microLife最新文献

{"title":"Inferring bacterial interspecific interactions from microcolony growth expansion.","authors":"Tania Miguel Trabajo, Isaline Guex, Manupriyam Dubey, Elvire Sarton-Lohéac, Helena Todorov, Xavier Richard, Christian Mazza, Jan Roelof van der Meer","doi":"10.1093/femsml/uqae020","DOIUrl":"10.1093/femsml/uqae020","url":null,"abstract":"<p><p>Bacterial species interactions significantly shape growth and behavior in communities, determining the emergence of community functions. Typically, these interactions are studied through bulk population measurements, overlooking the role of cell-to-cell variability and spatial context. This study uses real-time surface growth measurements of thousands of sparsely positioned microcolonies to investigate interactions and kinetic variations in monocultures and cocultures of <i>Pseudomonas putida</i> and <i>P. veronii</i> under substrate competition (succinate) or substrate independence (d-mannitol and putrescine). In monoculture, microcolonies exhibited expected substrate-dependent expansion rates, but individual colony sizes were affected by founder cell density, spatial positioning, growth rates, and lag times. In coculture, substrate competition favored <i>P. putida</i>, but unexpectedly, reduced the maximum growth rates of both species. In contrast, 10% of <i>P. veronii</i> microcolonies under competition grew larger than expected, likely due to founder cell phenotypic variation and stochastic spatial positioning. These effects were alleviated under substrate independence. A linear relationship between founder cell ratios and final colony area ratios in local neighborhoods (6.5-65 µm radius) was observed in coculture, with its slope reflecting interaction type and strength. Measured slopes in the <i>P. putida</i> to <i>P. veronii</i> biomass ratio under competition were one-third reduced compared to kinetic predictions using a cell-agent growth model, which exometabolite analysis and simulations suggested may be due to metabolite cross-feeding or inhibitory compound production. This indicates additional factors beyond inherent monoculture growth kinetics driving spatial interactions. Overall, the study demonstrates how microcolony growth experiments offer valuable insights into bacterial interactions, from local to community-level dynamics.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae020"},"PeriodicalIF":0.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acetylomics reveals an extensive acetylation diversity within <i>Pseudomonas aeruginosa</i>.","authors":"Nand Broeckaert, Hannelore Longin, Hanne Hendrix, Jeroen De Smet, Mirita Franz-Wachtel, Boris Maček, Vera van Noort, Rob Lavigne","doi":"10.1093/femsml/uqae018","DOIUrl":"10.1093/femsml/uqae018","url":null,"abstract":"<p><p>Bacteria employ a myriad of regulatory mechanisms to adapt to the continuously changing environments that they face. They can, for example, use post-translational modifications, such as Nε-lysine acetylation, to alter enzyme activity. Although a lot of progress has been made, the extent and role of lysine acetylation in many bacterial strains remains uncharted. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) in combination with the immunoprecipitation of acetylated peptides and LC-MS/MS to measure the first <i>Pseudomonas aeruginosa</i> PAO1 acetylome, revealing 1076 unique acetylation sites in 508 proteins. Next, we assessed interstrain acetylome differences within <i>P. aeruginosa</i> by comparing our PAO1 acetylome with two publicly available PA14 acetylomes, and postulate that the overall acetylation patterns are not driven by strain-specific factors. In addition, the comparison of the <i>P. aeruginosa</i> acetylome to 30 other bacterial acetylomes revealed that a high percentage of transcription related proteins are acetylated in the majority of bacterial species. This conservation could help prioritize the characterization of functional consequences of individual acetylation sites.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae018"},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial hub signaling compounds: natural products disproportionally shape microbiome composition and structure.","authors":"Axel A Brakhage","doi":"10.1093/femsml/uqae017","DOIUrl":"10.1093/femsml/uqae017","url":null,"abstract":"<p><p>Microbiomes are shaped by abiotic factors like nutrients, oxygen availability, pH, temperature, and so on, but also by biotic factors including low molecular weight organic compounds referred to as natural products (NPs). Based on genome analyses, millions of these compounds are predicted to exist in nature, some of them have found important applications e.g. as antibiotics. Based on recent data I propose a model that some of these compounds function as microbial hub signaling compounds, i.e. they have a higher hierarchical influence on microbiomes. These compounds have direct effects e.g. by inhibiting microorganisms and thereby exclude them from a microbiome (excluded). Some microorganisms do not respond at all (nonresponder), others respond by producing themselves NPs like a second wave of information molecules (message responder) influencing other microorganisms, but conceivably a more limited spectrum. Some microorganisms may respond to the hub compounds with their chemical modification (message modifiers). This way, the modified NPs may have themselves signaling function for a subset of microorganisms. Finally, it is also likely that NPs act as food source (C- and/or N-source) for microorganisms specialized on their degradation. As a consequence, such specialized microorganisms are selectively recruited to the microbiota.