Symbiont genomic features and localization in the bean beetle, < em > Callosobruchus maculatus < /em >
In this study, we applied community profiling using 16S rRNA gene sequencing to reveal a highly conserved bacterial assembly shared between larvae and adults. Dominated by Firmicutes and Proteobacteria, this community is localized extracellularly along the epithelial lining of the bean beetle's digestive tract. Our analysis revealed only one species, Staphylococcus gallinarum (phylum Firmicutes), is shared across all developmental stages. Isolation and whole genome sequencing of S. gallinarum from the beetle gut yielded a circular chromosome (2.8 Mb) and one plasmid (45 kb). The strain encoded complete biosynthetic pathway...
Source: Applied and Environmental Microbiology - April 17, 2021 Category: Microbiology Authors: Aileen Berasategui Abraham G Moller Benjamin Weiss Christopher W Beck Caroline Bauchiero Timothy D Read Nicole M Gerardo Hassan Salem Source Type: research

Construction of a fimbriae absent < em > Escherichia coli < /em > by deleting 64 genes and its application for efficient production of poly-3-hydroxybutyrate and L-threonine
In this study, each of the 12 operons was deleted in E. coli MG1655, and the resulting 12 deletion mutants all grew better than the wild type, especially in the nutrient-deficient M9 medium. When the plasmid pBHR68 containing the key genes for polyhydroxyalkanoate production was introduced into these 12 mutants, each mutant synthesized more polyhydroxyalkanoate than the wild type control. These results indicate that the fimbriae removal in E. coli benefits cell growth and polyhydroxyalkanoate production. Therefore, all the 12 chaperone-usher operons including 64 genes were deleted in MG1655, resulting the fimbriae absent s...
Source: Applied and Environmental Microbiology - April 17, 2021 Category: Microbiology Authors: Jun Qiao Xin Tan Hongyu Ren Zheng Wu Xiaoqing Hu Xiaoyuan Wang Source Type: research

High-resolution genomic comparisons within < em > Salmonella enterica < /em > serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period
In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism (SNP)-based maximum likelihood phylogeny and hierarchical clustering of core-genome multi-locus sequence typing. The importance of the aforementioned features on clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each sub-population. Our findings indicate that clonal expansion of Salmonella strains in cat...
Source: Applied and Environmental Microbiology - April 17, 2021 Category: Microbiology Authors: Gizem Levent Ashlynn Schlochtermeier Samuel E Ives Keri N Norman Sara D Lawhon Guy H Loneragan Robin C Anderson Javier Vinasco Henk C den Bakker H Morgan Scott Source Type: research

Molecular dissection of perithecial mating line development in < em > Colletotrichum fructicola < /em > , a species with a nontypical mating system featured by plus-to-minus switch and plus-minus mediated sexual enhancement
This study provides insights into mechanisms underlying the mysterious phenomenon of plus-minus mediated sexual enhancement being unique to Colletotrichum fungi.IMPORTANCEPlus-minus regulation of Colletotrichum sexual differentiation was reported in the early 1900s. Both plus and minus strains produce fertile perithecia in a homothallic but inefficient manner. However, when the two strain types encounter each other, efficient differentiation of fertile perithecia is triggered. The plus strain, by itself, can also generate minus ascospore progeny at high frequency. This nontypical mating system facilitates sexual reproducti...
Source: Applied and Environmental Microbiology - April 17, 2021 Category: Microbiology Authors: Xiaofei Liang Liqiang Yao Yuanyuan Kong Bingxuan Li Xiaojuan Hao Yuyi Lin Mengyu Cao Qiuyue Dong Rong Zhang Jeffrey A Rollins Guangyu Sun Source Type: research

Pyruvate production by < em > Escherichia coli < /em > using pyruvate dehydrogenase variants
This study describes an additional tool to modify central metabolism and direct metabolic flux to a product. We have shown that variants of the pyruvate dehydrogenase complex can direct metabolic flux away from cell growth to increase pyruvate production in Escherichia coli This approach could be paired with existing strategies to optimize metabolism and create industrially relevant and economically feasible processes.PMID:33863707 | DOI:10.1128/AEM.00487-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 17, 2021 Category: Microbiology Authors: W Chris Moxley Mark A Eiteman Source Type: research

