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Nguyen HT, Choi W, Kim EJ, Cho K. Microbial community niches on microplastics and prioritized environmental factors under various urban riverine conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157781. [PMID: 35926609 DOI: 10.1016/j.scitotenv.2022.157781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs) provide habitats to microorganisms in aquatic environments; distinct microbial niches have recently been elucidated. However, there is little known about the microbial communities on MPs under urban riverine conditions, in which environmental factors fluctuate. Therefore, this study investigated MP biofilm communities under various urban riverine conditions (i.e., organic content, salinity, and dissolved oxygen (DO) concentration) and evaluated the prioritized factors affecting plastisphere communities. Nine biofilm-forming reactors were operated under various environmental conditions. Under all testing conditions, biofilms grew on MPs with decreasing bacterial diversity. Interestingly, biofilm morphology and bacterial populations were driven by the environmental parameters. We found that plastisphere community structures were grouped according to the environmental conditions; organic content in the water was the most significant factor determining MP biofilm communities, followed by salinity and DO concentration. The principal plastisphere communities were Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes phyla. In-depth analyses of plastisphere communities revealed that biofilm-forming and plastic-degrading bacteria were the predominant microbes. In addition, potential pathogens were majorly discovered in the riverine waters with high organic content. Our results suggest that distinct plastisphere communities coexist with MP particles under certain riverine water conditions, implying that the varied MP biofilm communities may affect urban riverine ecology in a variety of ways.
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Affiliation(s)
- Hien Thi Nguyen
- Center for Water Cycle Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Woodan Choi
- Center for Water Cycle Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Eun-Ju Kim
- Center for Water Cycle Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Kyungjin Cho
- Center for Water Cycle Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea.
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2
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Lipko IA, Belykh OI. Environmental Features of Freshwater Planktonic Actinobacteria. CONTEMP PROBL ECOL+ 2021. [DOI: 10.1134/s1995425521020074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ting ASY, Zoqratt MZHM, Tan HS, Hermawan AA, Talei A, Khu ST. Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform. 3 Biotech 2021; 11:40. [PMID: 33479595 PMCID: PMC7794265 DOI: 10.1007/s13205-020-02617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/26/2020] [Indexed: 01/04/2023] Open
Abstract
Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02617-3.
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Affiliation(s)
- Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Andreas Aditya Hermawan
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Amin Talei
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Soon Thiam Khu
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
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Ouyang L, Chen H, Liu X, Wong MH, Xu F, Yang X, Xu W, Zeng Q, Wang W, Li S. Characteristics of spatial and seasonal bacterial community structures in a river under anthropogenic disturbances. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114818. [PMID: 32559870 DOI: 10.1016/j.envpol.2020.114818] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In this study, the seasonal characteristics of microbial community compositions at different sites in a river under anthropogenic disturbances (Maozhou River) were analyzed using Illumina HiSeq sequencing. Taxonomic analysis revealed that Proteobacteria was the most abundant phylum in all sites, followed by Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Firmicutes. The variations of the community diversities and compositions between the seasons were not significant. However, significant differences between sites as well as water and sediment samples were observed. These results indicated that sites under different levels of anthropogenic disturbances have selected distinct bacterial communities. pH, dissolved oxygen (DO), concentrations of total nitrogen (TN) and heavy metals were the main factors that influence the diversity and the composition of bacterial community. Specifically, the relative abundance of Proteobacteria was negatively correlated with pH and DO and positively correlated with TN, while Actinobacteria and Verrucomicrobia showed the opposite pattern. Moreover, positive correlations between the relative abundances of Firmicutes and Bacteroidetes and the concentration of heavy metals were also found. Results of functional prediction analysis showed no significant differences of the carbon, nitrogen and phosphorus metabolism across the sites and seasons. Potential pathogens such as Vibrio, Arcobacter, Acinetobacter and Pseudomonas were found in these samples, which may pose potential risks for environment and human health. This study reveals the effect of anthropogenic activities on the riverine bacterial community compositions and provides new insights into the relationships between the environmental factors and the bacterial community distributions in a freshwater ecosystem under anthropogenic disturbances.
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Affiliation(s)
- Liao Ouyang
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Huirong Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xinyue Liu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education and Research (CHEER), The Education University of HongKong, Taipo, Hong Kong, China
| | - Fangfang Xu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuewei Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Wang Xu
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Qinghuai Zeng
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Weimin Wang
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Shuangfei Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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5
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Sun R, Tu Z, Fan L, Qiao Z, Liu X, Hu S, Zheng G, Wu Y, Wang R, Mi X. The correlation analyses of bacterial community composition and spatial factors between freshwater and sediment in Poyang Lake wetland by using artificial neural network (ANN) modeling. Braz J Microbiol 2020; 51:1191-1207. [PMID: 32406050 DOI: 10.1007/s42770-020-00285-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
As one of the most important components of the lake ecosystem, microorganisms from the freshwater and sediment play an important role in many ecological processes. However, the difference and correlation of bacterial community between these two niches were not clear. This study investigated the diversity of microbial community of freshwater and sediment samples from fifteen locations in Poyang Lake wetland. The correlation between the bacterial community and physicochemical property of Poyang Lake wetland was analyzed by artificial neural network (ANN). Our results demonstrated that the freshwater and sediment bacterial community were dominated by groups of the Bacteroidetes (23.33%) and β-Proteobacteria (22.54%) separately, whereas, Canalipalpata, Bacillariophyta, Gemmatimonadetes, and Verrucomicrobia were detected in freshwater niches only. Phylogenetic analysis further indicated that bacterial composition in freshwater significantly differed with the sediment niches. There are 34 unique species accounted for 85% in fresh water samples and 28 unique species accounted for 82% in sediment samples. Cluster analysis further proved that all the samples from freshwater niches clustered closely together, far from the rest sediment samples. ANN analysis revealed that the freshwater with high N and P nutrients will greatly increase the diversity of the bacterial communities. In general, both environmental physicochemical properties, not each factor independently, contributed to the shift in the bacterial community structure. The five tributaries (Gan, Fu, Xin, Rao, Xiu Rivers) play a vital role in shaping the bacterial communities of Poyang Lake. This study provides new insights for understanding of microbial community compositions and structures of Poyang Lake wetland.
