Supplementary Material: Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine–freshwater barrier

This repository contains supplementary material related to the manuscript "Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine–freshwater barrier". 1) SupplementaryMaterial1_SupplementaryTables.xlsx Supplementary Material 1. Supplementary Tables. Supplementary Table S1. Sampling locations at Fåvne and Troll Wall vent fields.Supplementary Table S2. Gallionella MAGs used in this study. Supplementary Table S3. Zetaproteobacteria MAGs used in this study.Supplementary Table S4. Coverage and relative abundances of FeOB Gallionellaceae and Zetaproteobacteria MAGs from this study.Supplementary Table S5. Gallionellaceae MAGs recovered in this study. Supplementary Table S6. List of single-copy marker genes used for concatenated phylogeny of Gallionella. Supplementary Table S7. Functional enrichment of genes in Gallionella MAGs based on the environment. Supplementary Table S8. Functional enrichment of genes in Zetaproteobacteria MAGs based on the environment.Supplementary Table S9. Functional enrichment of genes in Mariprofundus MAGs based on the environment. Supplementary Table S10. Average MAG statistics of Gallionella and Zetaproteobacteria genomes. Supplementary Table S11. Isoelectric point (pI) relative frequencies of the predicted proteomes. 2) FigS1.pdf Fig S1. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 15 single copy gene markers (Table SX) using MAGs from this study and references. Sfz1-4/Sfb1-4: potential stalk formation genes in Zetaproteobacteria/Betaproteobacteria. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Jan Mayen vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup. 3) FigS2.pdf Fig S2. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 17 single copy gene markers using MAGs from this study and references. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup. 4) FigS3.pdf Fig S3. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 19 single copy gene markers using MAGs from this study and references. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup. 5) FigS4.pdf Fig S4. Phylogeny of class Zetaproteobacteria. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 12 single copy gene markers (Hribovšek et al., 2023) using MAGs from this study and references. Sfz1-6: potential stalk formation genes in Zetaproteobacteria. The environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model LG+F+R9. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. 6) FigS5.pdf Fig S5. Phylogeny of ectoine synthase genes. Ectoine synthase genes were extracted from MAGs from this study and references. Metadata on isolation source were collected from NCBI for genes closely related to ectoine synthase genes of Gallionella. Blue-marked sequences were extracted from MAGs reconstructed from Fåvne and Troll Wall vent field. The phylogenomics tree is based on an alignment of 177 sequences of comparable length at 130 positions using IQ-TREE v2.0.3. The maximum likelihood tree with substitution model LG+I+I+R4. