purpose. Initial velocity kinetic studies monitored the appearance of product ferric ions in the presence of catalytic quantities of cells. Cell-catalyzed iron oxidation obeyed the Michaelis-Menten equation with values for KM and Vmax of 71 &...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Blake RC, Guidry JJ, Anthony MD, Ban B, Smith KA, Walton NN, Painter RG Tags: Appl Environ Microbiol Source Type: research

Sphingobium sp. SYK-6 syringate O-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR.
In this study, we found that the transcription of desA, encoding syringate O-demethylase in SYK-6, is regulated by an IclR-type of transcriptional regulator, DesX. The findings of this study, combined with our previous results on desR (a MarR transcriptional regulator that controls the transcription of ligM and desB), provide an overall picture of the transcriptional regulatory systems for syringate and vanillate catabolism in SYK-6. PMID: 32917754 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Araki T, Tanatani K, Kamimura N, Otsuka Y, Yamaguchi M, Nakamura M, Masai E Tags: Appl Environ Microbiol Source Type: research

Risk factors associated with carbapenemase-producing Enterobacterales (CPE) positivity in the hospital wastewater environment.
This study was conducted at a hospital with endemic KPCO linked to wastewater reservoirs and robust patient perirectal screening for silent KPCO carriage. Over five months, both rooms occupied and not occupied by KPCO-positive patients were sampled at three wastewater sites within each room (sink drain, sink P-trap, and toilet or hopper). Risk factors for KPCO positivity were assessed using logistic regression. Whole genome sequencing (WGS) identified environmental seeding by KPCO-positive patients.Findings: 219/475(46%) room sampling events were KPCO-positive in at least one wastewater site. KPCO-positive patient exposure...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Park SC, Parikh H, Vegesana K, Stoesser N, Barry KE, Kotay SM, Dudley S, Peto TEA, Crook DW, Walker AS, Mathers AJ Tags: Appl Environ Microbiol Source Type: research

Molecular basis for substrate recognition and catalysis by a marine bacterial laminarinase.
In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of β-1, 3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine flavobacterium. The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling. PMID: 32917756 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Yang J, Xu Y, Miyakawa T, Long L, Tanokura M Tags: Appl Environ Microbiol Source Type: research

Thermoregulation of Biofilm Formation in Pseudomonas aeruginosa.
This study shows how biofilms are formed at various temperatures, and provides new insights to control biofilms using temperature. PMID: 32917757 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Kim S, Li XH, Hwang HJ, Lee JH Tags: Appl Environ Microbiol Source Type: research

Trehalose degradation in Cellvibrio japonicus exhibits no functional redundancy and is solely dependent on the Tre37A enzyme.
This study facilitates the development of a comprehensive metabolic model for α-linked disaccharides in C. japonicus, and more broadly expands our understanding of the strategies that saprophytic bacteria employ to capture diverse carbohydrates from the environment.IMPORTANCE The metabolism of α-diglucosides like trehalose is becoming increasingly important due to its inclusion in a number of foods and its prevalence in the environment. Bacteria able to utilize trehalose in the human gut possess a competitive advantage, as do saprophytic microbes in terrestrial environments. While the biochemical mechanism of t...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Garcia CA, Narrett JA, Gardner JG Tags: Appl Environ Microbiol Source Type: research

Potential applications of human viral metagenomics and reference materials: considerations for current and future viruses.
Abstract Viruses are ubiquitous particles comprised of genetic material that can infect bacteria, archaea, fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery, and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translate into biological ...
Source: Applied and Environmental Microbiology - September 11, 2020 Category: Microbiology Authors: Santiago-Rodriguez TM, Hollister EB Tags: Appl Environ Microbiol Source Type: research

Isolation and molecular characterization of novel monomeric fungal subtilisin inhibitor from a plant pathogenic fungus, Choanephora cucurbitarum.
Abstract The bacterial protease inhibitor domain, Streptomyces subtilisin inhibitor (SSI), is rarely found in fungi. Genome analysis of a fungal pathogen, Choanephora cucurbitarum KUS-F28377, revealed 11 SSI-like domains that are horizontally transferred and sequentially diverged during evolution. We investigated the molecular function of fungal SSI-like domains of C. cucurbitarum, designated as 'Choanepins'. Among the tested proteins, only choanepin9 showed inhibitory activity against subtilisin as the target protease, and accounting for 47% of the inhibitory activity of bacterial SSI. However, the binding affini...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Pathiraja D, Chun Y, Cho JH, Min B, Lee S, Park H, Byun J, Choi IG Tags: Appl Environ Microbiol Source Type: research