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Affiliation(s)
- Ran Sun
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Zuxin Tu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330029, China
| | - Lin Fan
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Zixia Qiao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Xiaoyan Liu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Sihai Hu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Guohua Zheng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330029, China.,Key Laboratory of Poyang Lake, Jiangxi Academy of Sciences, Nanchang, 330029, China
| | - Yaoguo Wu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China.
| | - Ruiwu Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'An, 710129, China.
| | - Xiaohui Mi
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 2020; 86:AEM.00140-20. [PMID: 32169939 DOI: 10.1128/aem.00140-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022] Open
Abstract
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.
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Shi M, Li J, Zhou Q, Wang G, Zhang W, Zhang Z, Gao Y, Yan S. Interactions between elevated CO 2 levels and floating aquatic plants on the alteration of bacterial function in carbon assimilation and decomposition in eutrophic waters. WATER RESEARCH 2020; 171:115398. [PMID: 31874391 DOI: 10.1016/j.watres.2019.115398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Elevated atmospheric CO2 concentration (eCO2) may have different effects on the bacterial community with regard to C assimilation and decomposition in eutrophic waters compared to that in fresh waters with intermediate levels of nutrients and oceans. Aquatic plant growth under eCO2 could further modify microbial activities associated with the C cycle in eutrophic waters. Therefore, there is an urgent need to further study how eCO2 and its interactions with the growth of aquatic plants affect the composition and function of the bacterial community involved in mediating the C cycle in eutrophic waters. Accordingly, we designed a microcosm experiment to investigate the effects of ambient and high CO2 concentrations on bacterial community composition and function in eutrophic waters with and without the growth of Eichhornia crassipes (Mart.) Solms. The results from 16S rRNA gene sequencing, function prediction, and q-PCR showed that eCO2 significantly increased the abundance of bacterial and functional genes involved in CO2 assimilation (photosynthetic bacteria; cbbL IA & IC, cbbL ID, cbbM, pufM) and C decomposition (Acidimicrobiia, Thermoleophilia, Gaiellales; ChiA), illustrating the functional enrichment with photoautotrophy, hydrocarbon degradation, cellulolysis, and aromatic hydrocarbon degradation. However, eCO2 decreased the abundance of some chemoautotrophic bacteria, including nitrifying bacteria (Nitrospirae, Nitrosomonadaceae). In contrast, the cultivation of E. crassipes decreased the abundance of photosynthetic bacteria but increased the abundance of bacteria involved in complex C decomposition associated with root exudates and degradation, e.g. Fibrobacteres, Sphingobacteriales, Sphingomonadales, and Rhizobiales. eCO2 and growth of E. crassipes had opposite effects on algal density in eutrophic waters, creating interactive effects that further decreased the diversity of the bacterial community and abundance of some CO2-assimilating bacteria with nitrifying characteristics (Nitrosomonadaceae) and some C-degrading bacteria (Fibrobacteres) with denitrifying properties (Flavobacteriaceae, Sphingomonadaceae, and Gemmobacter). Therefore, the interactions between aquatic plants and the bacterial community in eutrophic waters under eCO2 would be beneficial to the environment and help alleviate the greenhouse effect.
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Affiliation(s)
- Man Shi
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiangye Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qi Zhou
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Weiguo Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China
| | - Zhenhua Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yan Gao
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China.
| | - Shaohua Yan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China
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Fan L, Hu G, Qiu L, Meng S, Wu W, Zheng Y, Song C, Li D, Chen J. Variations in bacterioplankton communities in aquaculture ponds and the influencing factors during the peak period of culture. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113656. [PMID: 31796310 DOI: 10.1016/j.envpol.2019.113656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
An increase in nutrient input may disturb the bacterioplankton communities in freshwater aquaculture ponds during the peak period of culture. Water samples were collected from ponds of three cultivated species. After the samples were filtered and total DNA was extracted, Illumina high-throughput sequencing was used to profile the spatiotemporal distributions in bacterioplankton communities, the belt diversity, and the influencing factors during this period of time. The results showed that Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla. Biological differences in cultivated species were the main influencing factors that shaped bacterioplankton communities. Monthly variations and thermal stratification provided little and no contribution to bacterioplankton communities, respectively. CODmn, Chla, and TN were the most appropriate parameters to describe the environmental interpretation of bacterial ordinations, and CODmn was the predominant factor. In addition, the higher similarity between CODmn and Chla, shown by clustering analysis, indicated that the algae-bacteria symbiotic system may have an important role in material circulation in freshwater aquaculture pond water during the peak period of culture. The present study has helped to elucidate the biological characteristics of aquaculture tail water, and enriched the basic data provided by bacterioplankton studies.
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Affiliation(s)
- Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, Jiangsu Province, China.
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Paver SF, Newton RJ, Coleman ML. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry. Environ Microbiol 2019; 22:433-446. [PMID: 31736217 PMCID: PMC6973239 DOI: 10.1111/1462-2920.14862] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022]
Abstract
The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.
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Affiliation(s)
- Sara F Paver
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
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10
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Kauser I, Ciesielski M, Poretsky RS. Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river. PeerJ 2019; 7:e7455. [PMID: 31403004 PMCID: PMC6688595 DOI: 10.7717/peerj.7455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/10/2019] [Indexed: 12/04/2022] Open
Abstract
Background In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems. Methods Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR. Results We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and antibiotic resistance.
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Affiliation(s)
- Imrose Kauser
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Mark Ciesielski
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Rachel S Poretsky
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
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11
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Tsao HF, Scheikl U, Herbold C, Indra A, Walochnik J, Horn M. The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes. WATER RESEARCH 2019; 159:464-479. [PMID: 31128471 PMCID: PMC6554697 DOI: 10.1016/j.watres.2019.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 05/30/2023]
Abstract
Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.
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Affiliation(s)
- Han-Fei Tsao
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Ute Scheikl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander Indra
- Department of Mycobacteriology and Clinical Molecular Biology, AGES, Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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12
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Gonzalez E, Pitre FE, Brereton NJB. ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. Environ Microbiol 2019; 21:2440-2468. [PMID: 30990927 PMCID: PMC6851558 DOI: 10.1111/1462-2920.14632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 01/04/2023]
Abstract
Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.