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae017"},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial markets: socio-economic perspective in studying microbial communities.","authors":"Fariha Mostafa, Aileen Krüger, Tim Nies, Julia Frunzke, Kerstin Schipper, Anna Matuszyńska","doi":"10.1093/femsml/uqae016","DOIUrl":"10.1093/femsml/uqae016","url":null,"abstract":"<p><p>Studying microbial communities through a socio-economic lens, this paper draws parallels with human economic transactions and microbes' race for resources. Extending the 'Market Economy' concept of social science to microbial ecosystems, the paper aims to contribute to comprehending the collaborative and competitive dynamics among microorganisms. Created by a multidisciplinary team of an economist, microbiologists, and mathematicians, the paper also highlights the risks involved in employing a socio-economic perspective to explain the complexities of natural ecosystems. Navigating through microbial markets offers insights into the implications of these interactions while emphasizing the need for cautious interpretation within the broader ecological context. We hope that this paper will be a fruitful source of inspiration for future studies on microbial communities.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae016"},"PeriodicalIF":0.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resistance against aminoglycoside antibiotics via drug or target modification enables community-wide antiphage defense.","authors":"Larissa Kever, Qian Zhang, Aël Hardy, Philipp Westhoff, Yi Yu, Julia Frunzke","doi":"10.1093/femsml/uqae015","DOIUrl":"10.1093/femsml/uqae015","url":null,"abstract":"<p><p>The ongoing arms race between bacteria and phages has forced bacteria to evolve a sophisticated set of antiphage defense mechanisms that constitute the bacterial immune system. In our previous study, we highlighted the antiphage properties of aminoglycoside antibiotics, which are naturally secreted by <i>Streptomyces</i>. Successful inhibition of phage infection was achieved by addition of pure compounds and supernatants from a natural producer strain emphasizing the potential for community-wide antiphage defense. However, given the dual functionality of these compounds, neighboring bacterial cells require resistance to the antibacterial activity of aminoglycosides to benefit from the protection they confer against phages. In this study, we tested a variety of different aminoglycoside resistance mechanisms acting via drug or target (16S rRNA) modification and demonstrated that they do not interfere with the antiphage properties of the molecules. Furthermore, we confirmed the antiphage impact of aminoglycosides in a community context by coculturing phage-susceptible, apramycin-resistant <i>Streptomyces venezuelae</i> with the apramycin-producing strain <i>Streptoalloteichus tenebrarius</i>. Given the prevalence of aminoglycoside resistance among natural bacterial isolates, this study highlights the ecological relevance of chemical defense via aminoglycosides at the community level.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae015"},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B <i>Streptococcus</i>.","authors":"Terry Brissac, Cécile Guyonnet, Aymane Sadouni, Ariadna Hernández-Montoya, Elise Jacquemet, Rachel Legendre, Odile Sismeiro, Patrick Trieu-Cuot, Philippe Lanotte, Asmaa Tazi, Arnaud Firon","doi":"10.1093/femsml/uqae014","DOIUrl":"10.1093/femsml/uqae014","url":null,"abstract":"<p><p><i>Streptococcus agalactiae</i> is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we first report ß-lactam tolerance due to the inactivation of the c-di-AMP phosphodiesterase GdpP. Mechanistically, tolerance depends on antagonistic regulation by the repressor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB osmolyte transporter and the AmaP/Asp23/GlsB cell envelope stress complex. The BusR transcriptional response is synergistic with the simultaneous allosteric inhibition of potassium and osmolyte transporters by c-di-AMP, which individually contribute to low-level ß-lactam tolerance. Genome-wide transposon mutagenesis confirms the role of GdpP and highlights functional interactions between a lysozyme-like hydrolase, the KhpAB RNA chaperone and the protein S immunomodulator in the response of GBS to ß-lactam. Overall, we demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response at the transcriptional and post-translational levels to cell wall weakening caused by ß-lactam activity, and reveal additional mechanisms that could foster resistance.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae014"},"PeriodicalIF":0.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11238645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple variants of the type VII secretion system in Gram-positive bacteria.","authors":"Stephen R Garrett, Andrew B Higginson, Tracy Palmer","doi":"10.1093/femsml/uqae013","DOIUrl":"10.1093/femsml/uqae013","url":null,"abstract":"<p><p>Type VII secretion systems (T7SS) are found in bacteria across the Bacillota and Actinomycetota phyla and have been well described in <i>Staphylococcus aureus, Bacillus subtilis</i>, and pathogenic mycobacteria. The T7SS from Actinomycetota and Bacillota share two common components, a membrane-bound EccC/EssC ATPase and EsxA, a small helical hairpin protein of the WXG100 family. However, they also have additional phylum-specific components, and as a result they are termed the T7SSa (Actinomycetota) and T7SSb (Bacillota), respectively. Here, we identify additional organizations of the T7SS across these two phyla and describe eight additional T7SS subtypes, which we have named T7SSc-T7SSj. T7SSd is found exclusively in Actinomycetota including the <i>Olselnella</i> and <i>Bifodobacterium</i> genus, whereas the other seven are found only in Bacillota. All of the novel subtypes contain the canonical ATPase (TsxC) and the WXG100-family protein (TsxA). Most of them also contain a small ubiquitin-related protein, TsxB, related to the T7SSb EsaB/YukD component. Protein kinases, phosphatases, and forkhead-associated (FHA) proteins are often encoded in the novel T7SS gene clusters. Candidate substrates of these novel T7SS subtypes include LXG-domain and RHS proteins. Predicted substrates are frequently encoded alongside genes for additional small WXG100-related proteins that we speculate serve as cosecretion partners. Collectively our findings reveal unexpected diversity in the T7SS in Gram-positive bacteria.