Marine biofilms constitute a bank of hidden microbial diversity and functional potential

Weipeng Zhang; Wei Ding; Yong Xin Li; Chunkit Tam; Salim Bougouffa; Ruojun Wang; Bite Pei; Hoyin Chiang; Pokman Leung; Yanhong Lu; Jin Sun; He Fu; Vladimir B. Bajic; Hongbin Liu; Nicole S. Webster; Pei Yuan Qian

doi:10.1038/s41467-019-08463-z

Marine biofilms constitute a bank of hidden microbial diversity and functional potential

Weipeng Zhang, Wei Ding, Yong Xin Li, Chunkit Tam, Salim Bougouffa, Ruojun Wang, Bite Pei, Hoyin Chiang, Pokman Leung, Yanhong Lu, Jin Sun, He Fu, Vladimir B. Bajic, Hongbin Liu, Nicole S. Webster, Pei Yuan Qian^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

74 Scopus citations

Abstract

Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming ‘species’ that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.

Original language	English (US)
Article number	517
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-08463-z
State	Published - Dec 1 2019

Bibliographical note

Funding Information:
We thank Mr. Huihui Zhu, Ms. Yujia Nie, and Ms. Xin Gong from Novogene for DNA sequencing and technical support. We thank Mr. Bo Yang for technical support in construction of Linux platform. We thank Ms. Qian Ding, Dr. Zhiwu Sun, Dr. Tim Wong, and Dr. Zhaoming Gao for sample collection. The authors are also grateful for English editing by Ms. Alice Cheung. We also thank the fundings provided by the China Ocean Mineral Resources Research and Development Association (COMRRDA17SC01) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB06010102) to P.Y.Q.

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41467-019-08463-z

Cite this

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title = "Marine biofilms constitute a bank of hidden microbial diversity and functional potential",

abstract = "Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming {\textquoteleft}species{\textquoteright} that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.",

author = "Weipeng Zhang and Wei Ding and Li, {Yong Xin} and Chunkit Tam and Salim Bougouffa and Ruojun Wang and Bite Pei and Hoyin Chiang and Pokman Leung and Yanhong Lu and Jin Sun and He Fu and Bajic, {Vladimir B.} and Hongbin Liu and Webster, {Nicole S.} and Qian, {Pei Yuan}",

note = "Funding Information: We thank Mr. Huihui Zhu, Ms. Yujia Nie, and Ms. Xin Gong from Novogene for DNA sequencing and technical support. We thank Mr. Bo Yang for technical support in construction of Linux platform. We thank Ms. Qian Ding, Dr. Zhiwu Sun, Dr. Tim Wong, and Dr. Zhaoming Gao for sample collection. The authors are also grateful for English editing by Ms. Alice Cheung. We also thank the fundings provided by the China Ocean Mineral Resources Research and Development Association (COMRRDA17SC01) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB06010102) to P.Y.Q. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

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AB - Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming ‘species’ that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.

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Marine biofilms constitute a bank of hidden microbial diversity and functional potential

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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