Development of wastewater pooled surveillance of SARS-CoV-2 from congregate living settings
Appl Environ Microbiol. 2021 Apr 15:AEM.00433-21. doi: 10.1128/AEM.00433-21. Online ahead of print.ABSTRACTWastewater-based monitoring for SARS-CoV-2 at individual building-level could be an efficient, passive means of early detection of new cases in congregate living settings, but this approach has not been validated. Preliminary samples were collected from a hospital and a local municipal wastewater treatment plant. Molecular diagnostic methods were compared side-by-side to assess feasibility, performance and sensitivity. Refined sample collection and processing protocols were then used to monitor two occupied dormitory ...
Source: Applied and Environmental Microbiology - April 16, 2021 Category: Microbiology Authors: Lisa M Colosi Katie E Barry Shireen M Kotay Michael D Porter Melinda D Poulter Cameron Ratliff William Simmons Limor I Steinberg D Derek Wilson Rena Morse Paul Zmick Amy J Mathers Source Type: research

Development of wastewater pooled surveillance of SARS-CoV-2 from congregate living settings
Appl Environ Microbiol. 2021 Apr 15:AEM.00433-21. doi: 10.1128/AEM.00433-21. Online ahead of print.ABSTRACTWastewater-based monitoring for SARS-CoV-2 at individual building-level could be an efficient, passive means of early detection of new cases in congregate living settings, but this approach has not been validated. Preliminary samples were collected from a hospital and a local municipal wastewater treatment plant. Molecular diagnostic methods were compared side-by-side to assess feasibility, performance and sensitivity. Refined sample collection and processing protocols were then used to monitor two occupied dormitory ...
Source: Applied and Environmental Microbiology - April 16, 2021 Category: Microbiology Authors: Lisa M Colosi Katie E Barry Shireen M Kotay Michael D Porter Melinda D Poulter Cameron Ratliff William Simmons Limor I Steinberg D Derek Wilson Rena Morse Paul Zmick Amy J Mathers Source Type: research

Global diversity and biogeography of the < em > Zostera marina < /em > mycobiome
In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.PMID:33837008 | DOI:10.1128/AEM.02795-20 (Sou...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Cassandra L Ettinger Laura E Vann Jonathan A Eisen Source Type: research

Effect of Leu277 on Disproportionation and Hydrolysis Activity in < em > Bacillus stearothermophilus < /em > NO2 Cyclodextrin Glucosyltransferase
In this study, Leu277 of the CGTase from Bacillus stearothermophilus NO2, located near both the +2 subsite and the catalytic acid/base Glu253, was modified to assess the effect of side chain size at this position on disproportionation and hydrolysis activities. The best mutant, L277M, exhibited a reduced Km for the acceptor substrate maltose (0.48 mM versus 0.945 mM) and an increased k cat/Km (1175 s-1mM-1 versus 686.1 s-1mM-1), compared with those of the wild-type enzyme. The disproportionation to hydrolysis ratio of L277M was 2.4-fold greater than that of the wild-type. Existing structural data were combined with a multi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Demin Kong Lei Wang Lingqia Su Jing Wu Source Type: research

Proteolytic maturation of the Outer Membrane < em > c < /em > -type cytochrome OmcZ by Subtilisin-like Serine Protease is Essential for Optimal Current Production by < em > Geobacter sulfurreducens < /em >
This study identifies a subtilisin-like protease OzpA, which plays a role in cleaving OmcZ and generating the mature form of OmcZ (OmcZS). OzpA is essential for current production, and thus, the proteolytic maturation of OmcZ. This is a novel regulation of the c-type cytochrome for G. sulfurreducens extracellular electron transfer. This study also provide new insights into the design strategy and development of microbial extracellular electron transfer for an efficient energy conversion from chemical energy to electricity.PMID:33837010 | DOI:10.1128/AEM.02617-20 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Ayako Kai Takahiro Tokuishi Takashi Fujikawa Yoshihiro Kawano Toshiyuki Ueki Miyuki Nagamine Yoichi Sakakibara Masahito Suiko Kengo Inoue Source Type: research

Genetic suppression of lethal mutations in fatty acid biosynthesis mediated by a secondary lipid synthase
Appl Environ Microbiol. 2021 Apr 9:AEM.00035-21. doi: 10.1128/AEM.00035-21. Online ahead of print.ABSTRACTThe biosynthesis and incorporation of polyunsaturated fatty acids into phospholipid membranes is a unique feature of certain marine Gammaproteobacteria inhabiting high-pressure and/or low temperature environments. In these bacteria, monounsaturated and saturated fatty acids are produced via the classical dissociated Type II fatty acid synthase mechanism, while omega-3 polyunsaturated fatty acids such as EPA (20:5n-3) and DHA (22:6n-3) are produced by a hybrid polyketide/fatty acid synthase - encoded by the pfa genes - ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Marco N Allemann Eric E Allen Source Type: research

