Microbial vertical diversity in core sediments and its response to environmental factors near the hydrothermal field of the southern Okinawa Trough
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摘要: 近年来，海底热液环境中的微生物及其环境适应机制已经成为海洋科学研究的热点。目前，相关的研究主要集中在表层沉积物及微生物的水平分布多样性方面，而对柱状沉积物中微生物垂直分布多样性研究却很少。本文基于西太平洋冲绳海槽南部热液区附近S2站位的柱状沉积物样品，通过对其不同层位的样品进行分离培养和16S rRNA基因高通量测序，揭示了样品中可培养微生物和总体微生物的垂直群落分布特征，同时结合对样品主量元素、微量元素、碳氮含量等指标的评估和冗余分析等统计学方法，讨论了微生物群落结构及其对环境因子的响应。研究发现该位点的柱状沉积物有机质含量较为贫乏，存在两个富含Cu-Zn-Pb的层；各个层位的沉积物中微生物类群均以变形菌为主要类群，同时表层沉积物表现出更高的微生物多样性。此外研究还表明柱状沉积物中有机碳含量与其微生物的群落组成有着更为密切的关系。总之， 本研究的结果和获得的菌种资源为进一步深入研究海底热液环境中微生物参与元素地球化学循环的过程提供了一定的基础。Abstract: In recent years, microbe and its adaptation mechanism in submarine hydrothermal environment have become the focus of marine science research. At present, relevant researches focus on the horizontal distribution diversity of surface sediments and microorganisms, and only few researches on the vertical distribution diversity of microorganisms in columnar sediments. Based on the columnar sediment samples from the S2 station in the southern hydrothermal area of the Okinawa Trough in the western Pacific Ocean, we revealed the vertical community distribution characteristics of culturable microorganisms and the overall microorganisms in the samples through isolation, culture, and high-throughput sequencing of 16S rRNA gene from the samples at different levels. At the same time, the microbial community structure and its response to environmental factors were discussed by using statistical methods such as the evaluation of major elements, trace elements, carbon and nitrogen contents, and redundancy analysis. Results show that the organic matter content of the core sediment at this site is relatively poor, and Cu-Zn-Pb is rich in two layers; the microbial community of each layer is composed of mainly Proteobacteria, while the surface sediments exhibit higher microbial diversity. Meanwhile, it indicated a closer relationship between the organic carbon content of core sediments and the composition of their microbial communities. This study obtained bacterial strain resources and provided a basis for further research into microbial participation in the geochemical cycle of elements in submarine hydrothermal environment.
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图 2 基于16S rRNA基因序列构建的可培养细菌的系统发育树
分支1中包含的菌株有18A01、18E05、18S01、81A02、81E07-1、199A01、301A01、334E05、334M01、334S02、334S04、392A01、392E02、475E05和Alcanivorax xenomutans JC109T (HE601937)。
Figure 2. Phylogenetic tree of cultivable bacteria isolated from hydrothermal field sediment core in the southern Okinawa Trough based on the 16S rRNA gene sequences using the maximum-likelihood algorithm
GenBank accession numbers are shown in parentheses. Bar, 0.1 substitutions per nucleotide position. Branch 1 represented 18A01, 18E05, 18S01, 81A02, 81E07-1, 199A01, 301A01, 334E05, 334M01, 334S02, 334S04, 392A01, 392E02, 475E05, and Alcanivorax xenomutans JC109T (HE601937).