The impact of the human microbiome in forensic sciences: A systematic review.
This study throws light on the role of microbiome research in the postmortem interval during the process of decomposition; identifying death caused by drowning or sudden death; locating the geographical location of death; establishing a connection between human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori to ascertain personal identity or geographical location. Sev...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: García MG, Pérez-Cárceles MD, Osuna E, Legaz I Tags: Appl Environ Microbiol Source Type: research

Active Packaging of Immobilized Zinc Oxide Nanoparticles Controls Campylobacter jejuni in Raw Chicken Meat.
Abstract Zinc oxide nanoparticles (ZnO NPs) are regarded as a safe and stable antimicrobial that can inactivate bacteria by several potential working mechanisms. We aimed to include ZnO NPs into the packaging material to control Campylobacter in raw chicken meat. ZnO NPs were first incorporated into 3D paper tubes to identify the lethal concentration against C. jejuni, which was selected as the working concentration to develop 2D functionalized absorbing pads by ultrasound-assisted dipping technique. The functionalized pad was placed underneath raw chicken meat to inactivate C. jejuni and the predominant chicken m...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Hakeem MJ, Feng J, Nilghaz A, Ma L, Seah HC, Konkel ME, Lu X Tags: Appl Environ Microbiol Source Type: research

Magnetotactic bacteria accumulate a large pool of iron distinct from their magnetite crystals.
Abstract Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that form intracellular nanoparticles of magnetite (Fe3O4) or greigite (Fe3S4) in a genetically controlled manner. Magnetite and greigite synthesis requires MTB to transport a large amount of iron from the environment. Most intracellular iron was proposed to be contained within the crystals. However, recent mass spectrometry studies suggest that MTB may contain a large amount of iron that is not precipitated in crystals. Here, we attempt to resolve these discrepancies by performing chemical and magnetic assays to quantify the different iro...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Amor M, Ceballos A, Wan J, Simon CP, Aron AT, Chang CJ, Hellman F, Komeili A Tags: Appl Environ Microbiol Source Type: research

Mutant and recombinant phages selected from in vitro coevolution conditions overcome phage-resistant Listeria monocytogenes.
This study demonstrates that in vitro evolution of phages can be utilized to expand the host range and improve the long-term efficacy of phage-based control of L. monocytogenes This approach may also be applied to other phage-host systems for applications in biocontrol, detection, and phage therapy. PMID: 32887717 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Peters TL, Song Y, Bryan DW, Hudson LK, Denes TG Tags: Appl Environ Microbiol Source Type: research

Therapeutic Efficacy of Phage PIZ SAE-01E2 Against Abortion Caused by Salmonella abortus equi in Mice.
In this study, the preventive and therapeutic effects of phage PIZ SAE-01E2 against S. abortus equi in a mouse model of abortion was investigated. Phage PIZ SAE-01E2 was stable at different temperatures (4 ∼ 70 °C) and pH values (4 ∼ 10) and could lyse the majority of the tested Salmonella strains (25/28) of serotype O:4 and O:9. There is no lysogenic, toxin or antibiotic-resistant related gene in the genome of PIZ SAE-01E2. All of these characteristics indicated PIZ SAE-01E2 has potential for phage therapy. In in vivo experiments, 2 × 103 CFU/mouse of S. abortus equi ATCC 9842 was sufficient to lead to m...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Wang X, Ji Y, Su J, Xue Y, Xi H, Wang Z, Bi L, Zhao R, Zhang H, Yang L, Guo Z, Guan Y, Feng X, Sun C, Lei L, Ur Rahman S, Dong J, Han W, Gu J Tags: Appl Environ Microbiol Source Type: research