Bacillaene Mediates the Inhibitory Effect of < em > Bacillus subtilis < /em > on < em > Campylobacter jejuni < /em > Biofilms
In this study, we investigated the ability of the natural isolate Bacillus subtilis PS-216 to restrain Campylobacter jejuni biofilm formation and adhesion to abiotic surfaces as well as to disrupt pre-established C. jejuni biofilms. Using confocal laser scanning microscopy and colony counts, we demonstrate that the presence of B. subtilis PS-216 prevents C. jejuni biofilm formation, decreases growth of the pathogen by 4.2 log10 and disperses 26 h old pre-established C. jejuni biofilms. Furthermore, the co-inoculation of B. subtilis and C. jejuni interferes with the adhesion of C. jejuni to abiotic surfaces reducing it by 2...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: A Erega P Stefanic I Dogsa T Danev čič K Simunovic A Klan čnik S Smole Mo žina I Mandic Mulec Source Type: research

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling
Appl Environ Microbiol. 2021 Apr 9:AEM.00546-21. doi: 10.1128/AEM.00546-21. Online ahead of print.ABSTRACTThe phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct mi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Smruthi Karthikeyan Luis H Orellana Eric R Johnston Janet K Hatt Frank E L öffler H éctor L Ayala-Del-Río Grizelle Gonz ález Konstantinos T Konstantinidis Source Type: research

Warming shapes < em > nirS- < /em > and < em > nosZ < /em > -type denitrifier communities and stimulates N < sub > 2 < /sub > O emission in acidic paddy soil
This study demonstrated high temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and dev...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoyi Xing Yafang Tang Huifang Xu Hongling Qin Yi Liu Wenzhao Zhang Anlei Chen Baoli Zhu Source Type: research

Characterization of a lysozyme-like effector TseP and secretion co-dependence of the type VI secretion system in < em > Aeromonas dhakensis < /em > SSU
In this study, we identified a cell-wall lysing effector and by inactivating it and the other two known effectors, we have built a detoxified T6SS-active strain that may be used for protein delivery towards prokaryotic and eukaryotic recipient cells.PMID:33837015 | DOI:10.1128/AEM.00435-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoye Liang Tong-Tong Pei Zeng-Hang Wang Weiliang Xiong Li-Li Wu Ping Xu Shuangjun Lin Tao G Dong Source Type: research

Determination of antimicrobial resistance profiles and mechanisms of < em > Campylobacter jejuni < /em > using a Raman spectroscopy-based metabolomic approach
In this study, we have applied Raman spectroscopy and chemometrics to achieve a rapid, accurate, and easy-to-operate investigation on bacterial AMR profiles and mechanisms. Raman spectroscopy reduced the analysis time by an order of magnitude to obtain the same results from traditional culture-based antimicrobial susceptibility approaches. It offers great benefits as a high-throughput screening method in food chain surveillance and clinical diagnostics. Meanwhile, the AMR mechanisms towards two representative antibiotic classes, namely ampicillin and tetracycline, were revealed by Raman spectroscopy at metabolome level. Th...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Luyao Ma Lei Chen Keng C Chou Xiaonan Lu Source Type: research

Biosensor-based multi-gene pathway optimization for enhancing the production of glycolate
Appl Environ Microbiol. 2021 Apr 9:AEM.00113-21. doi: 10.1128/AEM.00113-21. Online ahead of print.ABSTRACTGlycolate is widely used in industry, especially in the fields of chemical cleaning, cosmetics, and medical materials, and has broad market prospects for the future. Recent advances in metabolic engineering and synthetic biology have significantly improved the titer and yield of glycolate. However, an expensive inducer was used in previous studies that is not feasible for use in large-scale industrial fermentations. To constitutively biosynthesize glycolate, the expression level of each gene of the glycolate synthetic ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Shumin Xu Linpei Zhang Shenghu Zhou Yu Deng Source Type: research

Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity
Appl Environ Microbiol. 2021 Apr 9:AEM.00471-21. doi: 10.1128/AEM.00471-21. Online ahead of print.ABSTRACTAcyl coenzyme A (CoA) binding protein (ACBP), also called diazepam-binding inhibitor (DBI) is a phylogenetically conserved protein that is expressed by all eukaryotic species as well as by some bacteria. Since elevated ACBP/DBI levels play a major role in the inhibition of autophagy, increase in appetite and lipoanabolism that accompany obesity, we wondered whether ACBP/DBI produced by the human microbiome might affect host weight. We found that the genomes of bacterial commensals rarely contain ACBP/DBI homologues, wh...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Andrew Maltez Thomas Francesco Asnicar Guido Kroemer Nicola Segata Source Type: research

