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Lancaster E, Winston R, Martin J, Lee J. Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses. WATER RESEARCH 2024; 259:121818. [PMID: 38815337 DOI: 10.1016/j.watres.2024.121818] [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: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.
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Affiliation(s)
- Emma Lancaster
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jay Martin
- Department of Food, Agricultural, and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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Davis SN, Klumker SM, Mitchell AA, Coppage MA, Labonté JM, Quigg A. Life in the PFAS lane: The impact of perfluoroalkyl substances on photosynthesis, cellular exudates, nutrient cycling, and composition of a marine microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171977. [PMID: 38547969 DOI: 10.1016/j.scitotenv.2024.171977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
Perfluoroalkyl substances (PFAS) are of great ecological concern, however, exploration of their impact on bacteria-phytoplankton consortia is limited. This study employed a bioassay approach to investigate the effect of unary exposures of increasing concentrations of PFAS (perfluorooctane sulfonate (PFOS) and 6:2 fluorotelomer sulfonate (6:2 FTS)) on microbial communities from the northwestern Gulf of Mexico. Each community was examined for changes in growth and photophysiology, exudate production and shifts in community structure (16S and 18S rRNA genes). 6:2 FTS did not alter the growth or health of phytoplankton communities, as there were no changes relative to the controls (no PFOS added). On the other hand, PFOS elicited significant phototoxicity (p < 0.05), altering PSII antennae size, lowering PSII connectivity, and decreasing photosynthetic efficiency over the incubation (four days). PFOS induced a cellular protective response, indicated by significant increases (p < 0.001) in the release of transparent exopolymer particles (TEP) compared to the control. Eukaryotic communities (18S rRNA gene) changed substantially (p < 0.05) and to a greater extent than prokaryotic communities (16S rRNA gene) in PFOS treatments. Community shifts were concentration-dependent for eukaryotes, with the low treatment (5 mg/L PFOS) dominated by Coscinodiscophyceae (40 %), and the high treatment (30 mg/L PFOS) marked by a Trebouxiophyceae (50 %) dominance. Prokaryotic community shifts were not concentration dependent, as both treatment levels became depleted in Cyanobacteriia and were dominated by members of the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. Further, PFOS significantly decreased (p < 0.05) the Shannon diversity and Pielou's evenness across treatments for eukaryotes, and in the low treatment (5 mg/L PFOS) for prokaryotes. These findings show that photophysiology was not impacted by 6:2 FTS but PFOS elicited toxicity that impacted photosynthesis, exudate release, and community composition. This research is crucial in understanding how PFOS impacts microbial communities.
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Affiliation(s)
- Sarah N Davis
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, USA.
| | - Shaley M Klumker
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, USA
| | - Alexis A Mitchell
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, USA
| | - Marshall A Coppage
- Department of Biological Sciences, University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Jessica M Labonté
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, USA
| | - Antonietta Quigg
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, USA; Department of Oceanography, Texas A&M University, 3146 TAMU, College Station, TX 77843, USA; Department of Ecology and Conservation Biology, Texas A&M University, 534 John Kimbrough Boulevard, College Station, TX 77843, USA
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Wu D, Zou Y, Xiao J, Mo L, Lek S, Chen B, Fu Q, Guo Z. The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China. Front Microbiol 2024; 15:1354784. [PMID: 38770023 PMCID: PMC11102952 DOI: 10.3389/fmicb.2024.1354784] [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: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.