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Affiliation(s)
- Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.,Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
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13
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Albert RA, McGuine M, Pavlons SC, Roecker J, Bruess J, Mossman S, Sun S, King M, Hong S, Farrance CE, Danner J, Joung Y, Shapiro N, Whitman WB, Busse HJ. Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2019; 69:1376-1383. [PMID: 30882299 DOI: 10.1099/ijsem.0.003319] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367T, Bosea lathyri LMG 26379T, Bosea lupini LMG 26383T, Bosea eneae CCUG 43111T, Bosea vestrisii CCUG 43114T and Boseamassiliensis CCUG 43117T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131T and Bosea vaviloviae Vaf-18T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5-35 °C, pH values of pH 5.5-8.0, a salt tolerance range of 0.0-1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131T (NRRL B-65405=LMG 30034).
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Affiliation(s)
- Richard A Albert
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA.,2Water Quality Center, Marquette University, Civil and Environmental Engineering, P.O. Box 1881 Milwaukee, WI, USA
| | - Molly McGuine
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C Pavlons
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jon Roecker
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jennifer Bruess
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shane Mossman
- 1Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Sona Sun
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Mike King
- 3Microbial Discovery Group, Franklin, WI, USA
| | - Sunhee Hong
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | | | - Joseph Danner
- 4Charles River Laboratories, Microbial Solutions, Newark, DE, USA
| | - Yochan Joung
- 5Department of Biological Sciences, College of Natural Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Nicole Shapiro
- 6DOE Joint Genomics Institute, Walnut Creek, CA 94598, USA
| | - William B Whitman
- 7Microbiology Department, Univeristy of Georgia, Athens, GA 30602, USA
| | - Hans-Jürgen Busse
- 8Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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14
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Batrich M, Maskeri L, Schubert R, Ho B, Kohout M, Abdeljaber M, Abuhasna A, Kholoki M, Psihogios P, Razzaq T, Sawhney S, Siddiqui S, Xoubi E, Cooper A, Hatzopoulos T, Putonti C. Pseudomonas Diversity Within Urban Freshwaters. Front Microbiol 2019; 10:195. [PMID: 30828321 PMCID: PMC6384249 DOI: 10.3389/fmicb.2019.00195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/23/2019] [Indexed: 11/23/2022] Open
Abstract
Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.
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Affiliation(s)
- Mary Batrich
- Niehoff School of Nursing, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Ryan Schubert
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Brian Ho
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Melanie Kohout
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Malik Abdeljaber
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Ahmed Abuhasna
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Mutah Kholoki
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Penelope Psihogios
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Tahir Razzaq
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Samrita Sawhney
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Salah Siddiqui
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Eyad Xoubi
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Alexandria Cooper
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thomas Hatzopoulos
- Department of Computer Science, Loyola University Chicago, Chicago, IL, United States
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States.,Department of Computer Science, Loyola University Chicago, Chicago, IL, United States.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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15
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Guo XP, Lu DP, Niu ZS, Feng JN, Chen YR, Tou FY, Liu M, Yang Y. Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. MARINE POLLUTION BULLETIN 2018; 126:141-149. [PMID: 29421081 DOI: 10.1016/j.marpolbul.2017.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 06/08/2023]
Abstract
This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO42- and total organic carbon, while bacterial diversity was significantly correlated with SO42- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO42-, salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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16
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Guo XP, Niu ZS, Lu DP, Feng JN, Chen YR, Tou FY, Liu M, Yang Y. Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China. MARINE POLLUTION BULLETIN 2017; 124:314-320. [PMID: 28755810 DOI: 10.1016/j.marpolbul.2017.07.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
In this study, the 16S rRNA-based Illumina MiSeq sequencing was used to investigate the bacterial community structure and composition of intertidal biofilm taken along the Yangtze Estuary. The results showed that 680,721 valid sequences of seven samples were assigned to 147,239 operational taxonomic units, which belonged to 49 phyla, 246 family and 314 genera. Compared to other studies on water and sediments in the study area, biofilms showed highest index of bacterial diversity and abundances. At different taxonomic levels, both dominant taxa and their abundances varied among the seven samples, with Proteobacteria as the dominant phylum in general. Principal component analysis and cluster analysis revealed that bacterial communities at WSK differed from those at other sampling sites. Salinity, dissolved oxygen, pH and nutrients were the vital environmental factors to influence the bacterial community structure of biofilms. These results may provide a new insight into the microbial ecology in estuarine environments.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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17
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Frindte K, Allgaier M, Grossart HP, Eckert W. Redox stability regulates community structure of active microbes at the sediment-water interface. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:798-804. [PMID: 27402503 DOI: 10.1111/1758-2229.12441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/02/2015] [Indexed: 06/06/2023]
Abstract
Changes in redox conditions occur in a wide range of microbial habitats, in particular at the sediment-water interface (SWI) of aquatic systems. A mesocosm study using intact sediment cores from Lake Stechlin (Germany) was performed to investigate the impact of redox changes on microbial communities at the SWI. The SWI was exposed to permanent oxic (OX) or anoxic (ANOX) or to variable (VR) redox conditions, and for molecular analysis sediment samples were taken at the start and after seven days of the treatment. We performed 16S rRNA amplicon sequencing to identify redox-specific changes in the composition of metabolically active microbes. Generally, the community of active microbes in the VR cores was similar to in the OX cores, but differed significantly from the ANOX cores. Interestingly, VR conditions resulted in a high fraction of a Crenothrix-like microorganism increasing in read abundance from 4 to 5% initially, up to 69% over the experimental period. This implies that periodic redox fluctuations select for specific bacteria in environments such as seiches-affected sediments of stratified lakes. In Lake Stechlin sediment cores, these redox fluctuations lead to increased activities of specific microorganisms and high organic matter turnover rates with profound implications for aquatic organic matter cycling.
