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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":"<p><p>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.</p>","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":"<p><p>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.</p>","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
Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming. 在短期、中期和长期变暖的情况下,亚北极土壤中的微生物核糖体都会枯竭。
IF 11 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae081
Andrea Söllinger, Laureen S Ahlers, Mathilde Borg Dahl, Páll Sigurðsson, Coline Le Noir de Carlan, Biplabi Bhattarai, Christoph Gall, Victoria S Martin, Cornelia Rottensteiner, Liabo L Motleleng, Eva Marie Breines, Erik Verbruggen, Ivika Ostonen, Bjarni D Sigurdsson, Andreas Richter, Alexander T Tveit
{"title":"Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming.","authors":"Andrea Söllinger, Laureen S Ahlers, Mathilde Borg Dahl, Páll Sigurðsson, Coline Le Noir de Carlan, Biplabi Bhattarai, Christoph Gall, Victoria S Martin, Cornelia Rottensteiner, Liabo L Motleleng, Eva Marie Breines, Erik Verbruggen, Ivika Ostonen, Bjarni D Sigurdsson, Andreas Richter, Alexander T Tveit","doi":"10.1093/ismejo/wrae081","DOIUrl":"10.1093/ismejo/wrae081","url":null,"abstract":"<p><p>Physiological responses of soil microorganisms to global warming are important for soil ecosystem function and the terrestrial carbon cycle. Here, we investigate the effects of weeks, years, and decades of soil warming across seasons and time on the microbial protein biosynthesis machineries (i.e. ribosomes), the most abundant cellular macromolecular complexes, using RNA:DNA and RNA:MBC (microbial biomass carbon) ratios as proxies for cellular ribosome contents. We compared warmed soils and non-warmed controls of 15 replicated subarctic grassland and forest soil temperature gradients subject to natural geothermal warming. RNA:DNA ratios tended to be lower in the warmed soils during summer and autumn, independent of warming duration (6 weeks, 8-14 years, and > 50 years), warming intensity (+3°C, +6°C, and +9°C), and ecosystem type. With increasing temperatures, RNA:MBC ratios were also decreasing. Additionally, seasonal RNA:DNA ratios of the consecutively sampled forest showed the same temperature-driven pattern. This suggests that subarctic soil microorganisms are depleted of ribosomes under warm conditions and the lack of consistent relationships with other physicochemical parameters besides temperature further suggests temperature as key driver. Furthermore, in incubation experiments, we measured significantly higher CO2 emission rates per unit of RNA from short- and long-term warmed soils compared to non-warmed controls. In conclusion, ribosome reduction may represent a widespread microbial physiological response to warming that offers a selective advantage at higher temperatures, as energy and matter can be reallocated from ribosome synthesis to other processes including substrate uptake and turnover. This way, ribosome reduction could have a substantial effect on soil carbon dynamics.</p>","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/PMC11126301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897331","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
Correction to: Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus? 更正:Pandoravirus massiliensis 中不完整的三羧酸循环和质子梯度:它还是病毒吗?
