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Martinez O, Bergen SR, Gareis JB. Comparison of Yamuna (India) and Mississippi River (United States of America) bacterial communities reveals greater diversity below the Yamunotri Glacier. PLoS One 2024; 19:e0304664. [PMID: 38968225 PMCID: PMC11226128 DOI: 10.1371/journal.pone.0304664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/15/2024] [Indexed: 07/07/2024] Open
Abstract
The Yamuna River in India and the Mississippi River in the United States hold significant commercial, cultural, and ecological importance. This preliminary survey compares the bacterial communities sampled in surface waters at 11 sites (Yamuna headwaters, Mississippi headwaters, Yamuna River Yamunotri Town, Mississippi River at Winona, Tons River, Yamuna River at Paonta Sahib, Yamuna River Delhi-1, Yamuna River Delhi-2, Yamuna River before Sangam, Sangam, Ganga River before Sangam). Bacterial 16S rDNA analyses demonstrate dominance of Proteobacteria and Bacteroidetes phyla. Actinobacteria were also dominant at sites near Sangam in India and sites in Minnesota. A dominance of Epsilonbacteraeota were found in Delhi, India. Principal component analysis (PCA) using unique operational taxonomic units (OTUs) resulted in the identification of 3 groups that included the Yamuna River locations in Delhi (Delhi locations), Yamuna headwaters and Yamuna River at Yamunotri (Yamuna River locations below the Glacier) and Mississippi, Ganga, Tons, and other Yamuna River locations. Diversity indices were significantly higher at the Yamuna River locations below the Glacier (Simpson D = 0.986 and Shannon H = 5.06) as compared (p value <0.001) to the Delhi locations (D = 0.951 and H = 4.23) and as compared (p value < 0.001) to Mississippi, Ganga, Tons, and other Yamuna River locations (D = 0.943 and H = 3.96). To our knowledge, this is the first survey to compare Mississippi and Yamuna River bacterial communities. We demonstrate higher diversity in the bacterial communities below the Yamunotri glacier in India.
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Affiliation(s)
- Osvaldo Martinez
- Biology Department, Winona State University, Winona, MN, United States of America
| | - Silas R. Bergen
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
| | - Jacob B. Gareis
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
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Wang H, Yan B, Wu Y, Yin M, Wang M, Fu C. Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China. Front Microbiol 2023; 14:1218806. [PMID: 37799598 PMCID: PMC10547884 DOI: 10.3389/fmicb.2023.1218806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/07/2023] Open
Abstract
River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.
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Affiliation(s)
- Huan Wang
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
- Chongqing Landscape and Gardening Research Institute, Chongqing, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, China
| | - Bin Yan
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Yan Wu
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Maoyun Yin
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Maoqing Wang
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Chuan Fu
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
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3
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Čačković A, Kajan K, Selak L, Marković T, Brozičević A, Pjevac P, Orlić S. Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem. mSphere 2023:e0060222. [PMID: 37097185 DOI: 10.1128/msphere.00602-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.
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Affiliation(s)
- Andrea Čačković
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Lorena Selak
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Andrijana Brozičević
- Scientific Research Center "Dr. Ivo Pevalek," Plitvice Lakes National Park, Plitvička Jezera, Croatia
| | - Petra Pjevac
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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Zhang H, Xu H, Wang S, Qin M, Zhao D, Wu QL, Zeng J. Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160418. [PMID: 36435238 DOI: 10.1016/j.scitotenv.2022.160418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.
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Affiliation(s)
- Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
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Bourhane Z, Cagnon C, Castañeda C, Rodríguez-Ochoa R, Álvaro-Fuentes J, Cravo-Laureau C, Duran R. Vertical organization of microbial communities in Salineta hypersaline wetland, Spain. Front Microbiol 2023; 14:869907. [PMID: 36778872 PMCID: PMC9911865 DOI: 10.3389/fmicb.2023.869907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.
