mLife最新文献

{"title":"Cultivating the uncultured: Harnessing the “sandwich agar plate” approach to isolate heme‐dependent bacteria from marine sediment","authors":"Jing Zhang, Qi-Yun Liang, Da-shuai Mu, Fengbai Lian, Ya Gong, Mengqi Ye, Guan‐Jun Chen, Yuqi Ye, Zong‐Jun Du","doi":"10.1002/mlf2.12093","DOIUrl":"https://doi.org/10.1002/mlf2.12093","url":null,"abstract":"In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the “sandwich agar plate method,” which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10‐fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth‐promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the “sandwich agar plate method” could be developed and used to isolate more uncultured bacteria.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139526417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing a high‐sensitivity NanoLuc‐based bioluminescence system for in vivo evaluation of antimicrobial treatment","authors":"Weilong Shang, Zhen Hu, Mengyang Li, Yuting Wang, Yifan Rao, Li Tan, Juan Chen, Xiaonan Huang, Lu Liu, He Liu, Zuwen Guo, Huagang Peng, Yi Yang, Qiwen Hu, Shu Li, Xiaomei Hu, Jiao Zou, Xiancai Rao","doi":"10.1002/mlf2.12091","DOIUrl":"https://doi.org/10.1002/mlf2.12091","url":null,"abstract":"Focal and systemic infections are serious threats to human health. Preclinical models enable the development of new drugs and therapeutic regimens. In vivo, animal bioluminescence (BL) imaging has been used with bacterial reporter strains to evaluate antimicrobial treatment effects. However, high‐sensitivity bioluminescent systems are required because of the limited tissue penetration and low brightness of the BL signals of existing approaches. Here, we report that NanoLuc (Nluc) showed better performance than LuxCDABE in bacteria. However, the retention rate of plasmid constructs in bacteria was low. To construct stable Staphylococcus aureus reporter strains, a partner protein enolase (Eno) was identified by screening of S. aureus strain USA300 for fusion expression of Nluc‐based luciferases, including Nluc, Teluc, and Antares2. Different substrates, such as hydrofurimazine (HFZ), furimazine (FUR), and diphenylterazine (DTZ), were used to optimize a stable reporter strain/substrate pair for BL imaging. S. aureus USA300/Eno‐Antares2/HFZ produced the highest number of photons of orange‐red light in vitro and enabled sensitive BL tracking of S. aureus in vivo, with sensitivities of approximately 10 CFU from mouse skin and 750 CFU from mouse kidneys. USA300/Eno‐Antares2/HFZ was a powerful combination based on the longitudinal evaluation of the therapeutic efficacy of antibiotics. The optimized S. aureus Eno‐Antares2/HFZ pair provides a technological advancement for the in vivo evaluation of antimicrobial treatment.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138955258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variation in resource competition traits among Microcystis strains is affected by their microbiomes","authors":"Dylan Baker, Casey Godwin, Muhtamim Khanam, Ashley M. Burtner, Gregory J. Dick, Vincent J. Denef","doi":"10.1002/mlf2.12094","DOIUrl":"https://doi.org/10.1002/mlf2.12094","url":null,"abstract":"Freshwater harmful algal blooms are often dominated by Microcystis, a phylogenetically cohesive group of cyanobacteria marked by extensive genetic and physiological diversity. We have previously shown that this genetic diversity and the presence of a microbiome of heterotrophic bacteria influences competitive interactions with eukaryotic phytoplankton. In this study, we sought to explain these observations by characterizing Monod equation parameters for resource usage (maximum growth rate μmax, half‐saturation value for growth Ks, and quota) as a function of N and P levels for four strains (NIES‐843, PCC 9701, PCC 7806 [WT], and PCC 7806 ΔmcyB) in presence and absence of a microbiome derived from Microcystis isolated from Lake Erie. Results indicated limited differences in maximum growth rates but more pronounced differences in half‐saturation values among Microcystis strains. The largest impact of the microbiome was reducing the minimal nitrogen concentration sustaining growth and reducing half saturation values, with variable results depending on the Microcystis strain. Microcystis strains also differed from each other in their N and P quotas and the extent to which microbiome presence affected them. Our data highlight the importance of the microbiome in altering Microcystis‐intrinsic traits, strain competitive hierarchies, and thus bloom dynamics. As quota, μmax, and Ks are commonly used in models for harmful algal blooms, our data suggest that model improvement may be possible by incorporating genotype dependencies of resource‐use parameters.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138965133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput, microscopy-based screening and quantification of genetic elements.","authors":"Rongrong Zhang, Yajia Huang, Mei Li, Lei Wang, Bing Li, Aiguo Xia, Ye Li, Shuai Yang, Fan Jin","doi":"10.1002/mlf2.12096","DOIUrl":"10.1002/mlf2.12096","url":null,"abstract":"<p><p>Synthetic biology relies on the screening and quantification of genetic components to assemble sophisticated gene circuits with specific functions. Microscopy is a powerful tool for characterizing complex cellular phenotypes with increasing spatial and temporal resolution to library screening of genetic elements. Microscopy-based assays are powerful tools for characterizing cellular phenotypes with spatial and temporal resolution and can be applied to large-scale samples for library screening of genetic elements. However, strategies for high-throughput microscopy experiments remain limited. Here, we present a high-throughput, microscopy-based platform that can simultaneously complete the preparation of an 8 × 12-well agarose pad plate, allowing for the screening of 96 independent strains or experimental conditions in a single experiment. Using this platform, we screened a library of natural intrinsic promoters from <i>Pseudomonas aeruginosa</i> and identified a small subset of robust promoters that drives stable levels of gene expression under varying growth conditions. Additionally, the platform allowed for single-cell measurement of genetic elements over time, enabling the identification of complex and dynamic phenotypes to map genotype in high throughput. We expected that the platform could be employed to accelerate the identification and characterization of genetic elements in various biological systems, as well as to understand the relationship between cellular phenotypes and internal states, including genotypes and gene expression programs.