NfoR, Chromate Reductase or FMN reductase?
Abstract Soil bacteria can detoxify Cr(VI) ions by reduction. Within the last two decades numerous reports of chromate reductase enzymes have been published. These reports purport catalytic reduction of chromate ions by specific enzymes. These enzymes each have sequence similarity to known-redox active flavoproteins. We investigated the enzyme NfoR from Staphlococcus aureus that was claimed to be upregulated in chromate rich soils and to have chromate reductase activity (Han H, Ling Z, Zhou T, Xu R, He Y, Liu P, Li X. 2017. Sci Rep 7:15481.). We show that NfoR has structural similarity to known FMN reductases and ...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: O'Neill AG, Beaupre BA, Zheng Y, Liu D, Moran GR Tags: Appl Environ Microbiol Source Type: research

Bacillus thuringiensis Cry1Ab domain III β-22 mutants with enhanced toxicity to Spodoptera frugiperda (J. E. Smith).
Bacillus thuringiensis Cry1Ab domain III β-22 mutants with enhanced toxicity to Spodoptera frugiperda (J. E. Smith). Appl Environ Microbiol. 2020 Sep 04;: Authors: Gómez I, Ocelotl J, Sánchez J, Aguilar-Medel S, Peña-Chora G, Lina-Garcia L, Bravo A, Soberón M Abstract The fall armyworm, Spodoptera frugiperda, is an invasive maize pest that has spread from the Americas into Africa and Asia causing severe crop damages worldwide. Most populations of S. frugiperda show low susceptibility to Bacillus thuringiensis (Bt) Cry1Ab or Cry1Ac toxins, which have been proved to be e...
Source: Applied and Environmental Microbiology - September 4, 2020 Category: Microbiology Authors: Gómez I, Ocelotl J, Sánchez J, Aguilar-Medel S, Peña-Chora G, Lina-Garcia L, Bravo A, Soberón M Tags: Appl Environ Microbiol Source Type: research

Involvement of the cell wall integrity pathway in protection against cadmium and arsenate stresses in Saccharomyces cerevisiae.
This study shows that, in yeast S. cerevisiae, the CWI pathway plays a protective role against cadmium and arsenate through the upregulation of genes involved in cell wall biosynthesis and cell cycle control, possibly in order to modulate cell wall reconstruction and cell cycle phase transition, respectively. These data provide insights into molecular mechanisms underlying adaptive response to cadmium and arsenate. PMID: 32859590 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Techo T, Charoenpuntaweesin S, Auesukaree C Tags: Appl Environ Microbiol Source Type: research

Structural and functional insights of iturin W, a novel lipopeptide produced by the deep-sea bacterium Bacillus sp. wsm-1.
In this study, we discovered a novel lipopeptide iturin W with promising prospect in biological control of plant diseases. Moreover, the effects of different carbon and nitrogen sources and amino acids on production of C14 iturin W and C15 iturin W would provide a reasonable basis for the optimization of fermentation process of lipopeptides. Notably, the structure of iturin W was different to any previously reported lipopeptides, suggesting deep-sea microorganisms might produce many novel natural products and have significant potentials to develop biological products in the future. PMID: 32859591 [PubMed - as supplied...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Zhou S, Liu G, Zheng R, Sun C, Wu S Tags: Appl Environ Microbiol Source Type: research

Salmonella enterica serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine.
In conclusion, the study findings showed that S. Typhimurium incited temporal and spatial modifications to the swine autochthonous microbiota, and to host defense responses, that were consistent with overcoming colonization resistance to incite salmonellosis in swine.IMPORTANCE Limited information is available on host and enteric microbiota responses incited by Salmonella enterica Typhimurium in swine, and possible mechanisms by which the bacterium overcomes colonization resistance to incite salmonellosis. Temporal characterization of a variety of host metrics in piglets (e.g. physiologic, histopathologic, and immunologic)...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Bescucci DM, Moote PE, Ortega Polo R, Uwiera RRE, Inglis GD Tags: Appl Environ Microbiol Source Type: research

Improving Arsenic Tolerance of Pyrococcus furiosus by the Heterologous Expression of a Respiratory Arsenate Reductase.
Abstract Arsenate is a notorious toxicant that is known to disrupt multiple biochemical pathways. Many microorganisms have developed mechanisms to detoxify arsenate using the ArsC-type arsenate reductase and some even use arsenate as a terminal electron acceptor for respiration involving the arsenate respiratory reductase (Arr). ArsC-type reductases have been studied extensively but the phylogenetically-unrelated Arr system is less investigated and has not been characterized from Archaea. Herein, we heterologously-expressed the genes encoding Arr from the crenarchaeon Pyrobaculum aerophilum in the euryarchaeon Pyr...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Haja DK, Wu CH, Ponomarenko O, Poole FL, George GN, Adams MWW Tags: Appl Environ Microbiol Source Type: research