Tobramycin Adaptation Enhances Policing of Social Cheaters in < em > Pseudomonas aeruginosa < /em >
Appl Environ Microbiol. 2021 Apr 9:AEM.00029-21. doi: 10.1128/AEM.00029-21. Online ahead of print.ABSTRACTThe Pseudomonas aeruginosa LasR-I quorum-sensing system regulates secreted proteases that can be exploited by cheaters, such as quorum sensing receptor-defective (lasR) mutants. lasR mutants emerge in populations growing on casein as a sole source of carbon and energy. These mutants are exploitative cheaters because they avoid the substantial cost of engaging in quorum sensing. Previous studies showed that quorum sensing increases resistance to some antibiotics, such as tobramycin. Here, we show that tobramycin suppres...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Rhea G Abisado John H Kimbrough Brielle M McKee Vaughn D Craddock Nicole E Smalley Ajai A Dandekar Josephine R Chandler Source Type: research

Effects of Different Land-use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils
Appl Environ Microbiol. 2021 Apr 9:AEM.00092-21. doi: 10.1128/AEM.00092-21. Online ahead of print.ABSTRACTLand-use types with different disturbance gradients show many variations in soil properties, but the effects of different land-use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soils under three land-use types, forest, cropland, and greenhouse vegetable...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xinli Wang Yun Wang Fei Zhu Chi Zhang Peiyao Wang Xuan Zhang Source Type: research

Global diversity and biogeography of the < em > Zostera marina < /em > mycobiome
In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.PMID:33837008 | DOI:10.1128/AEM.02795-20 (Sou...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Cassandra L Ettinger Laura E Vann Jonathan A Eisen Source Type: research

Effect of Leu277 on Disproportionation and Hydrolysis Activity in < em > Bacillus stearothermophilus < /em > NO2 Cyclodextrin Glucosyltransferase
In this study, Leu277 of the CGTase from Bacillus stearothermophilus NO2, located near both the +2 subsite and the catalytic acid/base Glu253, was modified to assess the effect of side chain size at this position on disproportionation and hydrolysis activities. The best mutant, L277M, exhibited a reduced Km for the acceptor substrate maltose (0.48 mM versus 0.945 mM) and an increased k cat/Km (1175 s-1mM-1 versus 686.1 s-1mM-1), compared with those of the wild-type enzyme. The disproportionation to hydrolysis ratio of L277M was 2.4-fold greater than that of the wild-type. Existing structural data were combined with a multi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Demin Kong Lei Wang Lingqia Su Jing Wu Source Type: research

Proteolytic maturation of the Outer Membrane < em > c < /em > -type cytochrome OmcZ by Subtilisin-like Serine Protease is Essential for Optimal Current Production by < em > Geobacter sulfurreducens < /em >
This study identifies a subtilisin-like protease OzpA, which plays a role in cleaving OmcZ and generating the mature form of OmcZ (OmcZS). OzpA is essential for current production, and thus, the proteolytic maturation of OmcZ. This is a novel regulation of the c-type cytochrome for G. sulfurreducens extracellular electron transfer. This study also provide new insights into the design strategy and development of microbial extracellular electron transfer for an efficient energy conversion from chemical energy to electricity.PMID:33837010 | DOI:10.1128/AEM.02617-20 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Ayako Kai Takahiro Tokuishi Takashi Fujikawa Yoshihiro Kawano Toshiyuki Ueki Miyuki Nagamine Yoichi Sakakibara Masahito Suiko Kengo Inoue Source Type: research

Genetic suppression of lethal mutations in fatty acid biosynthesis mediated by a secondary lipid synthase
Appl Environ Microbiol. 2021 Apr 9:AEM.00035-21. doi: 10.1128/AEM.00035-21. Online ahead of print.ABSTRACTThe biosynthesis and incorporation of polyunsaturated fatty acids into phospholipid membranes is a unique feature of certain marine Gammaproteobacteria inhabiting high-pressure and/or low temperature environments. In these bacteria, monounsaturated and saturated fatty acids are produced via the classical dissociated Type II fatty acid synthase mechanism, while omega-3 polyunsaturated fatty acids such as EPA (20:5n-3) and DHA (22:6n-3) are produced by a hybrid polyketide/fatty acid synthase - encoded by the pfa genes - ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Marco N Allemann Eric E Allen Source Type: research

