ISME Journal最新文献_第7页

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles. 大规模单病毒基因组学揭示了河水病毒隐藏的多样性和多样化的基因特征。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae124

Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama

{"title":"Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.","authors":"Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-Ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama","doi":"10.1093/ismejo/wrae124","DOIUrl":"10.1093/ismejo/wrae124","url":null,"abstract":"Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.","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/PMC11283719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555842","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

Diversity alone does not reliably indicate the healthiness of an animal microbiome. 仅凭多样性并不能可靠地说明动物微生物群的健康状况。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae133

Claire E Williams, Tobin J Hammer, Candace L Williams

引用次数: 0

Comment on "Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone" by Yuanxu Song et al. 就宋元旭等人《依赖腐殖酸的乙酰甲烷虫呼吸生长涉及吡咯喹啉醌》发表的评论

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae020

Derek R Lovley, Dawn E Holmes

引用次数: 0

Response to comment on "Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone" by Yuanxu Song et al. 对Yuanxu song等人关于 "Methanosarcina acetivorans的腐殖酸依赖性呼吸生长涉及吡咯喹啉醌 "的评论的回应

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae019

Yuanxu Song, Rui Huang, Ling Li, Mingyu Wang, Shuguang Wang, James G Ferry, Zhen Yan

引用次数: 0

Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality. 噬菌体抗性与固氮作用之间的权衡推动了蓝藻异囊功能所必需基因的进化。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrad008

Dikla Kolan, Esther Cattan-Tsaushu, Hagay Enav, Zohar Freiman, Nechama Malinsky-Rushansky, Shira Ninio, Sarit Avrani

{"title":"Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality.","authors":"Dikla Kolan, Esther Cattan-Tsaushu, Hagay Enav, Zohar Freiman, Nechama Malinsky-Rushansky, Shira Ninio, Sarit Avrani","doi":"10.1093/ismejo/wrad008","DOIUrl":"10.1093/ismejo/wrad008","url":null,"abstract":"Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.","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/PMC10811720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747727","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

Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. 需氧甲烷营养体在限氧淡水生境中的神秘持久性。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae041

Paula C J Reis, Jackson M Tsuji, Cerrise Weiblen, Sherry L Schiff, Matthew Scott, Lisa Y Stein, Josh D Neufeld

引用次数: 0

High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts. 高糖饮食导致家蝇幼虫肠道中有益益生菌的流失

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae193

Anna Voulgari-Kokota, Francesco Boatta, Ruud Rijkers, Bregje Wertheim, Leo W Beukeboom, Jacintha Ellers, Joana Falcao Salles

{"title":"High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts.","authors":"Anna Voulgari-Kokota, Francesco Boatta, Ruud Rijkers, Bregje Wertheim, Leo W Beukeboom, Jacintha Ellers, Joana Falcao Salles","doi":"10.1093/ismejo/wrae193","DOIUrl":"10.1093/ismejo/wrae193","url":null,"abstract":"The housefly (Musca domestica) is a common insect species with only a few recurrent bacterial taxa in its gut microbiota, because the numerous microbial acquisition routes in its septic habitats can favor transient microbes. Here, we investigated the role of the diet on the microbiota and the developmental success of a housefly strain reared on three substrates. We used a control wheat bran-based substrate, and added clotted cream and sucrose to make a high-fat, and a high-sugar substrate, respectively. The conducted survey revealed that, in contrast to the high-fat diet, the high-sugar diet caused lower developmental success and less diverse microbiota, in which several lactobacilli were replaced with Weissella bacterial phylotypes. Cultures with sucrose as the sole carbon source confirmed that a Weissella confusa strain, isolated from larvae, could utilize sucrose more efficiently than other tested lactic acid bacteria; a result also supported by gene function prediction analysis. Enhancing the rearing substrate with Limosilactobacillus fermentum and Lactiplantibacillus plantarum strains, which were isolated from control larvae, could not only revert the negative effect of the high-sucrose diet on development, but also increase the gut bacterial diversity. In our study, we show that the microbiota shifts in response to the high-sucrose diet did not benefit the host, that showed lower developmental success. In contrast, high-sucrose favored specific components of the microbiota, that continued to be enriched even after multiple generations, outcompeting beneficial bacteria. Also, microbiome manipulation showed the potential of probiotics to rescue host performance and restore the microbiome.","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/PMC11495414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373436","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

Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host. 大型附着细胞器介导 Nanobdellota 古菌 YN1 与宿主之间的相互作用。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae154

Matthew D Johnson, Hiroyuki D Sakai, Bindusmita Paul, Takuro Nunoura, Somavally Dalvi, Manasi Mudaliyar, Doulin C Shepherd, Michiru Shimizu, Shubha Udupa, Moriya Ohkuma, Norio Kurosawa, Debnath Ghosal

{"title":"Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host.","authors":"Matthew D Johnson, Hiroyuki D Sakai, Bindusmita Paul, Takuro Nunoura, Somavally Dalvi, Manasi Mudaliyar, Doulin C Shepherd, Michiru Shimizu, Shubha Udupa, Moriya Ohkuma, Norio Kurosawa, Debnath Ghosal","doi":"10.1093/ismejo/wrae154","DOIUrl":"10.1093/ismejo/wrae154","url":null,"abstract":"DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here, we successfully isolated and cultivated a coculture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterized the coculture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (cryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together, our results unravel the molecular and structural basis of ectosymbiotic relationship between YN1 and YN1HA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships.","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/PMC11420986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903447","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

Gut microbiota contribute to variations in honey bee foraging intensity. 肠道微生物群导致蜜蜂觅食强度的变化。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae030

Cassondra L Vernier, Lan Anh Nguyen, Tim Gernat, Amy Cash Ahmed, Zhenqing Chen, Gene E Robinson

{"title":"Gut microbiota contribute to variations in honey bee foraging intensity.","authors":"Cassondra L Vernier, Lan Anh Nguyen, Tim Gernat, Amy Cash Ahmed, Zhenqing Chen, Gene E Robinson","doi":"10.1093/ismejo/wrae030","DOIUrl":"10.1093/ismejo/wrae030","url":null,"abstract":"Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. Although many studies have reported that experimental disruptions to the gut microbial community result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, because of their simple gut microbiota and complex division of labor characterized by colony-level variation in behavioral phenotypes. Although previous studies report correlational differences in gut microbial community associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between European honey bees (Apis mellifera). We found that gut microbial community structure differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in gut microbial community composition were associated with task experience. Moreover, single-microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused effects on foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral trait variation.","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/PMC11008687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984419","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

Active prophages in coral-associated Halomonas capable of lateral transduction. 珊瑚相关卤单胞菌中能进行横向转导的活性噬菌体。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae085

Ziyao Liu, Kaihao Tang, Yiqing Zhou, Tianlang Liu, Yunxue Guo, Duoting Wu, Xiaoxue Wang

{"title":"Active prophages in coral-associated Halomonas capable of lateral transduction.","authors":"Ziyao Liu, Kaihao Tang, Yiqing Zhou, Tianlang Liu, Yunxue Guo, Duoting Wu, Xiaoxue Wang","doi":"10.1093/ismejo/wrae085","DOIUrl":"10.1093/ismejo/wrae085","url":null,"abstract":"Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.","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/PMC11131426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140917344","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