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图 4 基于科水平的物种聚类显示的样品中不同细菌所占的比例
Figure 4. Relative abundance of bacteria in the samples on family level
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图 5 基于物种相对丰度的不同层位样品间的主坐标分析
Figure 5. Principal coordinate analysis (PCoA) on each sample based on the microbial relative abundance
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图 6 基于科水平差异物种相对丰度的样本聚类热图
Figure 6. Cluster heatmap based on relative abundance of differential species at family level
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图 7 样品、微生物种群及环境因子RDA图
Figure 7. Redundancy analysis on the relationships between environmental factors and relative abundance at family level
表 1 本研究使用样品的地球化学组成
Table 1 Geochemical compositions of the samples used in this study
样品深
度/cmbsf18 30 81 100 110 171 181 190 199 240 248 267 288 301 311 334 380 392 475 Na2O/% 2.03 1.98 1.81 1.9 1.86 1.98 1.8 1.84 1.84 1.79 1.79 1.78 1.95 1.89 1.96 1.83 1.89 2.02 1.88 MgO/% 2.64 2.3 2.49 2.5 2.59 2.03 2.43 2.65 2.58 2.4 2.38 2.41 2.71 2.58 2.48 2.39 2.54 2.57 2.49 Al2O3/% 16.32 15.39 16.33 15.77 15.23 14.25 16.11 16.65 16.31 16.37 16.2 16.41 16.13 15.92 15.31 15.98 15.96 15.9 16.37 SiO2/% 58.88 60.43 59.27 59.7 59.17 62.59 59.43 58.05 57.99 59.26 59.53 59.27 59.12 58.48 58.99 59.51 59.62 58.96 58.55 Fe2O3/% 6.43 5.85 6.43 6.03 5.98 5.09 6.21 6.41 6.43 6.31 6.18 6.23 6.32 6.23 5.8 6.14 6.26 6.24 6.26 K2O/% 3.26 2.97 3.27 3.11 3.09 2.76 3.26 3.46 3.35 3.29 3.23 3.26 3.28 3.23 3.04 3.21 3.24 3.17 3.28 CaO/% 2.21 2.67 2.4 2.66 3.52 2.92 2.6 2.66 2.92 2.55 2.6 2.49 2.41 3.13 3.46 2.68 2.52 2.62 2.75 P/10−6 706.1 714.3 684.3 674 632.5 623.6 631.4 607.2 635.4 642 649.2 689.1 646.6 602.5 653.1 620.1 623 899 618.5 S/10−6 761.1 859.7 649.3 841 804.9 956.8 567.1 580.2 657.2 517.6 559 569.4 620.3 650.5 782.9 556.5 734.1 660.4 661.3 Cl/10−6 6037.2 6000 3860.6 4979.2 4420.3 5220.8 4230.2 5057 5537.6 3815.5 4061.6 4257.9 5084 5536.1 6376.4 4519.6 4159.3 6186.9 5395 Ti/10−6 4742.1 4697.5 4834.1 4714.8 4530.7 4377.6 4777.1 4603 4734.4 4868.5 4826 4845.9 4641.3 4639.4 4567 4743.7 4663.3 4562.8 4811.9 V/10−6 131.8 110 128.4 124.9 122.7 100.9 122.7 129.6 128.4 118.9 119.6 117.4 139.2 127.3 117 119.8 131.9 129.2 125 Cr/10−6 99.5 84.6 94.9 88.2 88.8 76.1 90.1 100.1 95.2 91.6 90.8 90 97.6 92.6 85.8 88.6 94.6 89.8 93.4 Mn/10−6 478.4 505.3 527.1 463 496.2 404.1 507 475 493.8 513.2 510.5 542.4 489.8 503.1 492.1 509.3 458.6 623.8 529.6 Co/10−6 16.5 16.6 18.6 16 21.8 13.9 16.6 16.7 16.1 15.6 15.6 17.7 17.7 17.5 16 17 16.7 16 16.8 Ni/10−6 40.3 35.8 40.8 37.2 36.9 30.8 37.5 39.9 38.5 38.5 37.3 37.5 39.4 39.5 35.9 36.9 38.8 37.3 39 Cu/10−6 48.9 28.2 38.5 36.5 35 18.9 26.3 40.1 28.6 28.9 25.4 26.5 57.9 28.5 25.2 26 44.3 43.9 27 Zn/10−6 130.8 95.9 117.6 113.9 110.4 83.4 103.3 126.8 107.2 108.3 103.2 105.5 154.7 107.4 95.7 102.5 135.4 129.5 105.4 Ga/10−6 21.2 19.7 22.5 20.2 20.9 18.3 21 22.9 21.6 22.8 20.9 21.6 21.3 21.7 19 21.5 22.2 20.7 21.7 As/10−6 17 15.5 19.4 12.3 10.5 8.3 12.2 14.8 12.5 12.6 12.2 13.2 17.3 11.6 9.2 11.5 14 14.7 