Bacillaene Mediates the Inhibitory Effect of < em > Bacillus subtilis < /em > on < em > Campylobacter jejuni < /em > Biofilms
In this study, we investigated the ability of the natural isolate Bacillus subtilis PS-216 to restrain Campylobacter jejuni biofilm formation and adhesion to abiotic surfaces as well as to disrupt pre-established C. jejuni biofilms. Using confocal laser scanning microscopy and colony counts, we demonstrate that the presence of B. subtilis PS-216 prevents C. jejuni biofilm formation, decreases growth of the pathogen by 4.2 log10 and disperses 26 h old pre-established C. jejuni biofilms. Furthermore, the co-inoculation of B. subtilis and C. jejuni interferes with the adhesion of C. jejuni to abiotic surfaces reducing it by 2...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: A Erega P Stefanic I Dogsa T Danev čič K Simunovic A Klan čnik S Smole Mo žina I Mandic Mulec Source Type: research

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling
Appl Environ Microbiol. 2021 Apr 9:AEM.00546-21. doi: 10.1128/AEM.00546-21. Online ahead of print.ABSTRACTThe phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct mi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Smruthi Karthikeyan Luis H Orellana Eric R Johnston Janet K Hatt Frank E L öffler H éctor L Ayala-Del-Río Grizelle Gonz ález Konstantinos T Konstantinidis Source Type: research

Warming shapes < em > nirS- < /em > and < em > nosZ < /em > -type denitrifier communities and stimulates N < sub > 2 < /sub > O emission in acidic paddy soil
This study demonstrated high temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and dev...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoyi Xing Yafang Tang Huifang Xu Hongling Qin Yi Liu Wenzhao Zhang Anlei Chen Baoli Zhu Source Type: research

Characterization of a lysozyme-like effector TseP and secretion co-dependence of the type VI secretion system in < em > Aeromonas dhakensis < /em > SSU
In this study, we identified a cell-wall lysing effector and by inactivating it and the other two known effectors, we have built a detoxified T6SS-active strain that may be used for protein delivery towards prokaryotic and eukaryotic recipient cells.PMID:33837015 | DOI:10.1128/AEM.00435-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoye Liang Tong-Tong Pei Zeng-Hang Wang Weiliang Xiong Li-Li Wu Ping Xu Shuangjun Lin Tao G Dong Source Type: research

Determination of antimicrobial resistance profiles and mechanisms of < em > Campylobacter jejuni < /em > using a Raman spectroscopy-based metabolomic approach
In this study, we have applied Raman spectroscopy and chemometrics to achieve a rapid, accurate, and easy-to-operate investigation on bacterial AMR profiles and mechanisms. Raman spectroscopy reduced the analysis time by an order of magnitude to obtain the same results from traditional culture-based antimicrobial susceptibility approaches. It offers great benefits as a high-throughput screening method in food chain surveillance and clinical diagnostics. Meanwhile, the AMR mechanisms towards two representative antibiotic classes, namely ampicillin and tetracycline, were revealed by Raman spectroscopy at metabolome level. Th...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Luyao Ma Lei Chen Keng C Chou Xiaonan Lu Source Type: research

Biosensor-based multi-gene pathway optimization for enhancing the production of glycolate
Appl Environ Microbiol. 2021 Apr 9:AEM.00113-21. doi: 10.1128/AEM.00113-21. Online ahead of print.ABSTRACTGlycolate is widely used in industry, especially in the fields of chemical cleaning, cosmetics, and medical materials, and has broad market prospects for the future. Recent advances in metabolic engineering and synthetic biology have significantly improved the titer and yield of glycolate. However, an expensive inducer was used in previous studies that is not feasible for use in large-scale industrial fermentations. To constitutively biosynthesize glycolate, the expression level of each gene of the glycolate synthetic ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Shumin Xu Linpei Zhang Shenghu Zhou Yu Deng Source Type: research

Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity
Appl Environ Microbiol. 2021 Apr 9:AEM.00471-21. doi: 10.1128/AEM.00471-21. Online ahead of print.ABSTRACTAcyl coenzyme A (CoA) binding protein (ACBP), also called diazepam-binding inhibitor (DBI) is a phylogenetically conserved protein that is expressed by all eukaryotic species as well as by some bacteria. Since elevated ACBP/DBI levels play a major role in the inhibition of autophagy, increase in appetite and lipoanabolism that accompany obesity, we wondered whether ACBP/DBI produced by the human microbiome might affect host weight. We found that the genomes of bacterial commensals rarely contain ACBP/DBI homologues, wh...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Andrew Maltez Thomas Francesco Asnicar Guido Kroemer Nicola Segata Source Type: research

