Metagenomic data of Microbiota in Mangrove Soil from Lukut River, Malaysia

Metagenomics sequencing
The assembled genome contained 6736 shared genes between soil 1 and soil 3, 203,682 shared genes between soil 1 and soil 2, and 66,383 shared genes between soil 2 and soil 3 (Figure 1).

Comparative analysis of metabolic pathways of bacterial diversity
Function annotation based on the KEGG, as shown in Figure 2, reveals that most of the core genes found in mangrove soils are involved in metabolic pathways. The highest genes are involved in carbohydrate metabolism and followed by amino acid metabolism. In addition, the functional annotation based on eggNOG shows the genome isolated from the soils of mangrove trees’ rhizosphere mostly contains genes that are associated with energy production and conversion, amino acid transport, metabolism, replication, recombination and repair, as well as carbohydrate transport and metabolism pathways (Figure 3). In this study, the functional annotation based on the CAZy reveals six CAZy main functions as follows: Glycoside Hydrolase (GH), Glycosyl Transferase (GT), Polysaccharide Lyase (PL), Carbohydrate Esterases (CE), Auxiliary Activities (AA) and Carbohydrate-Binding Modules (CBM) were found in collected mangrove soils (Figure 4).

Metabolic pathways show the signature of bacteria and their function
Carbon fixation was found to be the most prevalent pathway, followed by methane, nitrogen, sulfur, atrazine, and dioxin degradation pathways (Figure 5). Further analysis identified Chloroflexi, Gaiellales bacterium and Acidobacteria as the major microbial taxa affiliated with the carbon fixation pathway. Methanotrophic bacteria, including Methyloceanibacter caenitepidi, M. superfactus, and M. marginalis were also detected (Figure 6). Additionally, several nitrogen-fixing bacteria, such as Chloroflexi bacterium, Acidobacteria bacterium, Actinobacteria bacterium, Frankia sp., proteobacteria bacterium, Betaproteobacteria bacterium, Anaerolineae bacterium, Bradyrhizobium liaoningense, Bradyrhizobium sp., Methyloceanibacter caenitepidi, Methyloceanibacter marginalis, Methyloceanibacter superfactus, Pseudolabrys taiwanensis, Bradyrhizobium manausense, Solirubrobacter sp., Solirubrobacter soli, and Phycicoccus jejuensis were identified (Figure 6).

Furthermore, we also found the presence of sulfate-reducing bacteria (SRB), such as Thiohalobacter thiocyanaticus, Acidobacteria bacterium, Woeseia oceani, Desulfobacteraceae bacterium, Desulfobacterales bacterium, Mycolicibacterium rhodesiae, Gaiellales bacterium, Deltaproteobacteria bacterium and Myxococcales bacterium in the collected soil samples (Figure 6). The heatmap in Figure 6 also shows the presence of various bacterial species classified in the Actinobacteria phylum, including Phycicoccus jejuensis, Solirubrobacterales bacterium, Mycolicibacterium rhodesiae, M. mariokaense, Solirubrobacter sp. and S. soli in the collected soils.

宏基因组测序（Metagenomics sequencing）
组装得到的基因组中，土壤1与土壤3共享6736个基因，土壤1与土壤2共享203682个基因，土壤2与土壤3共享66383个基因（图1）。

细菌多样性代谢通路比较分析
基于京都基因与基因组百科全书（KEGG）的功能注释如图2所示，结果显示红树林土壤中发现的绝大多数核心基因均参与各类代谢通路。其中参与碳水化合物代谢的基因数量最多，其次为氨基酸代谢。此外，基于进化基因同源分组数据库（eggNOG）的功能注释结果表明，从红树林植物根际土壤分离得到的基因组，其携带的基因大多与能量产生与转换、氨基酸转运与代谢、复制、重组与修复，以及碳水化合物转运与代谢通路相关（图3）。本研究中，基于碳水化合物活性酶数据库（CAZy）的功能注释结果显示，采集的红树林土壤中共存在6类主要的CAZy功能模块，分别为糖苷水解酶（Glycoside Hydrolase，GH）、糖基转移酶（Glycosyl Transferase，GT）、多糖裂解酶（Polysaccharide Lyase，PL）、碳水化合物酯酶（Carbohydrate Esterases，CE）、辅助活性模块（Auxiliary Activities，AA）以及碳水化合物结合模块（Carbohydrate-Binding Modules，CBM）（图4）。

代谢通路体现细菌特征及其功能
研究发现固碳通路是最为普遍的代谢通路，其次为甲烷、氮、硫、阿特拉津以及二噁英降解通路（图5）。进一步分析表明，隶属于绿弯菌门（Chloroflexi）、盖氏杆菌目（Gaiellales）细菌及酸杆菌门（Acidobacteria）的微生物类群是参与固碳通路的主要类群。同时还检测到了包括海洋甲基杆菌属（Methyloceanibacter）的Caenitepidi海洋甲基杆菌（M. caenitepidi）、超级海洋甲基杆菌（M. superfactus）以及边缘海洋甲基杆菌（M. marginalis）在内的甲烷氧化细菌（图6）。此外，本研究还鉴定出多种固氮细菌，包括绿弯菌门细菌、酸杆菌门细菌、放线菌门细菌、弗兰克氏菌属（Frankia sp.）、变形菌门细菌、β-变形菌纲细菌、厌氧绳菌纲细菌、辽宁慢生根瘤菌（Bradyrhizobium liaoningense）、慢生根瘤菌属未定种（Bradyrhizobium sp.）、上述三种海洋甲基杆菌、台湾假拉夫菌（Pseudolabrys taiwanensis）、马瑙斯慢生根瘤菌（Bradyrhizobium manausense）、土红杆菌属未定种（Solirubrobacter sp.）、土壤土红杆菌（Solirubrobacter soli）以及济州拟球菌（Phycicoccus jejuensis）（图6）。

此外，本研究还在采集的土壤样本中检测到硫酸盐还原细菌（SRB），包括硫氰酸根还原盐杆菌（Thiohalobacter thiocyanaticus）、酸杆菌门细菌、海洋Woeseia菌（Woeseia oceani）、脱硫杆菌科细菌（Desulfobacteraceae bacterium）、脱硫杆菌目细菌（Desulfobacterales bacterium）、罗得西亚分枝杆菌样菌（Mycolicibacterium rhodesiae）、盖氏杆菌目细菌、δ-变形菌纲细菌以及粘球菌目细菌（Myxococcales bacterium）（图6）。图6的热图同时显示，采集的土壤中存在多种隶属于放线菌门（Actinobacteria）的细菌物种，包括济州拟球菌、索里红杆菌目（Solirubrobacterales）未定种细菌、罗得西亚分枝杆菌样菌、马里欧卡分枝杆菌（Mycolicibacterium mariokaense）、土红杆菌属未定种以及土壤土红杆菌。