Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.

IF 13.8 1区生物学 Q1 MICROBIOLOGY

Microbiome Pub Date : 2024-08-10 DOI:10.1186/s40168-024-01867-0

Hongjae Park, Paul-Adrian Bulzu, Tanja Shabarova, Vinicius S Kavagutti, Rohit Ghai, Vojtěch Kasalický, Jitka Jezberová

{"title":"Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.","authors":"Hongjae Park, Paul-Adrian Bulzu, Tanja Shabarova, Vinicius S Kavagutti, Rohit Ghai, Vojtěch Kasalický, Jitka Jezberová","doi":"10.1186/s40168-024-01867-0","DOIUrl":null,"url":null,"abstract":"Background: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.Results: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.Conclusions: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8000,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316352/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbiome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s40168-024-01867-0","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.

Results: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.

Conclusions: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.

查看原文本刊更多论文

揭示淡水微囊藻共生相互作用和生态位适应的基因组基础。

背景：前绿球藻属、中绿球藻属和蓝藻属中的微囊藻是水生生态系统中最普遍的光合生物。然而，由于对不同内陆水体的取样不均衡、不充分，对其淡水种群的研究仍然很少：在这项研究中，我们从中欧地区收集的非异源培养物中获得了 170 个高质量的淡水微囊藻基因组。此外，我们还发现了 33 个潜在共生伙伴的基因组，它们分别隶属于假单胞菌属、中生孢子菌属、酸性菌属和嗜氢菌属这四个菌属。共生相互作用的基因组基础涉及异养生物从皮囊蓝藻获得的营养物质中获益，同时提供 ROS 的解毒作用。微囊藻的全球丰度模式揭示了与营养状态、温度和 pH 值等关键环境因素相关的重要生态型。微囊藻在（超）富营养化水体中的适应性可归因于它们的群居生活方式和 CRISPR-Cas 系统。短花青素细菌中最常见的 CRISPR-Cas 亚型是 I-G 和 I-E，它们似乎是从其他细菌门通过水平基因转移获得的：我们的发现为了解淡水生态系统中最普遍的光自养菌的种群多样性、生态学和进化策略提供了新的视角。视频摘要

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Microbiome MICROBIOLOGY-

CiteScore

21.90

自引率

2.60%

发文量

198

审稿时长

4 weeks

期刊介绍： Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.