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Affiliation(s)
- Zeina Bourhane
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rafael Rodríguez-Ochoa
- Departamento de Medio Ambiente y Ciencias del Suelo, Universidad de Lleida, Lleida, Spain
| | | | | | - Robert Duran
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
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Panda A, Tuller T. Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis. NPJ Biofilms Microbiomes 2023; 9:5. [PMID: 36693851 PMCID: PMC9873608 DOI: 10.1038/s41522-023-00372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.
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Affiliation(s)
- Arup Panda
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, 69978, Israel.
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7
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Wang S, Jiao C, Zhao D, Zeng J, Xing P, Liu Y, Wu QL. Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157446. [PMID: 35863578 DOI: 10.1016/j.scitotenv.2022.157446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.
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Affiliation(s)
- Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, China.; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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8
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Du C, Li G, Xia R, Li C, Zhu Q, Li X, Li J, Zhao C, Tian Z, Zhang L. New insights into cyanobacterial blooms and the response of associated microbial communities in freshwater ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119781. [PMID: 35841988 DOI: 10.1016/j.envpol.2022.119781] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacterial blooms are important environmental problems in aquatic ecosystems. Researchers have found that cyanobacterial blooms cannot be completely prevented by controlling and/or eliminating pollutants (nutrients). Thus, more in-depth basic research on the mechanism of cyanobacterial blooms is urgently needed. Cyanobacteria, being primordial microorganisms, provide habitats and have various forms of interactions (reciprocity and competition) with microorganisms, thus having a significant impact on themselves. However, little is known about how environmental conditions and microbial communities in both water and sediment jointly affect cyanobacterial blooms or about the co-occurrence patterns and interactions of microbial communities. We investigated changes in environmental factors and microbial communities in water and sediment during different cyanobacterial blooms and revealed their interacting effects on cyanobacteria. Cyanobacteria had greater competitive and growth advantages than other microorganisms and had antagonistic and aggressive effects on them when resources (such as nutrients) were abundant. Furthermore, microbial networks from cyanobacterial degradation periods may be more complex and stable than those from bloom periods, with more positive links among the microbial networks, suggesting that microbial community structures strengthen interconnections with each other to degrade cyanobacteria. In addition, we found that sediment-enriched cyanobacteria play a key role in cyanobacterial blooms, and sediment microorganisms promote the nutrient release, further promoting cyanobacterial blooms in the water bodies. The study contributes to further our understanding of the mechanisms for cyanobacterial blooms and microbial community structural composition, co-occurrence patterns, and responses to cyanobacteria. These results can contribute to future management strategies for controlling cyanobacterial blooms in freshwater ecosystems.
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Affiliation(s)
- Caili Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Guowen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Rui Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Caole Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Qiuheng Zhu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Academy of Environmental Sciences, College of Water Sciences, Beijing Normal University, Beijing, 100012, China
| | - Xiaoguang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jiaxi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Chen Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zhenjun Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Academy of Environmental Sciences, College of Water Sciences, Beijing Normal University, Beijing, 100012, China
| | - Lieyu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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9
