来自墨西哥湾北部“死亡区”的宏基因组组装和原核宏基因组组装基因组序列
Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico "Dead Zone".
作者信息
Thrash J Cameron, Baker Brett J, Seitz Kiley W, Temperton Ben, Campbell Lauren Gillies, Rabalais Nancy N, Henrissat Bernard, Mason Olivia U
机构信息
Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.
Marine Science Institute, University of Texas, Austin, Port Aransas, Texas, USA.
出版信息
Microbiol Resour Announc. 2018 Sep 6;7(9). doi: 10.1128/MRA.01033-18. eCollection 2018 Sep.
Abstract
Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Our data set from within the second largest human-caused hypoxic region provides opportunities to more deeply explore the microbiology of these systems.
摘要
全球范围内，溶解氧下降的沿海地区数量在增加，且情况愈发严重。然而，尽管微生物代谢在沿海低氧环境中十分重要，但针对此的宏基因组学调查却很少。我们从第二大人为造成的低氧区域获取的数据集，为更深入探究这些系统的微生物学提供了契机。
相似文献
1
Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico "Dead Zone".来自墨西哥湾北部“死亡区”的宏基因组组装和原核宏基因组组装基因组序列
Microbiol Resour Announc. 2018 Sep 6;7(9). doi: 10.1128/MRA.01033-18. eCollection 2018 Sep.
2
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".未培养细菌浮游生物谱系在墨西哥湾“死亡区”的代谢作用。
mBio. 2017 Sep 12;8(5):e01017-17. doi: 10.1128/mBio.01017-17.
3
Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico.墨西哥湾北部缺氧区的古菌富集。
Environ Microbiol. 2015 Oct;17(10):3847-56. doi: 10.1111/1462-2920.12853. Epub 2015 Apr 27.
4
Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure.墨西哥湾缺氧区的年度范围影响微生物群落结构。
PLoS One. 2019 Apr 25;14(4):e0209055. doi: 10.1371/journal.pone.0209055. eCollection 2019.
5
Absence of hypoxia events in the adjacent coastal waters of Grijalva-Usumacinta river, Southern Gulf of Mexico.墨西哥湾南部格里哈尔瓦-乌苏马辛塔河邻近沿海海域无缺氧事件。
Mar Pollut Bull. 2020 Jul;156:111174. doi: 10.1016/j.marpolbul.2020.111174. Epub 2020 May 6.
6
Region-wide impairment of Atlantic croaker testicular development and sperm production in the northern Gulf of Mexico hypoxic dead zone.墨西哥湾北部缺氧死亡区影响大西洋军曹鱼的区域性睾丸发育和精子生成。
Mar Environ Res. 2010;69 Suppl:S59-62. doi: 10.1016/j.marenvres.2009.10.017. Epub 2009 Oct 25.
7
Impaired gamete production and viability in Atlantic croaker collected throughout the 20,000 km(2) hypoxic region in the northern Gulf of Mexico.在墨西哥湾北部20000平方公里的缺氧区域采集的大西洋鲱鱼，其配子产生和活力受损。
Mar Pollut Bull. 2015 Dec 15;101(1):182-192. doi: 10.1016/j.marpolbul.2015.11.001. Epub 2015 Nov 4.
8
Cost-effective targeting of conservation investments to reduce the northern Gulf of Mexico hypoxic zone.针对保护投资的成本效益目标，以减少墨西哥湾北部缺氧区。
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18530-5. doi: 10.1073/pnas.1405837111. Epub 2014 Dec 15.
9
Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia.墨西哥湾北部沉积物中暴露于低氧环境的细菌和古菌群落的变化。
Geobiology. 2015 Sep;13(5):478-93. doi: 10.1111/gbi.12142. Epub 2015 May 5.
10
Time-Evolving, Spatially Explicit Forecasts of the Northern Gulf of Mexico Hypoxic Zone.时间演变的墨西哥湾北部缺氧区的空间显式预测。
Environ Sci Technol. 2019 Dec 17;53(24):14449-14458. doi: 10.1021/acs.est.9b05790. Epub 2019 Nov 27.