Ferric Uptake Regulator Fur Coordinates Siderophore Production, Defense against Iron Toxicity and Oxidative Stress, and Contributes to Virulence in Chromobacterium violaceum.
Abstract Iron is a highly reactive metal that participates in several processes in prokaryotic and eukaryotic cells. Hosts and pathogens compete for iron in the context of infection. Chromobacterium violaceum, an environmental Gram-negative bacterial pathogen, relies on siderophores to overcome iron limitation in the host. In this work, we studied the role of the Ferric Uptake Regulator Fur in the physiology and virulence of C. violaceum A Δfur null mutant strain showed decreased growth and fitness under regular in vitro growth conditions and presented high sensitivity to iron and oxidative stresses. Further...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: de Souza Santos RER, Batista BB, da Silva Neto JF Tags: Appl Environ Microbiol Source Type: research

Genetic and Physiological Characterization of the Antibacterial Activity of Bacillus inaquosorum Strain T1 Effective Against pirABVp -Bearing Vibrio parahaemolyticus.
In this study we focus on the inhibitory activity of Bacillus inaquosorum strain T1, which hinders V. parahaemolyticus growth in co-culture experiments in a density-dependent manner; inhibition was also observed using cell-free supernatants from T1 stationary phase cultures. Using mariner-based transposon mutagenesis, 17 mutants were identified having complete or partial loss of inhibitory activity. Of those displaying total loss of activity, 13 had insertions within a 42.6 kb DNA region comprising 15 genes whose deduced products were homologous to non-ribosomal polypeptide synthetases (NRPSs), polyketide synthases (PKSs) ...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Avery SE, Ruzbarsky SP, Hise AM, Schreier HJ Tags: Appl Environ Microbiol Source Type: research

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae.
In this study, we investigated the potential of the fungal strain Metarhizium anisopliae CQMa421 to control rice planthoppers under field conditions and its effects on rice microbiota. This fungus suppressed rice planthoppers during this period, and its control efficiency was more than 60% 7 days post application and did not significantly differ from that of the chemical treatment except in 2019. Both treatments showed a lower population of rice planthoppers than the controls. After application, M. anisopliae was maintained on rice plants for approximately 14 days, showing a decreasing trend over time. Furthermore, the res...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Peng Y, Tang J, Hong M, Xie J Tags: Appl Environ Microbiol Source Type: research

Endosymbionts of vent-dwelling metazoans in PACManus-diversity and potential adaptive features revealed by genome analysis.
This study also revealed three novel genomes of symbionts from the snails of A. boucheti Combined with a dataset of other ectosymbiont and free-living bacteria, genome comparisons of the snail endosymbionts pointed to several genetic traits that may have contributed to the lifestyle shift into the epithelial cells in ϵ-proteobacteria These findings could increase our understanding of invertebrate-endosymbiont in deep-sea ecosystems. PMID: 32859597 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Li L, Wang M, Li L, Du Z, Sun Y, Wang X, Zhang X, Li C Tags: Appl Environ Microbiol Source Type: research

Processing has differential effects on microbiota accessible carbohydrates in whole grains during in vitro fermentation.
Abstract Whole grains are generally low in non-digestible carbohydrates that are available for fermentation by the gut microbiota, or microbiota accessible carbohydrates (MAC). However, there is potential to increase MAC in whole grains through food processing. Five processing methods: boiling, extrusion, sourdough bread, unleavened bread, and yeast bread, were applied to whole wheat flour and then subjected to in vitro digestion followed by fermentation using fecal microbiomes from 10 subjects. The microbiomes separated into 2 groups: those that showed high carbohydrate-utilization (CU) and those that exhibited l...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Smith C, Van Haute MJ, Rose DJ Tags: Appl Environ Microbiol Source Type: research

