ISME Journal最新文献_第10页

Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. 不同的微生物群落与毫米级土壤团聚体中有机物的特性有关。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae156

Eva Simon, Ksenia Guseva, Sean Darcy, Lauren Alteio, Petra Pjevac, Hannes Schmidt, Kian Jenab, Christian Ranits, Christina Kaiser

{"title":"Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates.","authors":"Eva Simon, Ksenia Guseva, Sean Darcy, Lauren Alteio, Petra Pjevac, Hannes Schmidt, Kian Jenab, Christian Ranits, Christina Kaiser","doi":"10.1093/ismejo/wrae156","DOIUrl":"10.1093/ismejo/wrae156","url":null,"abstract":"Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11325450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions. 通过硫胺素生物合成和硫胺素介导的代谢相互作用实现细菌生长和环境适应。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae157

Xihui Xu, Can Li, Weimiao Cao, Lulu Yan, Lulu Cao, Qi Han, Minling Gao, Yahua Chen, Zhenguo Shen, Jiandong Jiang, Chen Chen

{"title":"Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions.","authors":"Xihui Xu, Can Li, Weimiao Cao, Lulu Yan, Lulu Cao, Qi Han, Minling Gao, Yahua Chen, Zhenguo Shen, Jiandong Jiang, Chen Chen","doi":"10.1093/ismejo/wrae157","DOIUrl":"10.1093/ismejo/wrae157","url":null,"abstract":"Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life's early evolution. However, the biological adaptations occurring during this crucial transition remain largely unexplored. Thiamine is an important cofactor involved in central carbon metabolism and aerobic respiration. Here, we explored the phylogenetic and global distribution of thiamine-auxotrophic and thiamine-prototrophic bacteria based on the thiamine biosynthetic pathway in 154 838 bacterial genomes. We observed strong coincidences of the origin of thiamine-synthetic bacteria with the \"Great Oxygenation Event,\" indicating that thiamine biosynthesis in bacteria emerged as an adaptation to aerobic respiration. Furthermore, we demonstrated that thiamine-mediated metabolic interactions are fundamental factors influencing the assembly and diversity of bacterial communities by a global survey across 4245 soil samples. Through our newly established stable isotope probing-metabolic modeling method, we uncovered the active utilization of thiamine-mediated metabolic interactions by bacterial communities in response to changing environments, thus revealing an environmental adaptation strategy employed by bacteria at the community level. Our study demonstrates the widespread thiamine-mediated metabolic interactions in bacterial communities and their crucial roles in setting the stage for an evolutionary transition from anaerobic to aerobic lifestyles and subsequent environmental adaptation. These findings provide new insights into early bacterial evolution and their subsequent growth and adaptations to environments.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community. 一个深淡水湖中巨型病毒的时空动态揭示了一个独特的暗水群落。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae182

Liwen Zhang, Lingjie Meng, Yue Fang, Hiroyuki Ogata, Yusuke Okazaki

{"title":"Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community.","authors":"Liwen Zhang, Lingjie Meng, Yue Fang, Hiroyuki Ogata, Yusuke Okazaki","doi":"10.1093/ismejo/wrae182","DOIUrl":"10.1093/ismejo/wrae182","url":null,"abstract":"Giant viruses (GVs) significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about GVs of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment of genetic diversity. We sought to bridge this knowledge gap and overcome previous technical limitations. We subjected spatiotemporal (2 depths × 12 months) samples from Lake Biwa to metagenome-assembled genome reconstruction enhanced by long-read metagenomics. This yielded 293 GV metagenome-assembled genomes. Of these, 285 included previously unknown species in five orders of nucleocytoviruses and the first representatives of freshwater mirusviruses, which exhibited marked divergence from marine-derived lineages. The good performance of our long-read metagenomic assembly was demonstrated by the detection of 42 (14.3%) genomes composed of single contigs with completeness values >90%. GVs were partitioned across water depths, with most species specific to either the sunlit epilimnion or the dark hypolimnion. Epilimnion-specific members tended to be transient and exhibit short and intense abundance peaks, in line with the fact that they regulate the surface algal blooms. During the spring bloom, mirusviruses and members of three nucleocytovirus families were among the most abundant viruses. In contrast, hypolimnion-specific ones, including a mirusvirus genome, were typically more persistent in the hypolimnion throughout the water-stratified period, suggesting that they infect hosts specific to the hypolimnion and play previously unexplored ecological roles in dark water microbial ecosystems.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria. Cyanorhodopsin-II 代表了蓝藻中的一个吸黄质子泵浦罗丹素支系。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae175

Masumi Hasegawa-Takano, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Marie Kurihara, Yu Nakajima, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa

{"title":"Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria.","authors":"Masumi Hasegawa-Takano, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Marie Kurihara, Yu Nakajima, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa","doi":"10.1093/ismejo/wrae175","DOIUrl":"10.1093/ismejo/wrae175","url":null,"abstract":"Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142559189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sheaths are diverse and abundant cell surface layers in archaea. 鞘是古细菌中种类繁多的细胞表层。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae225