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Affiliation(s)
- Katharina Frindte
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, Bonn University, Nussallee 13, Bonn, 53115, Germany
| | - Martin Allgaier
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, Berlin, 14195, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, Stechlin, 16775, Germany
- Institute of Biochemistry and Biology, Potsdam University, Am Neuen Palais 10, Potsdam, 14469, Germany
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
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18
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Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rosselló-Mora R, Busse HJ. Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas. Int J Syst Evol Microbiol 2016; 66:4027-4032. [DOI: 10.1099/ijsem.0.001305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Richard A. Albert
- Water Quality Center, Marquette University, Civil & Environmental Engineering, P.O. Box 1881, Milwaukee, WI, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nancy E. Waas
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C. Pavlons
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jamie L. Pearson
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jon Roecker
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nikklas Tewalt
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Natalie Cleeve
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Ramon Rosselló-Mora
- Grup de Microbiologia Marina, Institut Mediterrani d'Estudis Avançats, E-07190 Esporles, Mallorca, Spain
| | - Hans-Jürgen Busse
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Hungary
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19
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Hoostal MJ, Bouzat JL. Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants. MICROBIAL ECOLOGY 2016; 72:559-570. [PMID: 27430632 DOI: 10.1007/s00248-016-0812-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Biphenyl dioxygenases, encoded by the bphA gene, initiate the oxidation of polychlorinated biphenyls (PCBs) and specify the substrate range of PCB congeners metabolized by bacteria. Increased bphA gene diversity within microbial communities may allow a broader range of PCB congeners to be catabolized, thus resulting in greater PCB degradation. To assess the role of PCBs in modulating bphA gene diversity, 16S ribosomal RNA (rRNA) gene and bphA environmental DNA libraries were generated from bacterial communities in sediments with a steep gradient of PCB contamination. Multiple measures of sequence diversity revealed greater heterogeneity of bphA sequences in polluted compared to unpolluted locations. Codon-based signatures of selection in bphA sequences provided evidence of purifying selection. Unifrac analysis of 16S rRNA sequences revealed independent taxonomic lineages from polluted and unpolluted locations, consistent with the presence of locally adapted bacterial communities. Phylogenetic analysis of bphA sequences indicated that dioxygenases from sediments were closely related to previously characterized dioxygenases that metabolize PCBs and polynuclear aromatic hydrocarbons (PAHs), consistent with high levels of these contaminants within the studied sediments. Structural analyses indicated that the BphA protein of Rhodococcus jostii, capable of metabolizing both PCBs and PAHs, provided a more optimal modeling template for bphA sequences reported in this study than a BphA homologue with more restricted substrate specificity. Results from this study suggest that PCBs and PAHs may drive local adaptation of microbial communities by acting as strong selective agents for biphenyl dioxygenases capable of metabolizing a wide range of congeners.
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Affiliation(s)
- Matthew J Hoostal
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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20
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Kurilkina MI, Zakharova YR, Galachyants YP, Petrova DP, Bukin YS, Domysheva VM, Blinov VV, Likhoshway YV. Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing. FEMS Microbiol Ecol 2016; 92:fiw094. [PMID: 27162182 DOI: 10.1093/femsec/fiw094] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 01/01/2023] Open
Abstract
The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal.
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Affiliation(s)
- Maria I Kurilkina
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Valentina M Domysheva
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
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21
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Pavloudi C, Oulas A, Vasileiadou K, Sarropoulou E, Kotoulas G, Arvanitidis C. Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea). Mar Genomics 2016; 28:71-81. [PMID: 26831186 DOI: 10.1016/j.margen.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 11/27/2022]
Abstract
Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities.
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Affiliation(s)
- Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece; Biology Department, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece; Department of Microbial Ecophysiology, Faculty of Biology, University of Bremen, 28359, Bremen, Germany; Department of Biology, Faculty of Sciences, University of Ghent, 9000 Ghent, Belgium.
| | - Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Katerina Vasileiadou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
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22
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Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AKT, Farnleitner AH, Eiler A. Bacterial diversity along a 2600 km river continuum. Environ Microbiol 2015; 17:4994-5007. [PMID: 25922985 PMCID: PMC4918796 DOI: 10.1111/1462-2920.12886] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 04/21/2015] [Indexed: 11/26/2022]
Abstract
The bacterioplankton diversity in large rivers has thus far been under‐sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA‐gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free‐living and particle‐associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater‐affiliated bacteria. Based on views of the meta‐community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.
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Affiliation(s)
- Domenico Savio
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Research Group Environmental Microbiology and Molecular Ecology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Lucas Sinclair
- Department of Ecology and Genetics, Limnology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK
| | - Juraj Parajka
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Institute of Hydraulic Engineering and Water Resource Management, Vienna University of Technology, Vienna, Austria
| | - Georg H Reischer
- Research Group Environmental Microbiology and Molecular Ecology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.,Interuniversity Cooperation Centre Water and Health, www.waterandhealth.at, Medical University of Vienna, Vienna, Austria
| | - Philipp Stadler
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Institute for Water Quality, Resource and Waste Management, Vienna University of Technology, Vienna, Austria
| | - Alfred P Blaschke
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Institute of Hydraulic Engineering and Water Resource Management, Vienna University of Technology, Vienna, Austria
| | - Günter Blöschl
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Institute of Hydraulic Engineering and Water Resource Management, Vienna University of Technology, Vienna, Austria
| | - Robert L Mach
- Research Group Environmental Microbiology and Molecular Ecology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Alexander K T Kirschner
- Interuniversity Cooperation Centre Water and Health, www.waterandhealth.at, Medical University of Vienna, Vienna, Austria.,Institute for Hygiene and Applied Immunology, Water Hygiene, Medical University of Vienna, Vienna, Austria
| | - Andreas H Farnleitner
- Centre for Water Resource Systems (CWRS), Vienna University of Technology, Vienna, Austria.,Research Group Environmental Microbiology and Molecular Ecology, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.,Interuniversity Cooperation Centre Water and Health, www.waterandhealth.at, Medical University of Vienna, Vienna, Austria
| | - Alexander Eiler
- Department of Ecology and Genetics, Limnology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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23
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Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 505:435-45. [PMID: 25461045 DOI: 10.1016/j.scitotenv.2014.10.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/01/2014] [Accepted: 10/04/2014] [Indexed: 05/20/2023]
Abstract
Bacterial community structure (BCS) in freshwater ecosystems varies seasonally and due to physicochemical gradients, but metacommunity structure of a major river remains understudied. Here we characterize the BCS along the Mississippi River and contributing rivers in Minnesota over three years using Illumina next-generation sequencing, to determine how changes in environmental conditions as well as inputs from surrounding land and confluences impacted community structure. Contributions of sediment to water microbial diversity were also evaluated. Long-term variation in community membership was observed, and significant shifts in relative abundances of major freshwater taxa, including α-Proteobacteria, Burkholderiales, and Actinomycetales, were observed due to temporal and spatial variations. Environmental parameters (e.g. temperature, rainfall, and nutrient concentrations) primarily contributed to differences in phyla abundances (88% of variance), with minimal influence from spatial distance alone (<1% of variance). Furthermore, an annually-recurrent BCS was observed in late summer, further suggesting that seasonal dynamics strongly influence community composition. Sediment communities differed from those in the water, but contributed up to 50% to community composition in the water column. Among water sampling sites, 34% showed significant variability in BCS of replicate samples indicating variability among riverine communities due to heterogeneity in the water column. Results of this study highlight the need for a better understanding of spatial and temporal variations in riverine bacterial diversity associated with physicochemical gradients and reveal how communities in sediments, and potentially other environmental reservoirs, impact waterborne BCS. Techniques used in this study may prove useful to determine sources of microbes from sediments and soils to waterways, which will facilitate best management practices and total maximum daily load determinations.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Trevor J Gould
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States; Biology Program, University of Minnesota, St. Paul, MN, United States
| | - Ping Wang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Jane Phillips
- Biology Program, University of Minnesota, St. Paul, MN, United States
| | - James B Cotner
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States; Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN, United States.