Assessment of soil features on the growth of environmental nontuberculous mycobacterial isolates from Hawai'i.
Abstract Environmental nontuberculous mycobacteria (NTM) with the potential to cause opportunistic lung infections can reside in soil. This might be particularly relevant in Hawai'i, a geographic hot spot for NTM infections and whose soil composition differs from many other areas of the world. Soil components are likely to contribute to NTM prevalence in certain niches, as food sources or attachment scaffolds, but the particular types of soils, clays, and minerals that impact NTM growth are not well-defined. Hawai'i soil and chemically weathered rock (a.k.a., saprolite) samples were examined to characterize the mi...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Glickman CM, Virdi R, Hasan NA, Epperson LE, Brown L, Dawrs SN, Crooks JL, Chan ED, Strong M, Nelson ST, Honda JR Tags: Appl Environ Microbiol Source Type: research

Dissolved microcystin release coincident with lysis of a Microcystis-dominated bloom in western Lake Erie attributed to a novel cyanophage.
This study provides further evidence that viral activity in western Lake Erie plays a significant role in transformation of microcystins from particulate to the dissolved fraction and therefore requires monitoring efforts from local water treatment plants. Additionally, identification of multiple lytic cyanophages will enable the development of a qPCR toolbox to assess viral activity during cHABs.Importance Viral attack on cHABs may contribute to changes in community composition during blooms as well as bloom decline, yet loss of bloom biomass does not eliminate the threat of cHAB toxicity. Rather, it may increase risks to...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: McKindles KM, Manes MA, DeMarco JR, McClure A, McKay RM, Davis TW, Bullerjahn GS Tags: Appl Environ Microbiol Source Type: research

Dietary supplementation of sodium sulfate improves rumen fermentation, fiber digestibility and plasma metabolome through modulating rumen bacterial communities in steers.
Abstract Six steers were used to study the effects of dietary supplementation with sodium sulfate (Na2SO4) on rumen fermentation, nutrient digestion, rumen microbiota and plasma metabolites. The animals were fed a basal ration added with Na2SO4 at 0 [sulfur (S) content 0.115% DM], 20 (S 0.185% DM) and 40 g/d (S 0.255%DM), respectively, in a replicate 3 × 3 Latin square design. Results indicated that supplementing Na2SO4 increased the ruminal concentration of total volatile fatty acids, the molar proportions of acetate and butyrate, the ruminal concentrations of microbial protein, SO4 2--S and S2--S and the d...
Source: Applied and Environmental Microbiology - August 28, 2020 Category: Microbiology Authors: Zhao Y, Xie B, Gao J, Zhao G Tags: Appl Environ Microbiol Source Type: research

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq.
Abstract With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of this organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. These gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes co-exist making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzyme...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM, Keasling JD Tags: Appl Environ Microbiol Source Type: research

Quantification of Complete Ammonia Oxidizing (Comammox) Bacteria Clades and Strict Nitrite Oxidizers in Nitrospira Using Newly Designed Primers.
Abstract Complete ammonia oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from comammox Nitrospira has become problematic since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clades A- and B-specific primer sets targeting the α-subunit of ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting cya...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Jiang R, Wang JG, Zhu T, Zou B, Wang DQ, Rhee SK, An D, Ji ZY, Quan ZX Tags: Appl Environ Microbiol Source Type: research

The Interactive Effects of Crude Oil and Corexit 9500 on their Biodegradation in Arctic Seawater.
Abstract The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Gofstein TR, Perkins M, Field J, Leigh MB Tags: Appl Environ Microbiol Source Type: research

Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis.
an RA Abstract Imbalances within the dental biofilm trigger dental caries, currently considered a dysbiosis and the most prevalent non-communicable disease. There is still a gap in knowledge about the dynamics of enamel colonization by bacteria from the dental biofilm in caries. The aim, therefore, was to test whether the sequence of enamel colonization by a typically commensal and a cariogenic species modifies biofilm's cariogenicity. Dual-species biofilms of Streptococcus mutans (Sm) and Streptococcus sanguinis (Ss) on saliva-coated enamel slabs were inoculated in different sequences: Sm followed by Ss (Sm-Ss), ...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Díaz-Garrido N, Lozano CP, Kreth J, Giacaman RA Tags: Appl Environ Microbiol Source Type: research