Tobramycin Adaptation Enhances Policing of Social Cheaters in < em > Pseudomonas aeruginosa < /em >
Appl Environ Microbiol. 2021 Apr 9:AEM.00029-21. doi: 10.1128/AEM.00029-21. Online ahead of print.ABSTRACTThe Pseudomonas aeruginosa LasR-I quorum-sensing system regulates secreted proteases that can be exploited by cheaters, such as quorum sensing receptor-defective (lasR) mutants. lasR mutants emerge in populations growing on casein as a sole source of carbon and energy. These mutants are exploitative cheaters because they avoid the substantial cost of engaging in quorum sensing. Previous studies showed that quorum sensing increases resistance to some antibiotics, such as tobramycin. Here, we show that tobramycin suppres...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Rhea G Abisado John H Kimbrough Brielle M McKee Vaughn D Craddock Nicole E Smalley Ajai A Dandekar Josephine R Chandler Source Type: research

Effects of Different Land-use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils
Appl Environ Microbiol. 2021 Apr 9:AEM.00092-21. doi: 10.1128/AEM.00092-21. Online ahead of print.ABSTRACTLand-use types with different disturbance gradients show many variations in soil properties, but the effects of different land-use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soils under three land-use types, forest, cropland, and greenhouse vegetable...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xinli Wang Yun Wang Fei Zhu Chi Zhang Peiyao Wang Xuan Zhang Source Type: research

Global diversity and biogeography of the < em > Zostera marina < /em > mycobiome
In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.PMID:33837008 | DOI:10.1128/AEM.02795-20 (Sou...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Cassandra L Ettinger Laura E Vann Jonathan A Eisen Source Type: research

Effect of Leu277 on Disproportionation and Hydrolysis Activity in < em > Bacillus stearothermophilus < /em > NO2 Cyclodextrin Glucosyltransferase
In this study, Leu277 of the CGTase from Bacillus stearothermophilus NO2, located near both the +2 subsite and the catalytic acid/base Glu253, was modified to assess the effect of side chain size at this position on disproportionation and hydrolysis activities. The best mutant, L277M, exhibited a reduced Km for the acceptor substrate maltose (0.48 mM versus 0.945 mM) and an increased k cat/Km (1175 s-1mM-1 versus 686.1 s-1mM-1), compared with those of the wild-type enzyme. The disproportionation to hydrolysis ratio of L277M was 2.4-fold greater than that of the wild-type. Existing structural data were combined with a multi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Demin Kong Lei Wang Lingqia Su Jing Wu Source Type: research

Proteolytic maturation of the Outer Membrane < em > c < /em > -type cytochrome OmcZ by Subtilisin-like Serine Protease is Essential for Optimal Current Production by < em > Geobacter sulfurreducens < /em >
This study identifies a subtilisin-like protease OzpA, which plays a role in cleaving OmcZ and generating the mature form of OmcZ (OmcZS). OzpA is essential for current production, and thus, the proteolytic maturation of OmcZ. This is a novel regulation of the c-type cytochrome for G. sulfurreducens extracellular electron transfer. This study also provide new insights into the design strategy and development of microbial extracellular electron transfer for an efficient energy conversion from chemical energy to electricity.PMID:33837010 | DOI:10.1128/AEM.02617-20 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Ayako Kai Takahiro Tokuishi Takashi Fujikawa Yoshihiro Kawano Toshiyuki Ueki Miyuki Nagamine Yoichi Sakakibara Masahito Suiko Kengo Inoue Source Type: research

Genetic suppression of lethal mutations in fatty acid biosynthesis mediated by a secondary lipid synthase
Appl Environ Microbiol. 2021 Apr 9:AEM.00035-21. doi: 10.1128/AEM.00035-21. Online ahead of print.ABSTRACTThe biosynthesis and incorporation of polyunsaturated fatty acids into phospholipid membranes is a unique feature of certain marine Gammaproteobacteria inhabiting high-pressure and/or low temperature environments. In these bacteria, monounsaturated and saturated fatty acids are produced via the classical dissociated Type II fatty acid synthase mechanism, while omega-3 polyunsaturated fatty acids such as EPA (20:5n-3) and DHA (22:6n-3) are produced by a hybrid polyketide/fatty acid synthase - encoded by the pfa genes - ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Marco N Allemann Eric E Allen Source Type: research