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Affiliation(s)
- Di Wu
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ying Zou
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Juan Xiao
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ling Mo
- Institute of Environmental Sciences, Haikou, Hainan Province, China
| | - Sovan Lek
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Laboratoire Evolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Bo Chen
- National Health Commission of the People's Republic of China Key Laboratory of Control of Tropical Diseases Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Qiongyao Fu
- National Health Commission of the People's Republic of China Key Laboratory of Control of Tropical Diseases Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Zhiqiang Guo
- School of Life and Health Sciences, Key Laboratory of Tropical Biological Resources of Ministry of Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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Shang Y, Wang X, Wu X, Dou H, Wei Q, Wang Q, Liu G, Sun G, Wang L, Zhang H. Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors. Microbiol Spectr 2024; 12:e0324523. [PMID: 38602397 PMCID: PMC11064641 DOI: 10.1128/spectrum.03245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
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Affiliation(s)
- Yongquan Shang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Gang Liu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Guolei Sun
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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Hu L, He L, Cai L, Wang Y, Wu G, Zhang D, Pan X, Wang YZ. Deterioration of single-use biodegradable plastics in high-humidity air and freshwaters over one year: Significant disparities in surface physicochemical characteristics and degradation rates. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133170. [PMID: 38064942 DOI: 10.1016/j.jhazmat.2023.133170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 02/08/2024]
Abstract
More single-use plastics are accumulating in the environment, and likewise biodegradable plastics (BPs), which are being vigorously promoted, cannot escape the fate. Currently, studies on the actual degradation of BPs in open-air and freshwaters are underrepresented despite they are potentially headmost leakage and contamination sites for disposable BPs. Herein, we compared the degradation behavior of six BP materials and non-degradable polypropylene (PP) plastics over a 1-year in situ suspension in the high-humidity air, a eutrophic river, and an oligotrophic lake. Moreover, a 3-months laboratory incubation was performed to detect the release of dissolved organic carbon (DOC) from BPs. In both air and freshwaters, poly(p-dioxanone) (PPDO) degraded significantly while PP and polylactic acid (PLA) showed no signs of degradation. The average degradation rates of three poly(butylene adipate-co-terephthalate) (PBAT)-based films varied: 100% in river, 55% in lake, and 10% in air. In addition to PLA, surface chemical groups, hydrophilicity, and thermal stability of BPs changed, and microplastics were found on their surfaces. Correspondingly, BPs with faster degradation rates released relatively higher amounts of DOC. Environmental microbial and chemical characteristics may contribute to differences in BP degradation besides polymer specificity. Altogether, our results indicate the need for appropriate monitoring of BPs.
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Affiliation(s)
- Lingling Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; The Collaborative Innovation Center for Eco-Friendly and Fire-Safety Polymeric Materials (MoE), National Engineering Laboratory of Eco-Friendly Polymeric Materials (Sichuan), State Key Laboratory of Polymer Materials Engineering, College of Chemistry, Sichuan University, Chengdu 610064, China; Shaoxing Research Institute, Zhejiang University of Technology, Shaoxing 312000, China
| | - Linlin He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Li Cai
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yumeng Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Gang Wu
- The Collaborative Innovation Center for Eco-Friendly and Fire-Safety Polymeric Materials (MoE), National Engineering Laboratory of Eco-Friendly Polymeric Materials (Sichuan), State Key Laboratory of Polymer Materials Engineering, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Daoyong Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yu-Zhong Wang
- The Collaborative Innovation Center for Eco-Friendly and Fire-Safety Polymeric Materials (MoE), National Engineering Laboratory of Eco-Friendly Polymeric Materials (Sichuan), State Key Laboratory of Polymer Materials Engineering, College of Chemistry, Sichuan University, Chengdu 610064, China
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Spencer-Williams I, Meyer M, DePas W, Elliott E, Haig SJ. Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20360-20369. [PMID: 37970641 DOI: 10.1021/acs.est.3c05272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.