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Chen J, Wang P, Wang C, Wang X, Gao H, Cui G, Liu S, Yuan Q. How dam construction affects the activity of alkaline phosphatases in reservoir sediments: A study of two highly regulated rivers. ENVIRONMENTAL RESEARCH 2022; 207:112236. [PMID: 34678255 DOI: 10.1016/j.envres.2021.112236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Dam construction causes phosphorus (P) accumulation in reservoir sediments and significantly affects the generation of available P. However, the effect of dam construction on the activity of sediment alkaline phosphatase (ALP), which is encoded by the bacterial phoD gene and participates in P mineralization, in river sediments remains unclear. Here, we investigated the ALP activities in 78 sediment samples collected from the cascade reservoir regions located in the Lancang River and the Jinsha River, two highly regulated rivers in southwestern China. The abundance and community composition of phoD-harboring bacteria were determined based on the phoD gene using quantitative real-time PCR and MiSeq sequencing, respectively. Comparison of control and affected sites indicated that dam construction significantly increased sediment ALP activity in both rivers. The abundances of phoD-harboring bacteria increased and their community compositions varied in response to dam construction; the relative abundances of the dominant genera Methylobacterium and Bradyrhizobium were particularly higher in affected site than control site. Co-occurrence network analyses revealed much higher network connectivity and relative abundances of keystone species in affected sites. Some microbial factors including phoD-harboring bacterial abundances, network clustering coefficients, and relative abundance of keystone species were positively correlated with ALP activity. The relative abundance of keystone species was identified as the most important microbial factor contributing to variation in ALP activity based on structural equation modeling analysis. These findings enhance our understanding of how dam construction affects the functions of phoD-harboring bacteria and their role in the P biogeochemical cycle in highly regulated rivers.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Ge Cui
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
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10
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Zhang R, Xu X, Jia D, Lyu Y, Hu J, Chen Q, Sun W. Sediments alleviate the inhibition effects of antibiotics on denitrification: Functional gene, microbial community, and antibiotic resistance gene analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150092. [PMID: 34520908 DOI: 10.1016/j.scitotenv.2021.150092] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Both antibiotics and sediments can affect the denitrification in aquatic systems. However, little is known how antibiotics influence the denitrification in the presence of sediments. Here, the effects of antibiotics (sulfamethoxazole, tetracycline and ofloxacin) on denitrification in the absence and presence of sediments were investigated. The influencing mechanisms were revealed by quantifying the denitrification functional genes (DNGs), 16S-seq of bacteria, and antibiotic resistance genes (ARGs). The results showed that the presence of antibiotics inhibited NO3-N reduction by decreasing the abundances of narG, nirK, nosZ, total DNGs, and denitrifying bacteria. However, the inhibition effect was alleviated by sediments, which promoted the growth of bacteria and decreased the selective pressure of antibiotics as the vector of bacteria and antibiotics, thus increasing the abundances of denitrifying bacteria and all the DNGs. Partial least-squares path model disclosed that antibiotics had negative effects on bacteria, ARGs and DNGs, while sediments had negative effects on ARGs but positive effects on bacteria and DNGs. The network analysis further revealed the close relation of the genera Bacillus, Acinetobacter, and Enterobacter with the ARGs and DNGs. The findings are helpful to understand the denitrification in antibiotic-polluted natural waters.
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Affiliation(s)
- Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Dantong Jia
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Yitao Lyu
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Jingrun Hu
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China.
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11
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Caillon F, Besemer K, Peduzzi P, Schelker J. Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity. MICROBIAL ECOLOGY 2021; 82:591-601. [PMID: 33532913 PMCID: PMC8463373 DOI: 10.1007/s00248-021-01700-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/21/2021] [Indexed: 05/10/2023]
Abstract
Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.
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Affiliation(s)
- Florian Caillon
- WasserCluster Lunz/Biological Station GmbH, A-3293, Lunz am See, Austria.
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria.