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. 7) FigS6.pdf Fig S6. Relative frequencies of predicted isoelectric points (pI) in Gallionella MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation. 8) FigS7.png Fig S7. Relative frequencies of predicted isoelectric points (pI) in Mariprofundus MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation. 9) FigS8.png Fig S8. Relative frequencies of predicted isoelectric points (pI) in Zetaproteobacteria MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation. References Hribovšek, P., Olesin Denny, E., Dahle, H., Mall, A., Øfstegaard Viflot, T., Boonnawa, C., et al. (2023). Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 8, 2023.06.20.545787. doi:10.1128/msystems.00543-23.本仓库收录有与学术论文《跨越海水-淡水屏障的铁氧化细菌嘉利翁氏菌属（Gallionella）与ζ-变形菌纲（Zetaproteobacteria）的适应策略》相关的补充资料。 1) 补充材料1_补充表格.xlsx 补充材料1：补充表格 补充表S1：法夫讷（Fåvne）与特罗尔沃恩（Troll Wall）热液喷口区的采样点位。 补充表S2：本研究中使用的嘉利翁氏菌属（Gallionella）宏基因组组装基因组（Metagenome-Assembled Genome，以下简称MAG）。 补充表S3：本研究中使用的ζ-变形菌纲（Zetaproteobacteria）MAG。 补充表S4：本研究中铁氧化细菌嘉利翁氏菌科（Gallionellaceae）与ζ-变形菌纲MAG的覆盖度及相对丰度。 补充表S5：本研究中组装获得的嘉利翁氏菌科MAG。 补充表S6：用于嘉利翁氏菌属串联系统发育分析的单拷贝标记基因列表。 补充表S7：基于环境背景的嘉利翁氏菌属MAG基因功能富集分析结果。 补充表S8：基于环境背景的ζ-变形菌纲MAG基因功能富集分析结果。 补充表S9：基于环境背景的马氏杆菌属（Mariprofundus）MAG基因功能富集分析结果。 补充表S10：嘉利翁氏菌属与ζ-变形菌纲基因组的平均MAG统计信息。 补充表S11：预测蛋白质组的等电点（pI）相对频率分布。 2) 补充图S1.pdf 补充图S1：典型淡水β-变形菌纲（Betaproteobacteria）嘉利翁氏菌属的系统发育树。该系统发育基因组树基于本研究及参考基因组的MAG，以人工精选的15个单拷贝基因标记（表SX）的串联联配序列构建。Sfz1-4/Sfb1-4：ζ-变形菌纲/β-变形菌纲中的潜在菌柄形成基因。环境标注基于NCBI元数据。蓝色基因组均来自法夫讷喷口区与扬马延喷口区的组装结果。该最大似然树采用GTR20+F+R6替换模型。黑色节点圆圈代表支持值：SH类近似似然比检验高于80%，超快速自举检验高于95%，两种检验均进行1000次迭代。树的根基于非嘉利翁氏菌属的嘉利翁氏菌科MAG序列作为外类群。 3) 补充图S2.pdf 补充图S2：典型淡水β-变形菌纲嘉利翁氏菌属的系统发育树。该系统发育基因组树基于本研究及参考基因组的MAG，以人工精选的17个单拷贝基因标记的串联联配序列构建。环境标注基于NCBI元数据。蓝色基因组均来自法夫讷喷口区与特罗尔沃恩喷口区的组装结果。该最大似然树采用GTR20+F+R6替换模型。黑色节点圆圈代表支持值：SH类近似似然比检验高于80%，超快速自举检验高于95%，两种检验均进行1000次迭代。树的根基于非嘉利翁氏菌属的嘉利翁氏菌科MAG序列作为外类群。 4) 补充图S3.pdf 补充图S3：典型淡水β-变形菌纲嘉利翁氏菌属的系统发育树。该系统发育基因组树基于本研究及参考基因组的MAG，以人工精选的19个单拷贝基因标记的串联联配序列构建。环境标注基于NCBI元数据。蓝色基因组均来自法夫讷喷口区与特罗尔沃恩喷口区的组装结果。该最大似然树采用GTR20+F+R6替换模型。黑色节点圆圈代表支持值：SH类近似似然比检验高于80%，超快速自举检验高于95%，两种检验均进行1000次迭代。树的根基于非嘉利翁氏菌属的嘉利翁氏菌科MAG序列作为外类群。 5) 补充图S4.pdf 补充图S4：ζ-变形菌纲的系统发育树。该系统发育基因组树基于本研究及参考基因组的MAG，以人工精选的12个单拷贝基因标记（Hribovšek et al., 2023）的串联联配序列构建。Sfz1-6：ζ-变形菌纲中的潜在菌柄形成基因。环境标注基于NCBI元数据。蓝色基因组均来自法夫讷喷口区与特罗尔沃恩喷口区的组装结果。该最大似然树采用LG+F+R9替换模型。黑色节点圆圈代表支持值：SH类近似似然比检验高于80%，超快速自举检验高于95%，两种检验均进行1000次迭代。 6) 补充图S5.pdf 补充图S5：四氢嘧啶合酶基因的系统发育树。四氢嘧啶合酶基因提取自本研究及参考基因组的MAG。与嘉利翁氏菌属四氢嘧啶合酶基因密切相关的基因的分离源元数据采集自NCBI数据库。蓝色标记序列均来自法夫讷与特罗尔沃恩喷口区组装获得的MAG。该系统发育基因组树基于177条长度相当（130个位点）的序列，使用IQ-TREE v2.0.3软件构建。该最大似然树采用LG+I+I+R4替换模型。黑色节点圆圈代表支持值：SH类近似似然比检验高于80%，超快速自举检验高于95%，两种检验均进行1000次迭代。 7) 补充图S6.pdf 补充图S6：嘉利翁氏菌属MAG的预测蛋白质组等电点（pI）相对频率分布。筛选标准为完整性高于50%且污染率低于10%的MAG。按环境分组取平均值，误差棒代表标准差。 8) 补充图S7.png 补充图S7：马氏杆菌属MAG的预测蛋白质组等电点相对频率分布。筛选标准为完整性高于50%且污染率低于10%的MAG。按环境分组取平均值，误差棒代表标准差。 9) 补充图S8.png 补充图S8：ζ-变形菌纲MAG的预测蛋白质组等电点相对频率分布。筛选标准为完整性高于50%且污染率低于10%的MAG。按环境分组取平均值，误差棒代表标准差。 参考文献 [1] Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, et al. 2023. 栖息于法夫讷深海热液喷口区的潜在新型产鞘氢与铁氧化ζ-变形菌纲. mSystems 8:2023.06.20.545787. DOI:10.1128/msystems.00543-23.