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181760","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":"Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics","authors":"Jinting Liu, Guofang Xu, Siyan Zhao, Jianzhong He","doi":"10.1002/mlf2.12090","DOIUrl":"https://doi.org/10.1002/mlf2.12090","url":null,"abstract":"Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste‐activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long‐term operation. In this study, we found that short‐term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%−9.0%, whereas higher levels (30−200 particles/g sludge) suppressed methanogenesis by 15.2%−30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long‐term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long‐term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138998161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues","authors":"Konstantinos T. Konstantinidis","doi":"10.1002/mlf2.12088","DOIUrl":"https://doi.org/10.1002/mlf2.12088","url":null,"abstract":"Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence‐discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter “intermediate” organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often—but not always—appears to be around 85%–95% genome‐average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138979914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bZIP transcription factor ATF1 regulates blue light and oxidative stress responses in Trichoderma guizhouense","authors":"Yifan Li, Yanshen Li, Huanhong Lu, Tingting Sun, Jia Gao, Jian Zhang, Qirong Shen, Zhenzhong Yu","doi":"10.1002/mlf2.12089","DOIUrl":"https://doi.org/10.1002/mlf2.12089","url":null,"abstract":"In several filamentous fungi, incident light and environmental stress signaling share the mitogen‐activated protein kinase (MAPK) HOG (SAK) pathway. It has been revealed that short‐term illumination with blue light triggers the activation of the HOG pathway in Trichoderma spp. In this study, we demonstrate the crucial role of the basic leucine zipper transcription factor ATF1 in blue light responses and signaling downstream of the MAPK HOG1 in Trichoderma guizhouense. The lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial germination. Upon blue light or H2O2 stimuli, HOG1 interacted with ATF1 in the nucleus. Genome‐wide transcriptome analyses revealed that 61.8% (509 out of 824) and 85.2% (702 out of 824) of blue light‐regulated genes depended on ATF1 and HOG1, respectively, of which 58.4% (481 out of 824) were regulated by both of them. Our results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the dark. Additionally, the lack of ATF1 led to reduced oxidative stress resistance, probably because of the downregulation of catalase‐encoding genes. Overall, our results demonstrate that ATF1 is the downstream component of HOG1 and is responsible for blue light responses, conidial germination, vegetative growth, and oxidative stress resistance in T. guizhouense.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes.","authors":"Xiaoli Yu, Qichao Tu, Jihua Liu, Yisheng Peng, Cheng Wang, Fanshu Xiao, Yingli Lian, Xueqin Yang, Ruiwen Hu, Huang Yu, Lu Qian, Daoming Wu, Ziying He, Longfei Shu, Qiang He, Yun Tian, Faming Wang, Shanquan Wang, Bo Wu, Zhijian Huang, Jianguo He, Qingyun Yan, Zhili He","doi":"10.1002/mlf2.12077","DOIUrl":"10.1002/mlf2.12077","url":null,"abstract":"<p><p>Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH₄), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (<i>Kandelia obovata</i>, KO), the introduced mangrove (<i>Sonneratia apetala</i>, SA) rhizosphere microbiome had significantly (<i>p</i> < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH₄ cycling (e.g., <i>mcrABCDG</i> and <i>pmoABC</i>), N₂ fixation (<i>nifHDK</i>), and inorganic S cycling (<i>dsrAB</i>, <i>dsrC</i>, <i>dsrMKJOP</i>, <i>soxB</i>, <i>sqr</i>, and <i>fccAB</i>). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH₄, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87223601","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":"Roadmap to tackle antibiotic resistance in the environment under the One Health framework.","authors":"Liguan Li, Tong Zhang","doi":"10.1002/mlf2.12078","DOIUrl":"10.1002/mlf2.12078","url":null,"abstract":"<p><p>Antibiotic resistance has been recognized as a major challenge worldwide for humans. \"One Health\" has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a \"One Health\" roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk-assessment framework. The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the \"One Health\" framework provides a guide to tackle antibiotic resistance in the environment.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73199293","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":"Denitrification and the challenge of scaling microsite knowledge to the globe","authors":"G. Philip Robertson","doi":"10.1002/mlf2.12080","DOIUrl":"https://doi.org/10.1002/mlf2.12080","url":null,"abstract":"Abstract Our knowledge of microbial processes—who is responsible for what, the rates at which they occur, and the substrates consumed and products produced—is imperfect for many if not most taxa, but even less is known about how microsite processes scale to the ecosystem and thence the globe. In both natural and managed environments, scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes. But rarely is scaling straightforward: More often than not, process rates in situ are distributed in a highly skewed fashion, under the influence of multiple interacting controls, and thus often difficult to sample, quantify, and predict. To date, quantitative models of many important processes fail to capture daily, seasonal, and annual fluxes with the precision needed to effect meaningful management outcomes. Nitrogen cycle processes are a case in point, and denitrification is a prime example. Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process‐level knowledge gaps or predicting outcomes under novel environmental conditions. Hybrid models that incorporate well‐calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced. Incorporating trait‐based models into such efforts promises to improve predictions and understanding still further, but much more development is needed.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135588082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}