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24
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Fisher JC, Newton RJ, Dila DK, McLellan SL. Urban microbial ecology of a freshwater estuary of Lake Michigan. ELEMENTA (WASHINGTON, D.C.) 2015; 3:000064. [PMID: 26866046 PMCID: PMC4746012 DOI: 10.12952/journal.elementa.000064] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.
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Affiliation(s)
- Jenny C. Fisher
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Deborah K. Dila
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
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25
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Garcia JC, Ketover RDJ, Loh AN, Parsons ML, Urakawa H. Influence of freshwater discharge on the microbial degradation processes of dissolved organic nitrogen in a subtropical estuary. Antonie van Leeuwenhoek 2014; 107:613-32. [DOI: 10.1007/s10482-014-0357-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
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26
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Albert RA, Zitomer D, Dollhopf M, Schauer-Gimenez AE, Struble C, King M, Son S, Langer S, Busse HJ. Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water. Int J Syst Evol Microbiol 2014; 64:613-620. [PMID: 24170777 DOI: 10.1099/ijs.0.056663-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic bacterium appearing as curved rod-shaped cells was isolated from Lake Michigan water. It exhibited highest similarities with
Sediminibacterium ginsengisoli
DCY13T (94.4 %);
Sediminibacterium salmoneum
NJ-44T (93.6 %) and
Hydrotalea flava
CCUG 51397 T (93.1 %) while similarities with other recognized species were <92.0 %. The primary polar lipid was phosphatidylethanolamine, with moderate amounts of two unidentified glycolipids, three unknown polar lipids, one unknown aminophospholipid and one aminolipid. The primary respiratory quinone was MK-7 and sym-homospermidine was the primary polyamine. The major cellular fatty acids were iso-C15 : 1G, iso-C15 : 0, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, with moderate amounts of iso-C16 : 0. The presence of glycolipids differentiated the novel strains from related genera. The DNA mol% G+C content of the type strain MU-2T was 45.2. Results for other phenotypic and molecular analyses indicated that strain MU-2T is a representative of a novel genus and species for which the name Vibrionimonas magnilacihabitans is proposed. The type strain is MU-2T ( = NRRL B-59231 = DSM 22423).
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Affiliation(s)
- Richard A. Albert
- Water Quality Center 1515 West Wisconsin Avenue, Marquette University Milwaukee, WI, 53233 USA
| | - Daniel Zitomer
- Water Quality Center 1515 West Wisconsin Avenue, Marquette University Milwaukee, WI, 53233 USA
| | - Michael Dollhopf
- Water Quality Center 1515 West Wisconsin Avenue, Marquette University Milwaukee, WI, 53233 USA
| | - A. E. Schauer-Gimenez
- Water Quality Center 1515 West Wisconsin Avenue, Marquette University Milwaukee, WI, 53233 USA
| | - Craig Struble
- Department of Mathematics, Statistics and Computer Science, P.O. Box 1881, Marquette University, Milwaukee, WI 53201, USA
| | - Michael King
- Microbial Discovery Group 5200 West Ashland Way Franklin, WI, USA
| | - Sona Son
- Microbial Discovery Group 5200 West Ashland Way Franklin, WI, USA
| | - Stefan Langer
- Institute of Bacteriology, Mycology and Hygiene University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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27
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Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia. World J Microbiol Biotechnol 2013; 30:757-66. [DOI: 10.1007/s11274-013-1506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/21/2013] [Indexed: 01/13/2023]
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28
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Staley C, Unno T, Gould TJ, Jarvis B, Phillips J, Cotner JB, Sadowsky MJ. Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol 2013; 115:1147-58. [PMID: 23924231 DOI: 10.1111/jam.12323] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 11/29/2022]
Abstract
AIMS A next-generation, Illumina-based sequencing approach was used to characterize the bacterial community at ten sites along the Upper Mississippi River to evaluate shifts in the community potentially resulting from upstream inputs and land use changes. Furthermore, methodological parameters including filter size, sample volume and sample reproducibility were evaluated to determine the best sampling practices for community characterization. METHODS AND RESULTS Community structure and diversity in the river was determined using Illumina next-generation sequencing technology and the V6 hypervariable region of 16S rDNA. A total of 16,400 operational taxonomic units (OTUs) were observed (4594 ± 824 OTUs per sample). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia accounted for 93.6 ± 1.3% of all sequence reads, and 90.5 ± 2.5% belonged to OTUs shared among all sites (n = 552). Among nonshared sequence reads at each site, 33-49% were associated with potentially anthropogenic impacts upstream of the second sampling site. Alpha diversity decreased with distance from the pristine headwaters, while rainfall and pH were positively correlated with diversity. Replication and smaller filter pore sizes minimally influenced the characterization of community structure. CONCLUSIONS Shifts in community structure are related to changes in the relative abundance, rather than presence/absence of OTUs, suggesting a 'core bacterial community' is present throughout the Upper Mississippi River. SIGNIFICANCE AND IMPACT OF THE STUDY This study is among the first to characterize a large riverine bacterial community using a next-generation-sequencing approach and demonstrates that upstream influences and potentially anthropogenic impacts can influence the presence and relative abundance of OTUs downstream resulting in significant variation in community structure.