Bacillaene Mediates the Inhibitory Effect of < em > Bacillus subtilis < /em > on < em > Campylobacter jejuni < /em > Biofilms
In this study, we investigated the ability of the natural isolate Bacillus subtilis PS-216 to restrain Campylobacter jejuni biofilm formation and adhesion to abiotic surfaces as well as to disrupt pre-established C. jejuni biofilms. Using confocal laser scanning microscopy and colony counts, we demonstrate that the presence of B. subtilis PS-216 prevents C. jejuni biofilm formation, decreases growth of the pathogen by 4.2 log10 and disperses 26 h old pre-established C. jejuni biofilms. Furthermore, the co-inoculation of B. subtilis and C. jejuni interferes with the adhesion of C. jejuni to abiotic surfaces reducing it by 2...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: A Erega P Stefanic I Dogsa T Danev čič K Simunovic A Klan čnik S Smole Mo žina I Mandic Mulec Source Type: research

Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling
Appl Environ Microbiol. 2021 Apr 9:AEM.00546-21. doi: 10.1128/AEM.00546-21. Online ahead of print.ABSTRACTThe phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct mi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Smruthi Karthikeyan Luis H Orellana Eric R Johnston Janet K Hatt Frank E L öffler H éctor L Ayala-Del-Río Grizelle Gonz ález Konstantinos T Konstantinidis Source Type: research

Warming shapes < em > nirS- < /em > and < em > nosZ < /em > -type denitrifier communities and stimulates N < sub > 2 < /sub > O emission in acidic paddy soil
This study demonstrated high temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and dev...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoyi Xing Yafang Tang Huifang Xu Hongling Qin Yi Liu Wenzhao Zhang Anlei Chen Baoli Zhu Source Type: research

Characterization of a lysozyme-like effector TseP and secretion co-dependence of the type VI secretion system in < em > Aeromonas dhakensis < /em > SSU
In this study, we identified a cell-wall lysing effector and by inactivating it and the other two known effectors, we have built a detoxified T6SS-active strain that may be used for protein delivery towards prokaryotic and eukaryotic recipient cells.PMID:33837015 | DOI:10.1128/AEM.00435-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xiaoye Liang Tong-Tong Pei Zeng-Hang Wang Weiliang Xiong Li-Li Wu Ping Xu Shuangjun Lin Tao G Dong Source Type: research

Determination of antimicrobial resistance profiles and mechanisms of < em > Campylobacter jejuni < /em > using a Raman spectroscopy-based metabolomic approach
In this study, we have applied Raman spectroscopy and chemometrics to achieve a rapid, accurate, and easy-to-operate investigation on bacterial AMR profiles and mechanisms. Raman spectroscopy reduced the analysis time by an order of magnitude to obtain the same results from traditional culture-based antimicrobial susceptibility approaches. It offers great benefits as a high-throughput screening method in food chain surveillance and clinical diagnostics. Meanwhile, the AMR mechanisms towards two representative antibiotic classes, namely ampicillin and tetracycline, were revealed by Raman spectroscopy at metabolome level. Th...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Luyao Ma Lei Chen Keng C Chou Xiaonan Lu Source Type: research

Biosensor-based multi-gene pathway optimization for enhancing the production of glycolate
Appl Environ Microbiol. 2021 Apr 9:AEM.00113-21. doi: 10.1128/AEM.00113-21. Online ahead of print.ABSTRACTGlycolate is widely used in industry, especially in the fields of chemical cleaning, cosmetics, and medical materials, and has broad market prospects for the future. Recent advances in metabolic engineering and synthetic biology have significantly improved the titer and yield of glycolate. However, an expensive inducer was used in previous studies that is not feasible for use in large-scale industrial fermentations. To constitutively biosynthesize glycolate, the expression level of each gene of the glycolate synthetic ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Shumin Xu Linpei Zhang Shenghu Zhou Yu Deng Source Type: research

Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity
Appl Environ Microbiol. 2021 Apr 9:AEM.00471-21. doi: 10.1128/AEM.00471-21. Online ahead of print.ABSTRACTAcyl coenzyme A (CoA) binding protein (ACBP), also called diazepam-binding inhibitor (DBI) is a phylogenetically conserved protein that is expressed by all eukaryotic species as well as by some bacteria. Since elevated ACBP/DBI levels play a major role in the inhibition of autophagy, increase in appetite and lipoanabolism that accompany obesity, we wondered whether ACBP/DBI produced by the human microbiome might affect host weight. We found that the genomes of bacterial commensals rarely contain ACBP/DBI homologues, wh...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Andrew Maltez Thomas Francesco Asnicar Guido Kroemer Nicola Segata Source Type: research