| | - Katharina Besemer
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Peter Peduzzi
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Jakob Schelker
- WasserCluster Lunz/Biological Station GmbH, A-3293, Lunz am See, Austria
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
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12
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Zhang L, Cheng Y, Zhou Y, Lu W, Li J. Effect of different types of anthropogenic pollution on the bacterial community of urban rivers. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1322-1332. [PMID: 33484078 DOI: 10.1002/wer.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 06/12/2023]
Abstract
The health of urban rivers is threatened by multiple anthropogenic stressors. Bacterial communities in rivers can quickly respond to different types of polluted environments, making them useful for water quality assessments and predictive insights. However, research on river bacterial communities has largely ignored interactions between these communities. Here, 16S rRNA amplicon sequencing analysis is used to comprehensively analyze the bacterial communities in the water and sediments in different types of anthropogenically impacted urban river. The results show that distinct differences occur in the bacterial communities in the river sediment and water with different pollution types. The changes in the bacterial communities in sediments were more pronounced than those in the water. A modular analysis further showed that the microbial co-occurrence network under different types of pollution had a nonrandom modular structure, and this structure was mainly driven by classification correlation and bacterial function. Genes identified for nitrogen cycling in all the river water and sediment samples included major functional genes for nitrogen fixation, assimilatory nitrogen reduction, nitrification, denitrification, and ammonification. Carbon degradation genes were mainly observed in the carbon cycle. Taken together, the above findings provide further insights into microbial communities in urban river ecosystems under anthropogenic contamination. PRACTITIONER POINTS: The physical and chemical indicators of the four types of pollution drive bacterial community structure. Bacterial community has C, N, P metabolic genes indicating its ecological effect. River bacteria were connected more frequently in the same or similar type of pollution in the co-occurrence network. Microbe-environment correlations and microbe-microbe interactions were combined to determine crucial indicators.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, China
| | - Yu Cheng
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, China
| | - Yi Zhou
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, China
| | - Wenxuan Lu
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Jing Li
- Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
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Nogueira T, Botelho A. Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. Antibiotics (Basel) 2021; 10:787. [PMID: 34203511 PMCID: PMC8300701 DOI: 10.3390/antibiotics10070787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
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Affiliation(s)
- Teresa Nogueira
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Evolutionary Ecology of Microorganisms Group, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Botelho
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
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Yuan B, Wu W, Guo M, Zhou X, Xie S. Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China. PLoS One 2021; 16:e0253233. [PMID: 34129622 PMCID: PMC8205147 DOI: 10.1371/journal.pone.0253233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/31/2021] [Indexed: 11/19/2022] Open
Abstract
The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.
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Affiliation(s)
- Bo Yuan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Wei Wu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Mengjing Guo
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Xiaode Zhou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, China
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15
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Luo X, Xiang X, Yang Y, Huang G, Fu K, Che R, Chen L. Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network. FEMS Microbiol Ecol 2021; 96:5864679. [PMID: 32597955 DOI: 10.1093/femsec/fiaa132] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/28/2020] [Indexed: 12/11/2022] Open
Abstract
Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance-decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.
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Affiliation(s)
- Xia Luo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Xinyi Xiang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Yuanhao Yang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Guoyi Huang
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Kaidao Fu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Liqiang Chen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China.,Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
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Zheng Y, He W, Li B, Hur J, Guo H, Li X. Refractory Humic-like Substances: Tracking Environmental Impacts of Anthropogenic Groundwater Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15778-15788. [PMID: 33216533 DOI: 10.1021/acs.est.0c04561] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To unravel the crucial components of natural organic matter that respond to the process of anthropogenic groundwater recharge (AGR) from different recharge water sources, dissolved organic matter (DOM) and base-extractable particulate organic matter (POM) in groundwater and surface water were analyzed using excitation-emission matrix spectroscopy coupled with parallel factor analysis (EEM-PARAFAC). The EEM and traditional spectral indices of samples show that the fluorescent intensity, molecular weight, and humification degree of the DOM were relatively higher than those of the POM, and the groundwater in the reclaimed water recharge area (RWRA) was more contaminated than in the south-to-north water recharge area (SNWRA). PARAFAC analysis indicates that the DOM was dominated by an allochthonous humic-like substance (C1), whereas the POM was dominated by tryptophan-like substances associated with microbial activity (C2). Partitioning of PARAFAC components between DOM and POM showed that the humic-like substances (C1 and C4) were more likely to be distributed into a dissolved phase compared to the protein-like substances (C2 and C3), which suggested the potential use of C1 and C4 as a tracking indicator. In particular, the clear gradient distributions along both the hydrogeological profile and different aquifer systems in terms of the concentration and composition of C1 also discriminated between the RWRA and SNWRA with regard to the effects of various AGRs on the groundwater. The association between C1 and water-quality indicators revealed by principal component analysis further indicated that refractory humic-like substances would track the environmental impacts of intentional AGR processes.
