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Lanclos VC, Rasmussen AN, Kojima CY, Cheng C, Henson MW, Faircloth BC, Francis CA, Thrash JC. Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. THE ISME JOURNAL 2023; 17:620-629. [PMID: 36739346 PMCID: PMC10030771 DOI: 10.1038/s41396-023-01376-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
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Affiliation(s)
- V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Conner Y Kojima
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chuankai Cheng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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Li X, Liu Q, Yu X, Zhang C, Liu M, Zhou X, Gu C, Wang M, Shao H, Li J, Jiang Y. Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20615-20630. [PMID: 36255574 DOI: 10.1007/s11356-022-23572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.
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Affiliation(s)
- Xianrong Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chenru Zhang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chengxiang Gu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 2661000, China
| | - Hongbing Shao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jiansen Li
- Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea. WATER 2020. [DOI: 10.3390/w12020501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Baltic Sea represents one of the largest brackish ecosystems where various environmental factors control dynamic seasonal shifts in the structure, diversity, and function of the planktonic microbial communities. In this study, despite seasonal fluctuations, several bacterial populations (<2% of the total OTUs) that are highly dominant (25% of relative abundance) and highly frequently occurring (>85% of occurrence) over four seasons were identified. Mathematical models using occurrence frequency and relative abundance data were able to describe community assembly persisting over time. Further, this work uncovered one of the core bacterial populations phylogenetically affiliated to SAR11 subclade IIIa. The analysis of the hypervariable region of 16S rRNA gene and single copy housekeeping genes recovered from metagenomic datasets suggested that the population was unexpectedly evolutionarily closely related to those inhabiting a mesosaline lacustrine ecosystem rather than other marine/coastal members. Our metagenomic results further revealed that the newly-identified population was the major driver facilitating the seasonal shifts in the overall community structure over the brackish waters of the Baltic Sea. The core community uncovered in this study supports the presence of a brackish water microbiome distinguishable from other marine and freshwater counterparts and will be a useful sentinel for monitoring local/global environmental changes posed on brackish surface waters.
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Oh S, Hammes F, Liu WT. Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. WATER RESEARCH 2018; 128:278-285. [PMID: 29107912 DOI: 10.1016/j.watres.2017.10.054] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 05/08/2023]
Abstract
Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.
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Affiliation(s)
- Seungdae Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Frederik Hammes
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstr. 133, CH-8600 Dübendorf, Switzerland
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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