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Affiliation(s)
- C Staley
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
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29
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Du J, Xiao K, Li L, Ding X, Liu H, Lu Y, Zhou S. Temporal and spatial diversity of bacterial communities in coastal waters of the South china sea. PLoS One 2013; 8:e66968. [PMID: 23785512 PMCID: PMC3681761 DOI: 10.1371/journal.pone.0066968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/14/2013] [Indexed: 01/09/2023] Open
Abstract
Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns.
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Affiliation(s)
- Jikun Du
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Kai Xiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Pharmacology, Guangdong Medical College, Dongguan, China
- * E-mail: (LL); (SZ)
| | - Xian Ding
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Helu Liu
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Yongjun Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shining Zhou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (LL); (SZ)
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30
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Newton RJ, Bootsma MJ, Morrison HG, Sogin ML, McLellan SL. A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan. MICROBIAL ECOLOGY 2013; 65:1011-23. [PMID: 23475306 PMCID: PMC4084971 DOI: 10.1007/s00248-013-0200-9] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/13/2013] [Indexed: 05/04/2023]
Abstract
Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥ 97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee's urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to > 2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint in this ecosystem extends to at least 8 km offshore.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
| | - Melinda J. Bootsma
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mitchell L. Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sandra L. McLellan
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
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31
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Kasalický V, Jezbera J, Hahn MW, Šimek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One 2013; 8:e58209. [PMID: 23505469 PMCID: PMC3591437 DOI: 10.1371/journal.pone.0058209] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/30/2013] [Indexed: 01/30/2023] Open
Abstract
Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.
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Affiliation(s)
- Vojtěch Kasalický
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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32
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Albert RA, Waas NE, Pavlons SC, Pearson JL, Ketelboeter L, Rosselló-Móra R, Busse HJ. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2013; 63:952-958. [DOI: 10.1099/ijs.0.043844-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
A psychrophilic, Gram-negative bacterium, designated MOL-1T, was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1T has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of
Sphingobacterium shayense
HS39T,
S. lactis
WCC 4512T,
S. composti
T5-12T,
S. daejeonense
TR6-04T,
S. bambusae
IBFC2009T and
S. alimentarium
WCC 4521T. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1T represents a novel
Sphingobacterium
species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1T ( = NRRL B-59232T = DSM 22418T).
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Affiliation(s)
- Richard A. Albert
- Water Quality Center, Marquette University, Civil & Environmental Engineering, PO Box 1881 Milwaukee, WI 53233, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nancy E. Waas
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C. Pavlons
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jamie L. Pearson
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Laura Ketelboeter
- Department of Biological Sciences, UW-Milwaukee, Milwaukee, WI 53201, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Ramon Rosselló-Móra
- Grup de Microbiologia Marina, Institut Mediterrani d’Estudis Avançats, Mallorca, E-07190 Esporles, Spain
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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33
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Li SG, Zhou XW, Li PF, Han K, Li W, Li ZF, Wu ZH, Li YZ. The existence and diversity of myxobacteria in lake mud - a previously unexplored myxobacteria habitat. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:587-595. [PMID: 23760929 DOI: 10.1111/j.1758-2229.2012.00373.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/22/2012] [Indexed: 06/02/2023]
Abstract
Myxobacteria are widely distributed in soil and oceanic sediment with a phylogeographic separation at high levels of classification. However, it is unclear whether freshwater environments, from which there has been no isolation report of myxobacteria since 1981, are habitats for myxobacteria. In this study, we investigated the presence of myxobacteria in lake mud using a two-step strategy. First, we constructed two universal bacterial libraries from the V3-V4 (V34) and V6-V8 (V678) hypervariable regions of 16S rRNA gene sequences. High-throughput 454 pyrosequencing revealed that myxobacteria were one of the major bacterial groups in the lake mud. They accounted for 5.77% of the total sequences and 7.52% of the total operational taxonomic units (OTUs) at a phylogenetic distance of 0.03. The community composition and taxonomic structure of the mud myxobacterial community were further analysed using myxobacteria-enriched libraries targeting the V34 and V678 regions, which were amplified with Cystobacterineae- and Sorangineae-specific primer pairs respectively. Phylogenetic analysis showed that the limnetic myxobacteria exhibited closer relationships to their soil than their marine relatives, but there were also exclusive taxa of limnetic myxobacteria detected. These results, together with a survey on available GenBank data, indicate that lake mud is a primary habitat for myxobacteria.
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Affiliation(s)
- Shu-Guang Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
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34
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Brown BP, Brown SR, Senko JM. Microbial communities associated with wet flue gas desulfurization systems. Front Microbiol 2012; 3:412. [PMID: 23226147 PMCID: PMC3510643 DOI: 10.3389/fmicb.2012.00412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/14/2012] [Indexed: 02/01/2023] Open
Abstract
Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.
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Affiliation(s)
- Bryan P Brown
- Department of Biology, The University of Akron, Akron OH, USA
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Edberg F, Andersson AF, Holmström SJM. Bacterial community composition in the water column of a lake formed by a former uranium open pit mine. MICROBIAL ECOLOGY 2012; 64:870-880. [PMID: 22622763 DOI: 10.1007/s00248-012-0069-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 04/27/2012] [Indexed: 06/01/2023]
Abstract
Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.
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Affiliation(s)
- Frida Edberg
- Department of Applied Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
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Liu J, Yu J, Li D, Zhang Y, Yang M. Reduction of bromate in a biological activated carbon filter under high bulk dissolved oxygen conditions and characterization of bromate-reducing isolates. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Llorens-Marès T, Auguet JC, Casamayor EO. Winter to spring changes in the slush bacterial community composition of a high-mountain lake (Lake Redon, Pyrenees). ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:50-56. [PMID: 23757229 DOI: 10.1111/j.1758-2229.2011.00278.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial community composition was analysed in the slush layers of snow-covered Lake Redon (2240 m altitude, Limnological Observatory of the Pyrenees, LOOP, NE Spain) in winter and spring and compared with bacteria from the lake water column, using 16S rRNA gene clone libraries and CARD-FISH counts. The set of biological data was related to changes in bacterial production and to other relevant environmental variables measured in situ. In winter, up to 70% of the 16S rRNA sequences found in the slush were closely related to planktonic bacteria from the water column beneath the ice. Conversely, during spring ablation, 50% of the sequences had > 97% identity with bacteria from the cryosphere (i.e. globally distributed glaciers, snow and ice) and may have originated from remote aerosol deposition. The transition winter to spring was characterized by consistent community changes switching from assemblages dominated by Betaproteobacteria, Verrucomicrobia and Bacteroidetes during snowpack growth to communities essentially dominated by the Bacteroidetes of classes Cytophagia and Sphingobacteria. This strong bacterial composition switch was associated with consistent increases in bacterial abundance and production, and decreasing bacterial diversity.