11.7 Rb/10−6 150.6 135.9 153.3 141.8 140.8 122.5 152.7 163.4 158 157.3 151.8 152.6 150.5 151.1 137.3 150.6 149.7 144.6 154 Sr/10−6 144 149 149 149 170 149 149 155 159 151 152 147 151 162 167 152 151 155 155 Zr/10−6 194 208 190 203 189 236 196 170 177 192 198 196 184 179 200 194 189 191 187 Nb/10−6 18.3 21.6 18 17.3 17.7 17 18.8 17.7 20.4 18.5 19 18.7 17.8 19 18.9 18.5 21.1 17.8 18.2 U/10−6 3.7 3.8 3.5 3.5 3.9 2.9 3.8 3.9 4.2 4.1 3.8 3.8 3.8 3.8 3.4 3.8 3.9 3.6 3.6 Mo/10−6 1.2 1.5 1.3 1.1 1.3 1 1.4 1.5 1.6 1.3 1.3 1.3 1.4 1.4 1.3 1.3 1.7 1.2 1.3 Sn/10−6 10.1 9.7 8.3 7.3 10.6 8 12.2 14.6 13.6 9.5 11.1 14.2 10.9 14.4 15.2 10.8 18.7 13.6 10.9 Sb/10−6 15.2 9.6 9.3 7.1 10 11.2 13.4 18.3 13.8 7.7 12.3 15.7 11.8 20.6 17.2 13 24.5 15 14.9 Ba/10−6 524 474 521 493 507 430 517 549 515 509 500 497 562 504 487 503 537 518 500 Hf/10−6 5.5 5.9 5.4 6 5.5 6.7 5.5 5.1 5.1 5.7 5.9 5.5 5.3 5.4 5.8 5.5 5.2 5.6 5.3 W/10−6 2.9 7.3 5.1 12.1 9.1 12.9 4.4 2.4 6.3 4.3 4.2 6.9 11.6 3.2 7.6 4.3 4.4 6.6 4.6 Pb/10−6 93.5 33.6 55.9 58.3 49.9 27.6 36.8 61.1 37.5 37.4 33.8 34.5 116.9 39.3 36.7 38.7 92.3 94.9 36 Bi/10−6 0.5 0.2 1 1.3 1.4 2.4 1.2 1.6 0.3 1.3 1.5 0 0 0 0.7 1 0.6 1.3 0 Th/10−6 15.2 15 13.8 13.9 12.8 10.6 16.1 14 16.1 14.7 14.6 15.5 14.7 16.4 13.1 14.8 15.1 14.7 14.5 Ce/10−6 76.5 54.2 62.8 73.7 71.8 74.8 65.5 68.4 78.7 72.8 66.4 69.4 66.8 68.4 72.9 65.1 68 65.7 84.4 Nd/10−6 27.8 38.4 34 29.1 32.8 29.3 35.1 31 26.9 26.8 33.6 30.8 35.7 31.3 31.8 28 27.5 25.2 29.5 Y/10−6 26.8 27.4 26.8 27 25.5 26.1 26.8 24.4 26 26.2 27.7 27.2 25.8 25.8 26.1 26.7 25.4 25.6 27 La/10−6 44.7 36.3 44.3 35.3 36.4 40.3 41.2 36.4 44.6 44.8 39.8 42 37.7 38.1 33.8 40.8 38.2 44.6 43.8 Sc/10−6 13.9 15 16.6 14.7 15.5 10.6 16 15.6 16.1 13.6 12.9 17.5 13.4 14.3 12.8 15.9 15.1 15.4 14.3 TN/% 0.16 0.1 0.14 0.1 0.13 0.07 0.11 0.15 0.13 0.12 0.1 0.15 0.16 0.12 0.13 0.12 0.14 0.14 0.12 TC/% 1.43 1.1 1.29 1.24 1.58 1.16 1.33 1.54 1.33 1.39 1.38 1.63 1.43 1.62 1.64 1.41 1.52 1.43 1.52 TOC/% 1.05 0.7 0.91 0.69 0.92 0.67 0.82 0.93 0.85 0.66 0.86 1.01 0.96 0.98 0.86 0.85 1.04 1.02 0.9 
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表 2 基于16S rRNA基因序列的菌株分类鉴定信息
Table 2 Isolation and identification of strains based on 16S rRNA gene sequence analysis
菌株号 亲缘菌株 16S rRNA
基因相似性/%层位深度
/cmbsf16S rRNA基因
序列登录号18A01 Alcanivorax xenomutans JC109T 99.22 18 OQ186762 18E01 Bacillus tequilensis KCTC 13622T 99.79 18 OQ186763 18E02 Pelagibacterium halotolerans B2T 99.78 18 OQ186764 18E03 Bacillus altitudinis 41KF2bT 99.93 18 OQ186765 18E04 Pseudonocardia carboxydivorans Y8T 99.93 18 OQ186766 18E05 Alcanivorax xenomutans JC109T 100 18 OQ186767 18M01 Alcanivorax venustensis ISO4T 100 18 OQ186768 18S01 Alcanivorax xenomutans JC109T 100 18 OQ186769 81A02 Alcanivorax xenomutans JC109T 99.93 81 OQ186770 81E01 Rossellomorea aquimaris TF-12T 99.21 81 OQ186771 81E02 Sutcliffiella halmapala DSM 8723T 99.14 81 OQ186772 81E03 Rossellomorea aquimaris TF-12T 99.29 81 OQ186773 81E05 Fictibacillus arsenicus Con a/3T 99.71 81 OQ186774 81E06 Bacillus safensis subsp. safensis FO-36bT 99.86 81 