1
|
Wang Y, Li X, Chi Y, Song W, Yan Q, Huang J. Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions. Microorganisms 2022; 10:1176. [PMID: 35744694 PMCID: PMC9229623 DOI: 10.3390/microorganisms10061176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/04/2022] Open
Abstract
A long-standing dilemma for microbial analyses is how to handle and store samples, as it is widely assumed that the microbial diversity and community patterns would be affected by sample storage conditions. However, it is quite challenging to maintain consistency in field sampling, especially for water sample collection and storage. To obtain a comprehensive understanding of how sample storage conditions impact microbial community analyses and the magnitude of the potential storage effects, freshwater samples were collected and stored in bottles with lid closed and without lid at room temperature for up to 6 days. We revealed the dynamics of prokaryotic and eukaryotic microbial communities under different storage conditions over time. The eukaryotic microbial communities changed at a faster rate than the prokaryotic microbial communities during storage. The alpha diversity of the eukaryotic microbial communities was not substantially influenced by container status or storage time for up to 12 h, but the beta diversity differed significantly between the control and all treatment samples. By contrast, no significant changes of either the alpha or beta diversity of the prokaryotic microbial communities were observed within 12 h of room-temperature storage, regardless of the container status. The potential interactions between microbial taxa were more complex when samples were stored in sealed bottles, and the deterministic processes played an increasingly important role in shaping the freshwater microbial communities with storage time. Our results suggest that water samples collected and stored without refrigeration for no more than 12 h may still be useful for downstream analyses of prokaryotic microbial communities. If the eukaryotic microbial communities are desired, storage of water samples should be limited to 3 h at room temperature.
Collapse
Affiliation(s)
- Yunfeng Wang
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan 430062, China;
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China;
| | - Jie Huang
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
2
|
Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes. WATER 2022. [DOI: 10.3390/w14050723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO3−-N, NH4+-N, PO43−, and CODcr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO3−-N, and NH4+-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment.
Collapse
|