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Affiliation(s)
- Yaxin Zheng
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Wei He
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Binghua Li
- Department of Water Resources, Beijing Water Science and Technology Institute, Beijing 100048, China
| | - Jin Hur
- Department of Environment and Energy, Sejong University, Seoul 05006, South Korea
| | - Huaming Guo
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xiaomeng Li
- Ministry of Education Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q, Sun S. Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river. Environ Microbiol 2019; 22:832-849. [DOI: 10.1111/1462-2920.14795] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 08/08/2019] [Accepted: 08/27/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
| | - Shenghao Sun
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of EnvironmentHohai University 1 Xikang Road, Nanjing 210098 China
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18
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Bacterial Abundance and Physicochemical Characteristics of Water and Sediment Associated with Hydroelectric Dam on the Lancang River China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16112031. [PMID: 31181632 PMCID: PMC6603985 DOI: 10.3390/ijerph16112031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/31/2019] [Accepted: 06/02/2019] [Indexed: 11/17/2022]
Abstract
Research on bacterial abundance in water column and sediment of dammed rivers remain poorly understood, despite their importance to biogeochemical processes, benthic ecology, and bioremediation. The present study investigates the water and sediment bacteria by epifluorescence microscopy in the reservoir (above the dam site), as well as in the downstream river stretches (below-dam site) at the middle reach of Lancang River during the wet, the normal and the dry seasons. The results demonstrated that the reservoir operating regime (water discharge variations) and strong precipitation promoted significant differences in the conditions of the river below the dam, especially for the concentration of dissolved oxygen, redox potential, electric conductivity, turbidity, and total dissolved solids in water and concentration of microbial activity in sediment. The seasonal variations were also key factors influencing water quality at the below-dam sampling sites. Nutrients concentration did not induce a significant response in bacterial abundance when inorganic nutrients were sufficient. Bacterial density in sediment was regulated by hydropower-related discharge, particle size, and type of sediments, while bacterial abundances in water were strongly linked with the physicochemical characteristics of the water, such as total dissolved solids and conductivity.
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19
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Mathai PP, Dunn HM, Magnone P, Zhang Q, Ishii S, Chun CL, Sadowsky MJ. Association between submerged aquatic vegetation and elevated levels of Escherichia coli and potential bacterial pathogens in freshwater lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:319-324. [PMID: 30543981 DOI: 10.1016/j.scitotenv.2018.11.484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
Fecal indicator bacteria such as Escherichia coli have been reported to persist and potentially grow in a wide variety of secondary habitats, such as water, beach sand, sediment, periphyton and some algae. However, little is known about their association with submerged macrophytes and how this may influence water quality. In this study, we examined the association of E. coli and potential bacterial pathogens with Eurasian watermilfoil (EWM), an invasive, submerged, macrophyte that has spread across thousands of lakes in North America. EWM samples were collected from 10 lakes in Minnesota, once a month, for six consecutive months from early summer to late fall. Microbiota associated with EWM were examined using membrane filtration, quantitative PCR targeting various bacterial pathogens and host-associated marker genes, and high-throughput DNA sequencing. E. coli densities were generally elevated on EWM samples, and peaked during warmer months. Moreover, our results showed that EWM could serve as a temporal source for transmission of microbiota to the water column. Several potential pathogenic groups, including Aeromonas, Enterobacteriaceae, and Clostridium were present in significantly greater relative abundance on EWM than in water, and waterfowl was predicted to be the major source of fecal contamination. These findings have water quality implications with respect to the potential for submerged macrophytes to harbor and disperse E. coli and other bacterial pathogens in a large number of waterbodies.