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Affiliation(s)
- Isaiah Spencer-Williams
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mitchell Meyer
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - William DePas
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Emily Elliott
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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Yang S, Huang T, Zhang H, Guo H, Xu J, Cheng Y. Pollutants reduction via artificial mixing in a drinking water reservoir: Insights into bacterial metabolic activity, biodiversity, interactions and co-existence of core genera. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165473. [PMID: 37454840 DOI: 10.1016/j.scitotenv.2023.165473] [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: 04/17/2023] [Revised: 06/17/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Endogenous pollution due to long periods of hypolimnetic anoxia in stratified reservoirs has become a worldwide concern, which can threaten metabolic activity, biodiversity, water quality security, and ultimately human health. In the present study, an artificial mixing system applied in a drinking water reservoir was developed to reduce pollutants, and the biological mechanism involved was explored. After approximately 44 days of system operation, the reservoir content was completely mixed resulting in the disappearance of anoxic layers. Furthermore, the metabolic activity estimated by the Biolog-ECO microplate technique and biodiversity was enhanced. 16S rRNA gene sequencing indicated a great variability on the composition of bacterial communities. Co-occurrence network analysis showed that interactions among bacteria were significantly affected by the proposed mixing system. Bacteria exhibited a more mutualistic state and >10 keystone genera were identified. Pollutants, including nitrogen, phosphorus, organic matter, iron, and manganese decreased by 30.63-80.15 %. Redundancy discriminant analysis revealed that environmental factors, especially the temperature and dissolved oxygen, were crucial drivers of the bacterial community structure. Furthermore, Spearman's correlation analysis between predominant genera and pollutants suggested that core genus played a vital role in pollutant reduction. Overall, our findings highlight the importance and provide insights on the artificial mixing systems' microbial mechanisms of reducing pollutants in drinking water reservoirs.
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Affiliation(s)
- Shangye Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Haihan Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Honghong Guo
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jin Xu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ya Cheng
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, PR China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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Sushmitha TJ, Rajeev M, Murthy PS, Rao TS, Pandian SK. Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115433. [PMID: 37696079 DOI: 10.1016/j.ecoenv.2023.115433] [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: 03/01/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 ℃). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.
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Affiliation(s)
- T J Sushmitha
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Meora Rajeev
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Sriyutha Murthy
- Water & Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Toleti Subba Rao
- School of Arts & Sciences, Sai University, OMR, Paiyanur, 603105 Tamil Nadu, India
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Li M, Zhao T, Liang D, Dong D, Guo Z, Hua X, Zhong S. Diversity characterization of bacteria and fungi in water, sediments and biofilms from Songhua River in Northeast China. CHEMOSPHERE 2023; 338:139524. [PMID: 37467849 DOI: 10.1016/j.chemosphere.2023.139524] [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: 05/21/2023] [Revised: 06/18/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
Water, sediments, and biofilms are the typical microbial carriers in natural water environments. However, comparative analysis of the distribution of bacterial and fungal communities in different carriers within the same habitat is relatively lacking. Therefore, this study employed 16 S and ITS rRNA gene sequencing to identify bacterial and fungal community structures in water, sediments, and biofilm. The results show that (1) the OTUs numbers revealed that the bacterial abundance, at the levels of species, genus, and family, followed the order of sediments > water > biofilms, while the fungal abundance order was water > sediments > biofilms. In addition, bacteria were mainly present in sediments, while fungi were mainly present in water. (2) The α diversity index (Shannon, ACE, Simpson, and Chao1) order, for bacteria was: sediments > water > biofilms, indicating that the diversity and homogeneity of bacteria in sediments were relatively higher; for fungi was: water > sediments > biofilms, indicating that the diversity and abundance of fungi in water were high. (3) The core phylum of bacterial in the water, sediments, and biofilms was Cyanobacteria (31.3-46.1%) and Actinobacteria (27.6-36.1%); Proteobacteria (35.0-41.8%), Cyanobacteria (14.7-36.6%); and Proteobacteria (63.3-69.2%), respectively. (4) The mainly colonized fungal phyla in biofilms in the water, sediments, and biofilms were Basidiomycota (29.3-38.7%) and Ascomycota (16.2-27.7%); Zygomycota (13.1-17.5%), Basidiomycota (5.6-17.6%); and Zygomycota (23.8-44.2%). (5) There were significant species differences in bacterial and fungal communities in water, sediments, and biofilm by NMDS analysis. Findings are useful for guiding significance for the Biogeochemical cycle of elements, the environmental fate of pollutants, and the study of water ecosystems.