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Affiliation(s)
- Tomàs Llorens-Marès
- Limnological Observatory of the Pyrenees (LOOP) - Biogeodynamics & Biodiversity Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
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Drudge CN, Warren LA. Prokaryotic Horizontal Gene Transfer in Freshwater Lakes: Implications of Dynamic Biogeochemical Zonation. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jep.2012.312181] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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de Figueiredo DR, Ferreira RV, Cerqueira M, de Melo TC, Pereira MJ, Castro BB, Correia A. Impact of water quality on bacterioplankton assemblage along Cértima River Basin (central western Portugal) assessed by PCR-DGGE and multivariate analysis. ENVIRONMENTAL MONITORING AND ASSESSMENT 2012; 184:471-485. [PMID: 21431313 DOI: 10.1007/s10661-011-1981-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 02/24/2011] [Indexed: 05/30/2023]
Abstract
The information on bacterial community composition (BCC) in Portuguese water bodies is very scarce. Cértima River (central western Portugal) is known to have high levels of pollution, namely organic. In the present work, the BCC from a set of 16 water samples collected from Cértima River Basin and its main tributaries was characterized using 16S rDNA-denaturing gradient gel electrophoresis, a culture-independent molecular approach. Molecular data were related to environmental parameters through multivariate analysis to investigate potential impact of water pollution along the river. Principal component analysis using environmental data showed a water quality gradient from more pristine waters (at the mountain tributaries) to waters with increasingly eutrophic potential (such as Fermentelos Lake). This gradient was mainly defined by factors such as organic and inorganic nutrient sources, electrical conductivity, hydrogen carbonate concentration, and pH. Molecular results showed variations in BCC along Cértima River Basin but in the main river section, a Bacteroidetes phylotype (Flavobacterium sp.) proved to be dominant throughout the river course. Multivariate analysis suggests that spatial variation of BCC along the Cértima River Basin depended mainly on parameters such as Chl a, total suspended solid (TSS), total organic carbon, electrical conductivity, and HCO[Formula: see text] levels. Bacteroidetes phylotypes were all related to higher electrical conductivity and HCO[Formula: see text] levels although some of these were also correlated with high SO[Formula: see text] and others with high soluble reactive phosphorus, nitrate, TN, and Kjeld-N levels. The Gammaproteobacteria occurrence was correlated with high SO[Formula: see text] levels. One of the Betaproteobacteria phylotypes showed to correlate with low redox potential (E(h)) and high temperature, pH, TSS, and Chl a levels while another one showed a negative correlation with Chl a values.
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Affiliation(s)
- Daniela R de Figueiredo
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal.
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Hu Y, Li Y, Wang L, Tang Y, Chen J, Fu X, Le Y, Wu J. Variability of soil organic carbon reservation capability between coastal salt marsh and riverside freshwater wetland in Chongming Dongtan and its microbial mechanism. J Environ Sci (China) 2012; 24:1053-1063. [PMID: 23505873 DOI: 10.1016/s1001-0742(11)60877-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Two representative zones in Chongming Dongtan which faced the Yangtze River and East China Sea respectively were selected to study the variability of soil organic carbon (SOC) reservation capability between coastal wetland and riverside wetland in the Chongming Dongtan wetland as well as its mechanism by analyzing soil characteristics and plant biomass. The results showed the SOC content of riverside wetland was only 48.61% (P = 0.000 < 0.05) that of coastal wetland. As the organic matter inputs from plant litter of the coastal wetland and riverside wetland were approximately the same, the higher soil microbial respiration (SMR) of riverside wetland led to its lower SOC reservation capability. In the riverside wetland, the high soil microbial biomass, higher proportion of beta-Proteobacteria, which have strong carbon metabolism activity and the existence of some specific aerobic heterotrophic bacteria such as Bacilli and uncultured Lactococcus, were the important reasons for the higher SMR compared to the coastal wetland. There were additional differences in soil physical and chemical characteristics between the coastal wetland and riverside wetlands. Path analysis of predominant bacteria and microbial biomass showed that soil salinity influenced beta-Proteobacteria and microbial biomass most negatively among these physical and chemical factors. Therefore the low salinity of the riverside area was suitable for the growth of microorganisms, especially beta-Proteobacteria and some specific bacteria, which led to the high SMR and low SOC reservation capability when compared to the coastal area.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Graças DA, Miranda PR, Baraúna RA, McCulloch JA, Ghilardi R, Schneider MPC, Silva A. Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia. MICROBIAL ECOLOGY 2011; 62:853-861. [PMID: 21755290 DOI: 10.1007/s00248-011-9906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/10/2011] [Indexed: 05/31/2023]
Abstract
Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.
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Affiliation(s)
- Diego A Graças
- Universidade Federal do Pará. Instituto de Ciências Biológicas, 66075-900 Belém, Pará, Brazil
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Co-habiting amphibian species harbor unique skin bacterial communities in wild populations. ISME JOURNAL 2011; 6:588-96. [PMID: 21955991 PMCID: PMC3280140 DOI: 10.1038/ismej.2011.129] [Citation(s) in RCA: 195] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.
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Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Appl Environ Microbiol 2011; 77:6972-81. [PMID: 21803887 DOI: 10.1128/aem.05480-11] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within the Lachnospiraceae family, which was closely related to the genus Blautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for human Bacteroidales (based on the HF183 genetic marker), total Bacteroidales spp., and enterococci and the conventional Escherichia coli and enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and human Bacteroidales increased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.
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Wu L, Ge G, Zhu G, Gong S, Li S, Wan J. Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis. World J Microbiol Biotechnol 2011; 28:233-44. [PMID: 22806799 DOI: 10.1007/s11274-011-0812-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 06/01/2011] [Indexed: 11/26/2022]
Abstract
Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated by partially sequencing cloned 16SrRNA genes. Moreover, restriction fragment length polymorphism (RFLP) was applied in the 16SrRNA gene clones. In total, four clone libraries were constructed and 347 clones were screened by RFLP, yielding 153 operational taxonomic units, which mainly belonged to the proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Planctomycetes. Our results showed that Beta-proteobacteria was the most significant lineage, with dominant numbers of operational taxonomic units in the northern October 2006, southern October 2006 and May 2007 libraries. The highest bacterial diversity occurred in the library from the southern sub-basin in May 2007 and the lowest in the library from the northern sub-basin in May 2007. Horizontal and temporal differences associated with the concentration of total phosphorus, water temperature and pH suggested that the trophic state and the physicochemical properties of lake play key roles in sustaining bacterial community composition structure.