IF 11 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae095
{"title":"Correction to: Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?","authors":"","doi":"10.1093/ismejo/wrae095","DOIUrl":"10.1093/ismejo/wrae095","url":null,"abstract":"","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/PMC11159527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288893","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 adenine cross-feeding stems from a purine salvage bottleneck. 细菌腺嘌呤交叉进食源于嘌呤挽救瓶颈。
IF 11 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae034
Ying-Chih Chuang, Nicholas W Haas, Robert Pepin, Megan G Behringer, Yasuhiro Oda, Breah LaSarre, Caroline S Harwood, James B McKinlay
{"title":"Bacterial adenine cross-feeding stems from a purine salvage bottleneck.","authors":"Ying-Chih Chuang, Nicholas W Haas, Robert Pepin, Megan G Behringer, Yasuhiro Oda, Breah LaSarre, Caroline S Harwood, James B McKinlay","doi":"10.1093/ismejo/wrae034","DOIUrl":"10.1093/ismejo/wrae034","url":null,"abstract":"<p><p>Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue an Escherichia coli purine auxotroph. Here we found that an E. coli purine auxotroph can stably coexist with R. palustris due to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized by R. palustris under diverse growth conditions. Computational modeling suggested that adenine externalization occurs via diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that adenine accumulation and externalization stem from a salvage pathway bottleneck at the enzyme encoded by apt. Ectopic expression of apt eliminated adenine externalization, supporting our hypothesis. A comparison of 49 R. palustris strains suggested that purine externalization is relatively common, with 16 strains exhibiting the trait. Purine externalization was correlated with the genomic orientation of apt, but apt orientation alone could not always explain purine externalization. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.</p>","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/PMC10976475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061141","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
Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga. 细胞间的异质性促使宿主与病毒在开花藻类中共存。
IF 11 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae038
Nir Joffe, Constanze Kuhlisch, Guy Schleyer, Nadia S Ahlers, Adva Shemi, Assaf Vardi
{"title":"Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga.","authors":"Nir Joffe, Constanze Kuhlisch, Guy Schleyer, Nadia S Ahlers, Adva Shemi, Assaf Vardi","doi":"10.1093/ismejo/wrae038","DOIUrl":"10.1093/ismejo/wrae038","url":null,"abstract":"<p><p>Algal blooms drive global biogeochemical cycles of key nutrients and serve as hotspots for biological interactions in the ocean. The massive blooms of the cosmopolitan coccolithophore Emiliania huxleyi are often infected by the lytic E. huxleyi virus, which is a major mortality agent triggering bloom demise. This multi-annual \"boom and bust\" pattern of E. huxleyi blooms suggests that coexistence is essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from an E. huxleyi culture that recovered from viral infection. The recovered population coexists with the virus, as host cells continue to divide in parallel to viral production. By applying single-molecule fluorescence in situ hybridization (smFISH) to quantify the fraction of infected cells, and assessing infection-specific lipid biomarkers, we identified a small subpopulation of cells that were infected and produced new virions, whereas most of the host population could resist infection. To further assess population heterogeneity, we generated clonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to E. huxleyi virus infection. This unraveled substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, highlighting that infection outcome may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives the host-virus coexistence and demonstrate how the coexistence with a lytic virus provides an ecological advantage for the host by killing competing strains.</p>","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/PMC10980834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061142","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
High niche specificity and host genetic diversity of groundwater viruses. 地下水病毒的高度生态位特异性和宿主遗传多样性。
IF 11 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae035
Emilie Gios, Olivia E Mosley, Michael Hoggard, Kim M Handley
{"title":"High niche specificity and host genetic diversity of groundwater viruses.","authors":"Emilie Gios, Olivia E Mosley, Michael Hoggard, Kim M Handley","doi":"10.1093/ismejo/wrae035","DOIUrl":"10.1093/ismejo/wrae035","url":null,"abstract":"<p><p>Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.</p>","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/PMC10980836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140061143","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
Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability. 鼻腔共生菌通过限制嗜苷酸盐的供应来减少金黄色葡萄球菌的增殖。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae123
Yanfeng Zhao, Alina Bitzer, Jeffrey John Power, Darya Belikova, Benjamin Orlando Torres Salazar, Lea Antje Adolf, David Gerlach, Bernhard Krismer, Simon Heilbronner