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Affiliation(s)
- Prince P Mathai
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Hannah M Dunn
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Paolo Magnone
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Chan Lan Chun
- Department of Civil Engineering and National Resources Research Institute, University of Minnesota, Duluth, MN, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA; Department of Plant, and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
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Enterococcal Concentrations in a Coastal Ecosystem Are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources. Appl Environ Microbiol 2018; 84:AEM.01038-18. [PMID: 30006393 DOI: 10.1128/aem.01038-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/23/2018] [Indexed: 02/01/2023] Open
Abstract
Fecal pollution at coastal beaches requires management efforts to address public health and economic concerns. Feces-borne bacterial concentrations are influenced by different fecal sources, environmental conditions, and ecosystem reservoirs, making their public health significance convoluted. In this study, we sought to delineate the influences of these factors on enterococcal concentrations in southern Maine coastal recreational waters. Weekly water samples and water quality measurements were conducted at freshwater, estuarine, and marine beach sites from June through September 2016. The samples were analyzed for total and particle-associated enterococcal concentrations, total suspended solids, and microbial source tracking markers (PCR: Bac32, HF183, CF128, DF475, and Gull2; quantitative PCR [qPCR]: AllBac, HF183, and GFD). Water, soil, sediment, and marine sediment samples were also subjected to 16S rRNA sequencing and SourceTracker analysis to determine the influence from these environmental reservoirs on water sample microbial communities. Enterococcal and particle-associated enterococcal concentrations were elevated in freshwater, but the concentrations of suspended solids were relatively similar. Mammal fecal contamination was significantly elevated in the estuary, with human and bird fecal contaminant levels similar between sites. A partial least-squares regression model indicated particle-associated enterococcal and mammal marker concentrations had the most significant positive relationships with enterococcal concentrations across marine, estuary, and freshwater environments. Freshwater microbial communities were significantly influenced by underlying sediment, while estuarine/marine beach communities were influenced by freshwater, high tide height, and estuarine sediment. Elevated enterococcal levels were reflective of a combination of increased fecal source input, environmental sources, and environmental conditions, highlighting the need for encompassing microbial source tracking (MST) approaches for managing water quality issues.IMPORTANCE Enterococci have long been the federal standard in determining water quality at estuarine and marine environments. Although enterococci are highly abundant in the intestines of many animals, they are not exclusive to that environment and can persist and grow outside fecal tracts. This presents a management problem for areas that are largely impaired by nonpoint source contamination, as fecal sources might not be the root cause of contamination. This study employed different microbial source tracking methods for delineating the influences from fecal source input, environmental sources, and environmental conditions to determine which combination of variables are influencing enterococcal concentrations in recreational waters at a historically impaired coastal town. The results showed that fecal source input, environmental sources, and conditions all play roles in influencing enterococcal concentrations. This highlights the need to include an encompassing microbial source tracking approach to assess the effects of all important variables on enterococcal concentrations.