OQ186775 81E07-1 Alcanivorax xenomutans JC109T 99.93 81 OQ186777 81E07-2 Staphylococcus pseudoxylosus S04009T 99.86 81 OQ186778 81E08 Mesobacillus thioparans BMP-1T 99.71 81 OQ186779 81E09 Mesorhizobium sediminum YIM M12096T 99.77 81 OQ186780 110E01 Halomonas titanicae BH1T 99.44 110 OQ186781 110E02 Metabacillus idriensis SMC 4352-2T 99.93 110 OQ186782 110E03 Pseudonocardia carboxydivorans Y8T 100 110 OQ186783 110E04 Mesorhizobium sediminum YIM M12096T 99.77 110 OQ186784 110E05 Pelagibacterium halotolerans B2T 99.78 110 OQ186785 110E06 Sutcliffiella horikoshii DSM 8719T 99.29 110 OQ186786 110E07 Virgibacillus halodenitrificans DSM 10037T 99.93 110 OQ186787 181E01 Halomonas titanicae BH1T 100 181 OQ186788 181E02 Rossellomorea aquimaris TF-12T 99.36 181 OQ186789 181E03 Pseudonocardia carboxydivorans Y8T 99.79 181 OQ186790 181E04 Nitratireductor aquibiodomus JCM 21793T 99.08 181 OQ186791 181M01 Halomonas titanicae BH1T 100 181 OQ186792 181S01 Martelella mediterranea DSM 17316T 99.63 181 OQ186793 199A01 Alcanivorax xenomutans JC109T 100 199 OQ186794 199E01 Nitratireductor aquibiodomus JCM 21793T 99.17 199 OQ186795 199E02 Mesorhizobium sediminum YIM M12096T 99.77 199 OQ186796 199E03 Pseudonocardia carboxydivorans Y8T 99.78 199 OQ186797 199M01 Halomonas titanicae BH1T 100 199 OQ186798 248E02 Paenisporosarcina quisquiliarum SK 55T 99.38 248 OQ186799 248E04 Nitratireductor aquibiodomus JCM 21793T 99.03 248 OQ186800 248E05 Citromicrobium bathyomarinum JF-1T 99.7 248 OQ186801 301A01 Alcanivorax xenomutans JC109T 99.93 301 OQ186802 301E02 Paenisporosarcina macmurdoensis CMS 21wT 99.31 301 OQ186803 301E04 Paenisporosarcina macmurdoensis CMS 21wT 99.72 301 OQ186804 301E05 Pelagerythrobacter marinus H32T 99.93 301 OQ186805 301E06 Nitratireductor aquibiodomus JCM 21793T 98.94 301 OQ186806 334E03 Paenisporosarcina macmurdoensis CMS 21wT 99.15 334 OQ186807 334E04 Paenisporosarcina macmurdoensis CMS 21wT 99.14 334 OQ186808 334E05 Alcanivorax xenomutans JC109T 100 334 OQ186809 334M01 Alcanivorax xenomutans JC109T 99.93 334 OQ186810 334S02 Alcanivorax xenomutans JC109T 100 334 OQ186811 334S03 Muricauda ruestringensis DSM 13258T 98.48 334 OQ186812 334S04 Alcanivorax xenomutans JC109T 100 334 OQ186813 392A01 Alcanivorax xenomutans JC109T 99.93 392 OQ186814 392E01 Paenisporosarcina quisquiliarum SK 55T 99.71 392 OQ186815 392E02 Alcanivorax xenomutans JC109T 100 392 OQ186816 392E03 Pelagerythrobacter marinus H32T 100 392 OQ186817 392E04 Pelagibacterium nitratireducens JLT2005T 99.77 392 OQ186818 392E05 Paracoccus marcusii DSM 11574T 99.77 392 OQ186819 392E06 Paenisporosarcina quisquiliarum SK 55T 99.79 392 OQ186820 475E01 Alkalihalobacillus hwajinpoensis SW-72T 99.65 475 OQ186821 475E02 Thalassospira xiamenensis M-5T 99.65 475 OQ186822 475E03 Qipengyuania vulgaris 022 2-10T 99.85 475 OQ186823 475E04 Pelagibacterium nitratireducens JLT2005T 99.7 475 OQ186824 475S01 Alcanivorax xenomutans JC109T 99.93 475 OQ186825 475M01 Thalassospira xiamenensis M-5T 99.85 475 OQ186826
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