{"title":"Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability.","authors":"Yanfeng Zhao, Alina Bitzer, Jeffrey John Power, Darya Belikova, Benjamin Orlando Torres Salazar, Lea Antje Adolf, David Gerlach, Bernhard Krismer, Simon Heilbronner","doi":"10.1093/ismejo/wrae123","DOIUrl":"10.1093/ismejo/wrae123","url":null,"abstract":"<p><p>The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens, such as methicillin-resistant Staphylococcus aureus, can reside within the nasal microbiota, which increases the risk of infection. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic species and S. aureus, but the underlying molecular mechanisms remain poorly understood. The nasal cavity is iron-limited, and bacteria are known to produce iron-scavenging siderophores to proliferate in such environments. Siderophores are public goods that can be consumed by all members of a bacterial community. Accordingly, siderophores are known to mediate bacterial competition and collaboration, but their role in the nasal microbiome is unknown. Here, we show that siderophore acquisition is crucial for S. aureus nasal colonization in vivo. We screened 94 nasal bacterial strains from seven genera for their capacity to produce siderophores as well as to consume the siderophores produced by S. aureus. We found that 80% of the strains engaged in siderophore-mediated interactions with S. aureus. Non-pathogenic corynebacterial species were found to be prominent consumers of S. aureus siderophores. In co-culture experiments, consumption of siderophores by competitors reduced S. aureus growth in an iron-dependent fashion. Our data show a wide network of siderophore-mediated interactions between the species of the human nasal microbiome and provide mechanistic evidence for inter-species competition and collaboration impacting pathogen proliferation. This opens avenues for designing nasal probiotics to displace S. aureus from the nasal cavity of humans.</p>","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/PMC11296517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581442","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
Molecular basis of phenotypic plasticity in a marine ciliate. 海洋纤毛虫表型可塑性的分子基础
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae136
Jiao Pan, Yaohai Wang, Chao Li, Simo Zhang, Zhiqiang Ye, Jiahao Ni, Haichao Li, Yichen Li, Hongwei Yue, Chenchen Ruan, Dange Zhao, Yujian Jiang, Xiaolin Wu, Xiaopeng Shen, Rebecca A Zufall, Yu Zhang, Weiyi Li, Michael Lynch, Hongan Long
{"title":"Molecular basis of phenotypic plasticity in a marine ciliate.","authors":"Jiao Pan, Yaohai Wang, Chao Li, Simo Zhang, Zhiqiang Ye, Jiahao Ni, Haichao Li, Yichen Li, Hongwei Yue, Chenchen Ruan, Dange Zhao, Yujian Jiang, Xiaolin Wu, Xiaopeng Shen, Rebecca A Zufall, Yu Zhang, Weiyi Li, Michael Lynch, Hongan Long","doi":"10.1093/ismejo/wrae136","DOIUrl":"10.1093/ismejo/wrae136","url":null,"abstract":"<p><p>Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive in complex and highly fluctuating environments. However, its reaction norm, molecular basis, and evolution remain unclear in most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating the reaction norm, regulation, and evolution of phenotypic plasticity in the cosmopolitan marine free-living ciliates Glauconema spp., which undergo significant phenotypic changes in response to food shortages. This study led to the de novo assembly of macronuclear genomes using long-read sequencing, identified hundreds of differentially expressed genes associated with phenotypic plasticity in different life stages, validated the function of two of these genes, and revealed that the reaction norm of body shape in response to food density follows a power-law distribution. Purifying selection may be the dominant evolutionary force acting on the genes associated with phenotypic plasticity, and the overall data support the hypothesis that phenotypic plasticity is a trait maintained by natural selection. This study provides novel insight into the developmental genetics of phenotypic plasticity in non-model unicellular eukaryotes and sheds light on the complexity and long evolutionary history of this important survival strategy.</p>","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/PMC11308186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635637","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
Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance. 苍蝇肠道微生物组是抗生素耐药性传播的储存库和促进因素。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae128
Dehao Gan, Zhenyan Lin, Lingshuang Zeng, Hui Deng, Timothy R Walsh, Shungui Zhou, Qiu E Yang
{"title":"Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.","authors":"Dehao Gan, Zhenyan Lin, Lingshuang Zeng, Hui Deng, Timothy R Walsh, Shungui Zhou, Qiu E Yang","doi":"10.1093/ismejo/wrae128","DOIUrl":"10.1093/ismejo/wrae128","url":null,"abstract":"<p><p>Arthropods, such as houseflies, play a significant role in the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across One Health sectors, affecting animals and environmental habitats as well as humans. In this study, we investigated the in situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying an mcr-8 gene, pA/C_MCR-8) in the gut microbiota of houseflies (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing and whole-genome sequencing. Our findings demonstrate that the pA/C_MCR-8-positive Escherichia coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for 5 days; however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, is a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further support the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.</p>","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/PMC11456846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141728215","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
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