A new approach for evaluating electron transfer dynamics by using in-situ resonance Raman microscopy and chronoamperometry in conjunction with a dynamic model.
a U Abstract Geobacter sulfurreducens is a good candidate as a chassis-organism due to its ability to form thick, conductive biofilms, enabling long distance extracellular electron transfer (EET). Due to the complexity of EET pathways in G. sulfurreducens, a dynamic approach is required to study genetically modified EET rates in the biofilm. By coupling on-line resonance Raman microscopy with chronoamperometry, we were able to observe the dynamic discharge response in the biofilm's cytochromes to an increase in anode voltage. Measuring the heme redox state alongside the current allows for the fitting of a dynamic ...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Krige A, Ramser K, Sjöblom M, Christakopoulos P, Rova U Tags: Appl Environ Microbiol Source Type: research

Multiple drug-induced stress responses inhibit formation of Escherichia coli biofilms.
jik V Abstract In most ecosystems, bacteria primarily exist as structured surface-associated biofilms that can be highly tolerant to antibiotics and thus represent an important health issue. Here we explored drug repurposing as a strategy to identify new antibiofilm compounds, screening over 1000 compounds from the Prestwick Chemical Library of approved drugs for specific activities that prevent biofilm formation by Escherichia coli Most growth-inhibiting compounds, which include known antibacterial but also antiviral and other drugs, had also reduced biofilm formation. However, we also identified several drugs th...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Teteneva NA, Mart'yanov SV, Esteban López M, Kahnt J, Glatter T, Netrusov AI, Plakunov VK, Sourjik V Tags: Appl Environ Microbiol Source Type: research

Fungal-associated molecules induce key genes involved in the biosynthesis of the antifungal secondary metabolites nunamycin and nunapeptin in the biocontrol strain Pseudomonas fluorescens In5.
This study focusses on further unravelling the complex regulation governing CLP synthesis in P. fluorescens In5. Promoter fusions were used to show that the specific activator NunF is dependent on the global regulator of secondary metabolism GacA and is regulated by fungal-associated molecules and low temperatures. In contrast, GacA is stimulated by plant signalling molecules leading to the hypothesis that P. fluorescens is a hyphosphere-associated bacterium encoding transcription factor genes that respond to signals indicating the presence of fungi and oomycetes. Based on these findings, we present a model for how synthes...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Christiansen L, Alanin KS, Phippen CBW, Olsson S, Stougaard P, Hennessy RC Tags: Appl Environ Microbiol Source Type: research

A CRISPRi-dCas9 system for archaea and its use to examine gene function during nitrogen fixation by Methanosarcina acetivorans.
In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI1I2DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNA), one targeting the promoter and the other nifD Remarkably, growth of M. ac...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Dhamad AE, Lessner DJ Tags: Appl Environ Microbiol Source Type: research

Three Candidate Probiotic Strains Impact Gut Microbiota and Induce Anergy in Mice with Cow's Milk Allergy.
In this study, we evaluated their potential benefits in a curative mouse model of cow's milk allergy. When administered for 3-weeks after the sensitization process and a first allergic reaction, none of the strains modified the levels of sensitization and allergic markers. However, all three strains affected gut bacteria communities and modified immune and inflammatory responses leading to a tolerogenic profile. Interestingly, all three strains exerted a direct effect on dendritic cells which are known to play a major role in food sensitization through their potentially tolerogenic properties and anergic responses. Altoget...
Source: Applied and Environmental Microbiology - August 21, 2020 Category: Microbiology Authors: Esber N, Mauras A, Delannoy J, Labellie C, Mayeur C, Caillaud MA, Kashima T, Souchaud L, Nicolis I, Kapel N, Waligora-Dupriet AJ Tags: Appl Environ Microbiol Source Type: research

Correction for Gomez-Fernandez et al., "Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases".
Correction for Gomez-Fernandez et al., "Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases". Appl Environ Microbiol. 2020 Aug 18;86(17): Authors: Gomez-Fernandez BJ, Risso VA, Rueda A, Sanchez-Ruiz JM, Alcalde M PMID: 32816744 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 18, 2020 Category: Microbiology Authors: Gomez-Fernandez BJ, Risso VA, Rueda A, Sanchez-Ruiz JM, Alcalde M Tags: Appl Environ Microbiol Source Type: research