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Affiliation(s)
- Lan Wu
- The Key Laboratory of Molecular Biology and Gene Engineering, Nanchang University, No. 999, Xuefu da Road, Hongutang New District, Nanchang, 330031, People's Republic of China
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Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 2011; 75:14-49. [PMID: 21372319 PMCID: PMC3063352 DOI: 10.1128/mmbr.00028-10] [Citation(s) in RCA: 844] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stuart E. Jones
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Alexander Eiler
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Katherine D. McMahon
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stefan Bertilsson
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
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Haller L, Tonolla M, Zopfi J, Peduzzi R, Wildi W, Poté J. Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). WATER RESEARCH 2011; 45:1213-1228. [PMID: 21145090 DOI: 10.1016/j.watres.2010.11.018] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/08/2010] [Accepted: 11/14/2010] [Indexed: 05/27/2023]
Abstract
The aim of this study was to compare the composition of bacterial and archaeal communities in contaminated sediments (Vidy Bay) with uncontaminated sediments (Ouchy area) of Lake Geneva using 16S rRNA clone libraries. Sediments of both sites were analysed for physicochemical characteristics including porewater composition, organic carbon, and heavy metals. Results show high concentrations of contaminants in sediments from Vidy. Particularly, high contents of fresh organic matter and nutrients led to intense mineralisation, which was dominated by sulphate-reduction and methanogenesis. The bacterial diversity in Vidy sediments was significantly different from the communities in the uncontaminated sediments. Phylogenetic analysis revealed a large proportion of Betaproteobacteria clones in Vidy sediments related to Dechloromonas sp., a group of dechlorinating and contaminant degrading bacteria. Deltaproteobacteria, including clones related to sulphate-reducing bacteria and Fe(III)-reducing bacteria (Geobacter sp.) were also more abundant in the contaminated sediments. The archaeal communities consisted essentially of methanogenic Euryarchaeota, mainly found in the contaminated sediments rich in organic matter. Multiple factor analysis revealed that the microbial community composition and the environmental variables were correlated at the two sites, which suggests that in addition to environmental parameters, pollution may be one of the factors affecting microbial community structure.
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Affiliation(s)
- Laurence Haller
- University of Geneva, Institute F.A. Forel, 10 route de Suisse, CP 416, CH-1290 Versoix, Switzerland
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Waddell EJ, Elliott TJ, Sani RK, Vahrenkamp JM, Roggenthen WM, Anderson CM, Bang SS. Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota. ENVIRONMENTAL TECHNOLOGY 2010; 31:979-991. [PMID: 20662386 PMCID: PMC3565620 DOI: 10.1080/09593331003789511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota, typically identified from marine environments, and one OTU belonging to a potentially novel phylum that fell sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and were grouped most closely to an ammonia-oxidizing, carbon-fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that have often been identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulphur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community, with unique phylotypes identified within each sample.
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Affiliation(s)
- Evan J. Waddell
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | - Terran J. Elliott
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | | | - William M. Roggenthen
- Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | | | - Sookie S. Bang
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
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Nold SC, Pangborn JB, Zajack HA, Kendall ST, Rediske RR, Biddanda BA. Benthic bacterial diversity in submerged sinkhole ecosystems. Appl Environ Microbiol 2010; 76:347-51. [PMID: 19880643 PMCID: PMC2798655 DOI: 10.1128/aem.01186-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 10/19/2009] [Indexed: 11/20/2022] Open
Abstract
Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities.
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Affiliation(s)
- Stephen C Nold
- University of Wisconsin-Stout, 410 10th Avenue East, Menomonie, WI 54751, USA.
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Broad habitat range of the phylogenetically narrow R-BT065 cluster, representing a core group of the Betaproteobacterial genus Limnohabitans. Appl Environ Microbiol 2009; 76:631-9. [PMID: 19948856 DOI: 10.1128/aem.02203-09] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution of the phylogenetically narrow R-BT065 cluster (Betaproteobacteria) in 102 freshwater lakes, reservoirs, and various ponds located in central Europe (a total of 122 samples) was examined by using a cluster-specific fluorescence in situ hybridization probe. These habitats differ markedly in pH, conductivity, trophic status, surface area, altitude, bedrock type, and other limnological characteristics. Despite the broad ecological diversity of the habitats investigated, the cluster was detected in 96.7% of the systems, and its occurrence was not restricted to a certain habitat type. However, the relative proportions of the cluster in the total bacterioplankton were significantly lower in humic and acidified lakes than in pH-neutral or alkaline habitats. On average, the cluster accounted for 9.4% of the total bacterioplankton (range, 0 to 29%). The relative abundance and absolute abundance of these bacteria were significantly and positively related to higher pH, conductivity, and the proportion of low-molecular-weight compounds in dissolved organic carbon (DOC) and negatively related to the total DOC and dissolved aromatic carbon contents. Together, these parameters explained 55.3% of the variability in the occurrence of the cluster. Surprisingly, no clear relationship of the R-BT065 bacteria to factors indicating the trophic status of habitats (i.e., different forms of phosphorus and chlorophyll a content) was found. Based on our results and previously published data, we concluded that the R-BT065 cluster represents a ubiquitous, highly active segment of bacterioplankton in nonacidic lakes and ponds and that alga-derived substrates likely form the main pool of substrates responsible for its high growth potential and broad distribution in freshwater habitats.
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McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 2009; 12:378-92. [PMID: 19840106 DOI: 10.1111/j.1462-2920.2009.02075.x] [Citation(s) in RCA: 259] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 pyrosequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTPs) in metropolitan Milwaukee. The sewage profiles included a discernible human faecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae genera. The faecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human faecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in faecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI--servicing residential plus a combined sewer system) and South Shore (SS--servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human faecal microbes and enrichment of specific microbes from the environment to form a unique population structure.
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Affiliation(s)
- S L McLellan
- Great Lakes Water Institute, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA.
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