引用本文的文献
1
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.来自墨西哥湾北部沿海时间序列的宏基因组和1313个宏基因组组装基因组。
Sci Data. 2025 Aug 8;12(1):1388. doi: 10.1038/s41597-025-05736-9.
2
Microbial ecology of northern Gulf of Mexico estuarine waters.墨西哥湾北部河口水域的微生物生态学。
mSystems. 2024 Aug 20;9(8):e0131823. doi: 10.1128/msystems.01318-23. Epub 2024 Jul 9.
3
Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column.宏基因组学和宏转录组学揭示了墨西哥湾缺氧区和海洋水柱中广泛分布、活跃且新颖的甲烷营养菌。
FEMS Microbiol Ecol. 2023 Jan 24;99(2). doi: 10.1093/femsec/fiac153.
4
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments.海洋 DNA MAG 目录包含了超过 50000 个源自各种海洋环境的原核生物基因组。
Sci Data. 2022 Jun 17;9(1):305. doi: 10.1038/s41597-022-01392-5.
5
Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ().全球分布的OM252浮游细菌的生态生理学（）
mSystems. 2021 Jun 29;6(3):e0027621. doi: 10.1128/mSystems.00276-21.
6
Best Practices for Successfully Writing and Publishing a Genome Announcement in .成功撰写和发表基因组公告的最佳实践
Microbiol Resour Announc. 2020 Sep 3;9(36):e00763-20. doi: 10.1128/MRA.00763-20.
7
Contributions of single-cell genomics to our understanding of planktonic marine archaea.单细胞基因组学对我们理解浮游海洋古菌的贡献。
Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190096. doi: 10.1098/rstb.2019.0096. Epub 2019 Oct 7.
8
Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones.未培养的硝化螺旋菌类似种是贫氧带中主要的亚硝酸盐氧化菌。
ISME J. 2019 Oct;13(10):2391-2402. doi: 10.1038/s41396-019-0443-7. Epub 2019 May 22.
9
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach.揭示南极土壤中未被培养的大多数：迈向协同方法。
Front Microbiol. 2019 Feb 15;10:242. doi: 10.3389/fmicb.2019.00242. eCollection 2019.
本文引用的文献
1
Declining oxygen in the global ocean and coastal waters.全球海洋和沿海水域的氧气减少。
Science. 2018 Jan 5;359(6371). doi: 10.1126/science.aam7240.
2
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".未培养细菌浮游生物谱系在墨西哥湾“死亡区”的代谢作用。
mBio. 2017 Sep 12;8(5):e01017-17. doi: 10.1128/mBio.01017-17.
3
IMG/M: integrated genome and metagenome comparative data analysis system.IMG/M：综合基因组与宏基因组比较数据分析系统
Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13.
4
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.CheckM：评估从分离株、单细胞和宏基因组中获得的微生物基因组质量。
Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.
5
Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico.墨西哥湾北部缺氧区的古菌富集。
Environ Microbiol. 2015 Oct;17(10):3847-56. doi: 10.1111/1462-2920.12853. Epub 2015 Apr 27.
6
Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.浮游嗜酸菌纲的基因组：通过宏基因组学拓展海洋放线菌的视野
mBio. 2015 Feb 10;6(1):e02083-14. doi: 10.1128/mBio.02083-14.
7
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria.宏基因组学揭示了一类新的低 GC 及超小型海洋放线菌。
Sci Rep. 2013;3:2471. doi: 10.1038/srep02471.
8
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.IDBA-UD：一个用于具有高度不均匀深度的单细胞和宏基因组测序数据的从头组装程序。
Bioinformatics. 2012 Jun 1;28(11):1420-8. doi: 10.1093/bioinformatics/bts174. Epub 2012 Apr 11.
9
The genomic standards consortium: bringing standards to life for microbial ecology.基因组标准协会：让微生物生态学标准落地生根。
ISME J. 2011 Oct;5(10):1565-7. doi: 10.1038/ismej.2011.39. Epub 2011 Apr 7.
Zotero 插件