Sofia Medvedeva, Guillaume Borrel, Simonetta Gribaldo

{"title":"Sheaths are diverse and abundant cell surface layers in archaea.","authors":"Sofia Medvedeva, Guillaume Borrel, Simonetta Gribaldo","doi":"10.1093/ismejo/wrae225","DOIUrl":"10.1093/ismejo/wrae225","url":null,"abstract":"Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings. Here, we conducted a comprehensive survey of sheath-forming proteins (SH proteins) across archaeal genomes. Structural modeling reveals a rich diversity of SH proteins, indicating the presence of a sheath in members of the TACK superphylum (Thermoprotei), as well as in the methanotrophic ANME-1. SH proteins are present in up to 40 copies per genome and display diverse domain arrangements suggesting multifunctional roles within the sheath, and potential involvement in cell-cell interaction with syntrophic partners. We uncover a complex evolutionary dynamic, indicating active exchange of SH proteins in archaeal communities. We find that viruses infecting sheathed archaea encode a diversity of SH-like proteins and we use them as markers to identify 580 vOTUs potentially associated with sheathed archaea. Structural modeling suggests that viral SH proteins can form complexes with the host SH proteins. We propose a previously unreported egress strategy where the expression of viral SH-like proteins may disrupt the integrity of the host sheath and facilitate viral exit during lysis. Together, our results significantly expand knowledge of the diversity and evolution of the archaeal sheath, which has been largely understudied but might have an important role in shaping microbial communities.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. 枯草芽孢杆菌和边缘假单胞菌对铁的竞争形成了代谢拮抗。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrad001

Mark Lyng, Johan P B Jørgensen, Morten D Schostag, Scott A Jarmusch, Diana K C Aguilar, Carlos N Lozano-Andrade, Ákos T Kovács

{"title":"Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis.","authors":"Mark Lyng, Johan P B Jørgensen, Morten D Schostag, Scott A Jarmusch, Diana K C Aguilar, Carlos N Lozano-Andrade, Ákos T Kovács","doi":"10.1093/ismejo/wrad001","DOIUrl":"10.1093/ismejo/wrad001","url":null,"abstract":"Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10811728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration. 深海扇贝-细菌共生揭示了在没有细胞整合的情况下的强基因组耦合。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae048

Yi-Tao Lin, Jack Chi-Ho Ip, Xing He, Zhao-Ming Gao, Maeva Perez, Ting Xu, Jin Sun, Pei-Yuan Qian, Jian-Wen Qiu

{"title":"Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration.","authors":"Yi-Tao Lin, Jack Chi-Ho Ip, Xing He, Zhao-Ming Gao, Maeva Perez, Ting Xu, Jin Sun, Pei-Yuan Qian, Jian-Wen Qiu","doi":"10.1093/ismejo/wrae048","DOIUrl":"10.1093/ismejo/wrae048","url":null,"abstract":"Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10999363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140295079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Entomopathogenic pseudomonads can share an insect host with entomopathogenic nematodes and their mutualistic bacteria. 昆虫致病假单胞菌可与昆虫致病线虫及其互生细菌共享昆虫宿主。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae028

Maria Zwyssig, Anna Spescha, Tabea Patt, Adrian Belosevic, Ricardo A R Machado, Alice Regaiolo, Christoph Keel, Monika Maurhofer

{"title":"Entomopathogenic pseudomonads can share an insect host with entomopathogenic nematodes and their mutualistic bacteria.","authors":"Maria Zwyssig, Anna Spescha, Tabea Patt, Adrian Belosevic, Ricardo A R Machado, Alice Regaiolo, Christoph Keel, Monika Maurhofer","doi":"10.1093/ismejo/wrae028","DOIUrl":"10.1093/ismejo/wrae028","url":null,"abstract":"A promising strategy to overcome limitations in biological control of insect pests is the combined application of entomopathogenic pseudomonads (EPPs) and nematodes (EPNs) associated with mutualistic bacteria (NABs). Yet, little is known about interspecies interactions such as competition, coexistence, or even cooperation between these entomopathogens when they infect the same insect host. We investigated the dynamics of bacteria-bacteria interactions between the EPP Pseudomonas protegens CHA0 and the NAB Xenorhabdus bovienii SM5 isolated from the EPN Steinernema feltiae RS5. Bacterial populations were assessed over time in experimental systems of increasing complexity. In vitro, SM5 was outcompeted when CHA0 reached a certain cell density, resulting in the collapse of the SM5 population. In contrast, both bacteria were able to coexist upon haemolymph-injection into Galleria mellonella larvae, as found for three further EPP-NAB combinations. Finally, both bacteria were administered by natural infection routes i.e. orally for CHA0 and nematode-vectored for SM5 resulting in the addition of RS5 to the system. This did not alter bacterial coexistence nor did the presence of the EPP affect nematode reproductive success or progeny virulence. CHA0 benefited from RS5, probably by exploiting access routes formed by the nematodes penetrating the larval gut epithelium. Our results indicate that EPPs are able to share an insect host with EPNs and their mutualistic bacteria without major negative effects on the reproduction of any of the three entomopathogens or the fitness of the nematodes. This suggests that their combination is a promising strategy for biological insect pest control.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139933895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli. 质粒和染色体的适应性进化提高了大肠杆菌中携带 blaNDM 的共整合质粒的适合度。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae037

Ziyi Liu, Yanyun Gao, Mianzhi Wang, Yuan Liu, Fulin Wang, Jing Shi, Zhiqiang Wang, Ruichao Li

{"title":"Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli.","authors":"Ziyi Liu, Yanyun Gao, Mianzhi Wang, Yuan Liu, Fulin Wang, Jing Shi, Zhiqiang Wang, Ruichao Li","doi":"10.1093/ismejo/wrae037","DOIUrl":"10.1093/ismejo/wrae037","url":null,"abstract":"Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10976473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of airborne algicidal bacteria on marine phytoplankton blooms. 空气中的杀藻细菌对海洋浮游植物繁殖的影响。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae016

Naama Lang-Yona, J Michel Flores, Tal Sharon Nir-Zadock, Inbal Nussbaum, Ilan Koren, Assaf Vardi

引用次数: 0