在高温条件下发现的两个新支系提供了对累积杆菌系统发育和基因组学的新见解。

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-04-18 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae049
Xiaojing Xie, Xuhan Deng, Jinling Chen, Liping Chen, Jing Yuan, Hang Chen, Chaohai Wei, Xianghui Liu, Guanglei Qiu
{"title":"在高温条件下发现的两个新支系提供了对累积杆菌系统发育和基因组学的新见解。","authors":"Xiaojing Xie, Xuhan Deng, Jinling Chen, Liping Chen, Jing Yuan, Hang Chen, Chaohai Wei, Xianghui Liu, Guanglei Qiu","doi":"10.1093/ismeco/ycae049","DOIUrl":null,"url":null,"abstract":"<p><p><i>Candidatus</i> Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality <i>Ca</i>. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the <i>Ca</i>. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that <i>Ca</i>. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying <i>Ca</i>. Accumulibacter. A pan-genomic analysis with other <i>Ca</i>. Accumulibacter members suggested that all <i>Ca</i>. Accumulibacter likely has the potential to use dicarboxylic amino acids. <i>Ca</i>. Accumulibacter aalborgensis AALB and <i>Ca</i>. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for <i>Ca</i>. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of <i>Ca</i>. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1000,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131965/pdf/","citationCount":"0","resultStr":"{\"title\":\"Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into <i>Candidatus</i> Accumulibacter.\",\"authors\":\"Xiaojing Xie, Xuhan Deng, Jinling Chen, Liping Chen, Jing Yuan, Hang Chen, Chaohai Wei, Xianghui Liu, Guanglei Qiu\",\"doi\":\"10.1093/ismeco/ycae049\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><i>Candidatus</i> Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality <i>Ca</i>. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the <i>Ca</i>. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that <i>Ca</i>. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying <i>Ca</i>. Accumulibacter. A pan-genomic analysis with other <i>Ca</i>. Accumulibacter members suggested that all <i>Ca</i>. Accumulibacter likely has the potential to use dicarboxylic amino acids. <i>Ca</i>. Accumulibacter aalborgensis AALB and <i>Ca</i>. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for <i>Ca</i>. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of <i>Ca</i>. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.</p>\",\"PeriodicalId\":73516,\"journal\":{\"name\":\"ISME communications\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.1000,\"publicationDate\":\"2024-04-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131965/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ISME communications\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/ismeco/ycae049\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"ECOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ISME communications","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/ismeco/ycae049","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

积累菌是多磷酸盐积累生物中的一个重要属,在实验室和大规模强化生物除磷系统(EBPR)中发挥着关键作用。共有 10 个高质量的 Ca.从高温下运行的 EBPR 系统中恢复了共 10 个高质量的 Ca.Accumulibacter 的系统发育和基因组研究提供了重要信息。在这些基因组中,支系 IIF 成员 SCELSE-3、SCELSE-4 和 SCELSE-6 代表了迄今已知的编码完整反硝化途径的基因组,表明仅 Ca.仅 Accumulibacter 就能实现完全脱氮。支系 IIC 成员 SSA1、SCUT-1、SCELCE-2 和 SCELSE-8 缺乏整套反硝化基因,代表了迄今已知的非反硝化 Ca.Accumulibacter.与其他 Ca.Accumulibacter 成员的泛基因组分析表明,所有 Ca.Accumulibacter 可能具有使用二羧酸氨基酸的潜力。Ca.Accumulibacter aalborgensis AALB 和 Ca.AALB 和 Ca. Accumulibacter affinis BAT3C720 似乎是仅有的两个能够利用葡萄糖进行 EBPR 的成员。热休克蛋白 Hsp20 编码基因只存在于高温下恢复的基因组中,而在 IA、IC、IG、IIA、IIB、IID、IIG 和 II-I 支系成员中均不存在。该基因在支系 IIC 成员 SCUT-2 和 SCUT-3 中的高转录表明,它在 Ca.Accumulibacter.新发现的基因组(SCELSE-9 和 SCELSE-10)的支系特征不明确。使用正交群作为输入特征开发了五个机器学习模型。预测结果表明它们属于一个新的支系(IIK)。对 Ca.根据侧面衍生的多磷酸激酶 2 基因重新评估了 Accumulibacter 的系统发育,结果显示其在区分不同支系方面的分辨率有所提高。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter.

Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
自引率
0.00%
发文量
0
期刊最新文献
Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession. Introduction into natural environments shifts the gut microbiome of captivity-raised filter-feeding bivalves. Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments. Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis. Rhizospheric miRNAs affect the plant microbiota.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1