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q. Bacterial Communities in Riparian Sediments: A Large-Scale Longitudinal Distribution Pattern and Response to Dam Construction. Front Microbiol 2018; 9:999. [PMID: 29867892 PMCID: PMC5964209 DOI: 10.3389/fmicb.2018.00999] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/27/2018] [Indexed: 11/15/2022] Open
Abstract
Sediment microbes play major roles in riparian ecosystems; however, little is known about their longitudinal distribution pattern and their responses to dam construction, the most severe human disturbance in river basins. Here, we investigated the variability of sediment bacterial communities along a large-scale longitudinal gradient and between dam-controlled and dam-affected sites in riparian zone of the Lancang River, China. The abundance, activity and diversity of sediment bacteria gradually increased in a downstream direction, but were significantly lower in the dam-affected sites than in the dam-controlled sites. The bacterial community compositions differed significantly between the upper-middle-reach and downstream sites at all control sites, and also between the dam-affected and dam-controlled sites. In the cascade dam area, the relative importance of spatial distance and environmental heterogeneity for bacterial distribution differed between the dam-controlled and dam-affected sites. Spatial distance was the primary cause of variations in bacterial community in dam-controlled site. By contrast, the environmental heterogeneity had more control over the bacterial communities than did the spatial distance in dam-affected site. Network analysis showed that the bacterial community in the dam-affected sites had lower connectivity and stability when compared with that in dam-controlled sites. These results suggest the distinct variations in sediment bacterial community in dam-affected sites, which could enhance our understanding of potential ecological effects caused by dam construction.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
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22
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Comte J, Berga M, Severin I, Logue JB, Lindström ES. Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons. Environ Microbiol 2017; 19:2391-2404. [DOI: 10.1111/1462-2920.13749] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 03/28/2017] [Accepted: 04/02/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Jérôme Comte
- Department of Ecology and Genetics/Limnology; Uppsala University; Norbyvägen 18D Uppsala 75236 Sweden
| | - Mercè Berga
- Department of Ecology and Genetics/Limnology; Uppsala University; Norbyvägen 18D Uppsala 75236 Sweden
- Biological Oceanography, Leibniz-Institute for Baltic Sea Research; Warnemünde (IOW); Seestrasse 15 Rostock Germany
| | - Ina Severin
- Department of Ecology and Genetics/Limnology; Uppsala University; Norbyvägen 18D Uppsala 75236 Sweden
| | - Jürg Brendan Logue
- Department of Ecology and Genetics/Limnology; Uppsala University; Norbyvägen 18D Uppsala 75236 Sweden
| | - Eva S. Lindström
- Department of Ecology and Genetics/Limnology; Uppsala University; Norbyvägen 18D Uppsala 75236 Sweden
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23
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Dubinsky EA, Butkus SR, Andersen GL. Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification. WATER RESEARCH 2016; 105:56-64. [PMID: 27598696 DOI: 10.1016/j.watres.2016.08.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 06/06/2023]
Abstract
Sources of fecal indicator bacteria are difficult to identify in watersheds that are impacted by a variety of non-point sources. We developed a molecular source tracking test using the PhyloChip microarray that detects and distinguishes fecal bacteria from humans, birds, ruminants, horses, pigs and dogs with a single test. The multiplexed assay targets 9001 different 25-mer fragments of 16S rRNA genes that are common to the bacterial community of each source type. Both random forests and SourceTracker were tested as discrimination tools, with SourceTracker classification producing superior specificity and sensitivity for all source types. Validation with 12 different mammalian sources in mixtures found 100% correct identification of the dominant source and 84-100% specificity. The test was applied to identify sources of fecal indicator bacteria in the Russian River watershed in California. We found widespread contamination by human sources during the wet season proximal to settlements with antiquated septic infrastructure and during the dry season at beaches during intense recreational activity. The test was more sensitive than common fecal indicator tests that failed to identify potential risks at these sites. Conversely, upstream beaches and numerous creeks with less reliance on onsite wastewater treatment contained no fecal signal from humans or other animals; however these waters did contain high counts of fecal indicator bacteria after rain. Microbial community analysis revealed that increased E. coli and enterococci at these locations did not co-occur with common fecal bacteria, but rather co-varied with copiotrophic bacteria that are common in freshwaters with high nutrient and carbon loading, suggesting runoff likely promoted the growth of environmental strains of E. coli and enterococci. These results indicate that machine-learning classification of PhyloChip microarray data can outperform conventional single marker tests that are used to assess health risks, and is an effective tool for distinguishing numerous fecal and environmental sources of pathogen indicators.
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Affiliation(s)
- Eric A Dubinsky
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven R Butkus
- North Coast Regional Water Quality Control Board, Santa Rosa, CA 95403, USA
| | - Gary L Andersen
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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