Differences Between DNA- and RNA-Based Bacterial Communities in Marine Sediments

被引：2
作者：
Li M.-Y. [1 ,2 ,3 ]
Yang Y.-H. [1 ,2 ,3 ]
Mi T.-Z. [1 ,2 ,3 ]
He H. [4 ]
Zhen Y. [1 ,2 ,3 ]
机构：
[1] College of Environmental Science and Engineering, Ocean University of China, Qingdao
[2] Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao
[3] Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao
[4] College of Marine Life Science, Ocean University of China, Qingdao
来源：
Huanjing Kexue/Environmental Science | 2020年 / 41卷 / 05期
关键词：
Active; Bacterial community; DNA; RNA; Sediment;
D O I：
10.13227/j.hjkx.201911071
中图分类号：
学科分类号：
摘要：
Microorganisms in marine sediments play crucial roles in biogeochemical processes. Currently, 16S rRNA gene-based sequencing is popular for studying bacterial communities; however, the DNA used in analysis can include not only that from active microorganisms but also that from inactive microorganisms, while the RNA can represent active microorganisms and more recent activity in the environment; therefore, a study of the difference between the total bacterial community based on the 16S rRNA gene and the active bacterial community based on 16S rRNA will support a better understanding of bacterial community structure and function in marine sediments. In this study, the total and active bacterial community structures in surface sediments from the Bohai Sea and South Yellow Sea were investigated at DNA and RNA level using quantitative real-time polymerase chain reaction and Illumina high-throughput sequencing, respectively. The results show that the 16S rRNA gene abundances of bacterial communities are 1-2 orders of magnitude higher than the transcript abundances. The total bacterial community is more diverse compared to the active bacterial community, and there are distinct differences between them. The bacteria in the sediments take part in active chemoheterotrophy, sulfate reduction, and nitrification. Moreover, 16S rRNA gene-based sequencing misestimates some important functional microbiota when exploring bacterial community functions. The 'rare biosphere' in the total bacterial communities consists of actively transcriptional players, which could play key roles in biogeochemistry cycles. Overall, in the analysis of bacterial communities in marine sediments from a stable sedimentary environment, it is beneficial to use the 16S rRNA sequencing to reflect the true ecological status. © 2020, Science Press. All right reserved.
引用
收藏
页码：2485 / 2495
页数：10
相关论文
共 40 条
  • [1] Whitman W.B., Coleman D.C., Wiebe W.J., Prokaryotes: the unseen majority, Proceedings of the National Academy of Sciences of the United States of America, 95, 12, pp. 6578-6583, (1998)
  • [2] Falkowski P.G., Fenchel T., Delong E.F., The microbial engines that drive Earth's biogeochemical cycles, Science, 320, 5879, pp. 1034-1039, (2008)
  • [3] Zinger L., Amaral-Zettler L.A., Fuhrman J.A., Et al., Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems, PLoS One, 6, 9, (2011)
  • [4] Findlay R.H., Watling L., Seasonal variation in the structure of a marine benthic microbial community, Microbial Ecology, 36, 1, pp. 23-30, (1998)
  • [5] Qian P., Wang S.P., Liang C.L., Et al., Seasonal distribution characteristics of bacterial communities of coastal surface sediments of Xiangshan, Ningbo, Journal of Ningbo University (Natural Science & Engineering Edition), 30, 6, pp. 28-35, (2017)
  • [6] Fu L.L., Zhen Y., He H., Et al., Distribution characteristics of anaerobic ammonia oxidation bacteria in sediments from the adjacent seas of Yangtze estuary, Environmental Science, 37, 10, pp. 3914-3922, (2016)
  • [7] Liu J.W., Liu X.S., Wang M., Et al., Bacterial and archaeal communities in sediments of the north Chinese marginal seas, Microbial Ecology, 70, 1, pp. 105-117, (2015)
  • [8] Catania V., Sara G., Settanni L., Et al., Bacterial communities in sediment of a Mediterranean marine protected area, Canadian Journal of Microbiology, 63, 4, pp. 303-311, (2016)
  • [9] Rubio-Portillo E., Villamor A., Fernandez-Gonzalez V., Et al., Exploring changes in bacterial communities to assess the influence of fish farming on marine sediments, Aquaculture, 506, pp. 459-464, (2019)
  • [10] He H., Li M.Y., Zhen Y., Et al., Bacterial and archaeal communities in sediments from the adjacent waters of Rushan Bay (China) revealed by Illumina sequencing, Geomicrobiology Journal, pp. 1-15, (2019)
1234