Tobramycin Adaptation Enhances Policing of Social Cheaters in < em > Pseudomonas aeruginosa < /em >
Appl Environ Microbiol. 2021 Apr 9:AEM.00029-21. doi: 10.1128/AEM.00029-21. Online ahead of print.ABSTRACTThe Pseudomonas aeruginosa LasR-I quorum-sensing system regulates secreted proteases that can be exploited by cheaters, such as quorum sensing receptor-defective (lasR) mutants. lasR mutants emerge in populations growing on casein as a sole source of carbon and energy. These mutants are exploitative cheaters because they avoid the substantial cost of engaging in quorum sensing. Previous studies showed that quorum sensing increases resistance to some antibiotics, such as tobramycin. Here, we show that tobramycin suppres...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Rhea G Abisado John H Kimbrough Brielle M McKee Vaughn D Craddock Nicole E Smalley Ajai A Dandekar Josephine R Chandler Source Type: research

Effects of Different Land-use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils
Appl Environ Microbiol. 2021 Apr 9:AEM.00092-21. doi: 10.1128/AEM.00092-21. Online ahead of print.ABSTRACTLand-use types with different disturbance gradients show many variations in soil properties, but the effects of different land-use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soils under three land-use types, forest, cropland, and greenhouse vegetable...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Xinli Wang Yun Wang Fei Zhu Chi Zhang Peiyao Wang Xuan Zhang Source Type: research

Global diversity and biogeography of the < em > Zostera marina < /em > mycobiome
In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.PMID:33837008 | DOI:10.1128/AEM.02795-20 (Sou...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Cassandra L Ettinger Laura E Vann Jonathan A Eisen Source Type: research

Effect of Leu277 on Disproportionation and Hydrolysis Activity in < em > Bacillus stearothermophilus < /em > NO2 Cyclodextrin Glucosyltransferase
In this study, Leu277 of the CGTase from Bacillus stearothermophilus NO2, located near both the +2 subsite and the catalytic acid/base Glu253, was modified to assess the effect of side chain size at this position on disproportionation and hydrolysis activities. The best mutant, L277M, exhibited a reduced Km for the acceptor substrate maltose (0.48 mM versus 0.945 mM) and an increased k cat/Km (1175 s-1mM-1 versus 686.1 s-1mM-1), compared with those of the wild-type enzyme. The disproportionation to hydrolysis ratio of L277M was 2.4-fold greater than that of the wild-type. Existing structural data were combined with a multi...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Demin Kong Lei Wang Lingqia Su Jing Wu Source Type: research

Proteolytic maturation of the Outer Membrane < em > c < /em > -type cytochrome OmcZ by Subtilisin-like Serine Protease is Essential for Optimal Current Production by < em > Geobacter sulfurreducens < /em >
This study identifies a subtilisin-like protease OzpA, which plays a role in cleaving OmcZ and generating the mature form of OmcZ (OmcZS). OzpA is essential for current production, and thus, the proteolytic maturation of OmcZ. This is a novel regulation of the c-type cytochrome for G. sulfurreducens extracellular electron transfer. This study also provide new insights into the design strategy and development of microbial extracellular electron transfer for an efficient energy conversion from chemical energy to electricity.PMID:33837010 | DOI:10.1128/AEM.02617-20 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Ayako Kai Takahiro Tokuishi Takashi Fujikawa Yoshihiro Kawano Toshiyuki Ueki Miyuki Nagamine Yoichi Sakakibara Masahito Suiko Kengo Inoue Source Type: research

Genetic suppression of lethal mutations in fatty acid biosynthesis mediated by a secondary lipid synthase
Appl Environ Microbiol. 2021 Apr 9:AEM.00035-21. doi: 10.1128/AEM.00035-21. Online ahead of print.ABSTRACTThe biosynthesis and incorporation of polyunsaturated fatty acids into phospholipid membranes is a unique feature of certain marine Gammaproteobacteria inhabiting high-pressure and/or low temperature environments. In these bacteria, monounsaturated and saturated fatty acids are produced via the classical dissociated Type II fatty acid synthase mechanism, while omega-3 polyunsaturated fatty acids such as EPA (20:5n-3) and DHA (22:6n-3) are produced by a hybrid polyketide/fatty acid synthase - encoded by the pfa genes - ...
Source: Applied and Environmental Microbiology - April 10, 2021 Category: Microbiology Authors: Marco N Allemann Eric E Allen Source Type: research