Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing.

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2018-01

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Abstract

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons.Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014-16 El Niño event.

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10.7717/peerj.4671

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O'Connell, Lauren, Song Gao, Donald McCorquodale, Jay Fleisher and Jose V Lopez (2018). Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing. PeerJ, 6(5). 10.7717/peerj.4671 Retrieved from https://hdl.handle.net/10161/17102.

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Scholars@Duke

Gao

Song Gao

Professor of Environmental Science at Duke Kunshan University

Song Gao
Professor of Environmental Science/Chemistry, DKU
Postdoctoral Scholar, California Institute of Technology (Atmospheric Chemistry / Environmental Engineering)
Ph.D., University of Washington (Analytical/Environmental Chemistry)
B.S., University of Science and Technology of China (Materials Science /Chemistry Track, with Honors)

Welcome to my Duke Scholar page. Prior to joining DKU, I served on the chemistry and environmental science faculty in both liberal arts and research universities, including Stetson University (#4 Best Regional Universities South - US News 2023) in the US, as well as Hong Kong University of Science and Technology (#40 QS Top Global Universities 2023).
 
My group's research takes an interdisciplinary approach, combining field, laboratory and modeling studies, to understanding the scientific mechanisms behind environmental pollution and finding remediation solutions. My peer-reviewed publications focus on the physicochemical mechanisms of smog pollution, molecular nature and chemical transformation of secondary aerosols, remediation technologies in removing halogenated compounds in groundwater.  These publications are widely cited globally: by google scholar, one of them has ~600 citations, and another five publications with over 300 citations each.

I have also taken on a keen interest to formulate science-based environmental policies. My latest research involves developing a novel scientific/policy framework to reduce plastics pollution at the upstream, uncovering previously missing links between synthetic chemistry and atmospheric chemistry, ultimately coordinating global treaties on ozone protection, climate mitigation and plastics reduction. This research has culminated in a paper being published at the Proceedings of the National Academy of Sciences of the United States (PNAS) in 2021 with a DKU undergraduate as a co-author (now studying environmental engineering at Stanford University), and an invited book chapter in celebrating the 35th Anniversary of the Montreal Protocol by United Nations Environment Programme (UNEP). In addition, a new book that I co-authored, "SOLVE: Environmental Science Problems", was recently published by the University Science Books in the US.

I have received research funding from the United States National Science Foundation (US NSF) and Hong Kong Research Grants Council, and have served as a reviewer for US NSF grants and various international journals, a Section Editor for Case Studies in the Environment (University of California Press), and an Associate Editor for Journal of Environmental Studies and Sciences (Springer).   

I am also passionate about teaching, having taught both undergraduate and graduate courses in chemistry, environmental science and energy, and supervised student research at both graduate and undergraduate levels. Three DKU graduates in 2022, who did their undergraduate SW thesis research under my mentorship, are now studying in applied math, environmental engineering and information technology strategy, respectively, in top universities in the US. Two previous students received Green Chemistry Scholarships awarded by US National Science Foundation /American Chemical Society.  Disseminating knowledge on chemical and earth sciences, in an intriguing and articulate manner whilst ensuring the rigor of learning, has never ceased to gratify me, and I intend to continue this exploratory journey with my students.  

In spare time, I enjoy attending concerts and playing the keyboard. Without elaborating, may I simply say that Bach, Mendelssohn, and Brahms (among all other great composers), with their music so profoundly enriching and enjoyable whilst deeply resonating with laws and patterns in the sciences, are perfect reminders of how various fields and domains are fundamentally connected; yet it is a lifelong journey to decipher the embedded interconnections, complexities and implications.




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