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae013"},"PeriodicalIF":0.0,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11217815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cyanobacterial chemotaxis-like system controls phototactic orientation via phosphorylation of two antagonistic response regulators.","authors":"Yu Han, Jonas Hammerl, Felicitas E Flemming, Nils Schuergers, Annegret Wilde","doi":"10.1093/femsml/uqae012","DOIUrl":"10.1093/femsml/uqae012","url":null,"abstract":"<p><p>Photosynthetic cyanobacteria exhibit phototaxis, utilizing type IV pili (T4P) to navigate either toward or away from a light source. The Tax1 system is a chemotaxis-like signal transduction pathway that controls the switch in cell polarity, which is crucial for positive phototaxis in <i>Synechocystis</i> sp. PCC 6803. The system consists of the blue/green light sensor PixJ, which controls the histidine kinase PixL and two CheY-like response regulators, PixG and PixH. However, the molecular mechanism by which Tax1 regulates T4P activity and polarity is poorly understood. Here, we investigated the phosphotransfer between PixL and its cognate response regulators <i>in vitro</i> and analyzed the localization and function of wild-type and phosphorylation-deficient PixG and PixH during phototaxis. We found that both PixG and PixH are phosphorylated by PixL but have different roles in phototaxis regulation. Only phosphorylated PixG interacts with the T4P motor protein PilB1 and localizes to the leading cell pole under directional light, thereby promoting positive phototaxis. In contrast, PixH is a negative regulator of PixG phosphorylation and inhibits positive phototaxis. We also demonstrated that the C-terminal receiver domain of PixL is essential for positive phototaxis, and modulates the kinase activity of PixL. Our findings reveal the molecular basis of positive phototaxis regulation by the Tax1 system and provide insights into the division of labor between PatA-type and CheY-like response regulators in cyanobacterial chemotaxis-like systems. Furthermore, these findings highlight similarities in the regulation of movement direction during twitching motility in phototactic and chemotactic bacteria.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae012"},"PeriodicalIF":0.0,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11181946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: multireceptor phage cocktail against <i>Salmonella enterica</i> to circumvent phage resistance.","authors":"","doi":"10.1093/femsml/uqae010","DOIUrl":"https://doi.org/10.1093/femsml/uqae010","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/femsml/uqae003.].</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae010"},"PeriodicalIF":0.0,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11110844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141082925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time-series metaproteogenomics of a high-CO₂ aquifer reveals active viruses with fluctuating abundances and broad host ranges.","authors":"Carrie Julia Moore, Till L V Bornemann, Perla Abigail Figueroa-Gonzalez, Sarah P Esser, Cristina Moraru, André Rodrigues Soares, Tjorven Hinzke, Anke Trautwein-Schult, Sandra Maaß, Dörte Becher, Joern Starke, Julia Plewka, Lousia Rothe, Alexander J Probst","doi":"10.1093/femsml/uqae011","DOIUrl":"10.1093/femsml/uqae011","url":null,"abstract":"<p><p>Ecosystems subject to mantle degassing are of particular interest for understanding global biogeochemistry, as their microbiomes are shaped by prolonged exposure to high CO₂ and have recently been suggested to be highly active. While the genetic diversity of bacteria and archaea in these deep biosphere systems have been studied extensively, little is known about how viruses impact these microbial communities. Here, we show that the viral community in a high-CO₂ cold-water geyser (Wallender Born, Germany) undergoes substantial fluctuations over a period of 12 days, although the corresponding prokaryotic community remains stable, indicating a newly observed \"infect to keep in check\" strategy that maintains prokaryotic community structure. We characterized the viral community using metagenomics and metaproteomics, revealing 8 654 viral operational taxonomic units (vOTUs). CRISPR spacer-to-protospacer matching linked 278 vOTUs to 32 hosts, with many vOTUs sharing hosts from different families. High levels of viral structural proteins present in the metaproteome (several structurally annotated based on AlphaFold models) indicate active virion production at the time of sampling. Viral genomes expressed many proteins involved in DNA metabolism and manipulation, and encoded for auxiliary metabolic genes, which likely bolster phosphate and sulfur metabolism of their hosts. The active viral community encodes genes to facilitate acquisition and transformation of host nutrients, and appears to consist of many nutrient-demanding members, based on abundant virion proteins. These findings indicate viruses are inextricably linked to the biogeochemical cycling in this high-CO₂ environment and substantially contribute to prokaryotic community stability in the deep biosphere hotspots.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae011"},"PeriodicalIF":0.0,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11162154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}