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Affiliation(s)
- Ming Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; Gong Qing Institute of Science and Technology, Nanchang, 330044, China; Jilin Agricultural Science and Technology University, Chang Chun, 130018, China; Key Laboratory of Songliao Aquatic Environment Ministry of Education, School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Tianyu Zhao
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Dapeng Liang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Deming Dong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Zhiyong Guo
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Xiuyi Hua
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China.
| | - Shuang Zhong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China.
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Zhang H, Zhao D, Ma M, Huang T, Li H, Ni T, Liu X, Ma B, Zhang Y, Li X, Lei X, Jin Y. Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131429. [PMID: 37099929 DOI: 10.1016/j.jhazmat.2023.131429] [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: 02/07/2023] [Revised: 03/19/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Daijuan Zhao
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Manli Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Haiyun Li
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tongchao Ni
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiang Liu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Xuan Li
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Xiaohui Lei
- Department of Rehabilitation, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Yaofeng Jin
- Department of Pathology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
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11
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Roda-Garcia JJ, Haro-Moreno JM, López-Pérez M. Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota. Front Microbiol 2023; 14:1159270. [PMID: 37234526 PMCID: PMC10205998 DOI: 10.3389/fmicb.2023.1159270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.
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12
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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13
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He S, Linz AM, Stevens SLR, Tran PQ, Moya-Flores F, Oyserman BO, Dwulit-Smith JR, Forest KT, McMahon KD. Diversity, distribution, and expression of opsin genes in freshwater lakes. Mol Ecol 2023; 32:2798-2817. [PMID: 36799010 DOI: 10.1111/mec.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have nontypical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.
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Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexandra M Linz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah L R Stevens
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Francisco Moya-Flores
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ben O Oyserman
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeffrey R Dwulit-Smith
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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14
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Feng J, Zhou L, Zhao X, Chen J, Li Z, Liu Y, Ou L, Xie Z, Wang M, Yin X, Zhang X, Li Y, Luo M, Zeng L, Yan Q, Xie L, Sun L. Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons. Front Microbiol 2023; 14:1091818. [PMID: 36865780 PMCID: PMC9971975 DOI: 10.3389/fmicb.2023.1091818] [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: 11/07/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.
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Affiliation(s)
- Jie Feng
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Letian Zhou
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Jianyi Chen
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Zhi Li
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Ou
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Zixin Xie
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Miao Wang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xue Yin
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yan Li
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lidong Zeng
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Linshen Xie
- State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Academy of Environmental Sciences, Shenzhen, China,*Correspondence: Linshen Xie,
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China,*Correspondence: Linshen Xie,
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15
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Crevecoeur S, Edge TA, Watson LC, Watson SB, Greer CW, Ciborowski JJH, Diep N, Dove A, Drouillard KG, Frenken T, McKay RM, Zastepa A, Comte J. Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum. Front Microbiol 2023; 14:1073753. [PMID: 36846788 PMCID: PMC9947797 DOI: 10.3389/fmicb.2023.1073753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.
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Affiliation(s)
- Sophie Crevecoeur
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada,*Correspondence: Sophie Crevecoeur, ✉
| | - Thomas A. Edge
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Linet Cynthia Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Susan B. Watson
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Charles W. Greer
- Energy, Mining and Environment, National Research Council of Canada, Montreal, QC, Canada
| | - Jan J. H. Ciborowski
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada,Department of Biological Sciences University of Calgary, Calgary, AB, Canada
| | - Ngan Diep
- Ontario Ministry of the Environment, Conservation and Parks, Environmental Monitoring and Reporting Branch, Etobicoke, ON, Canada
| | - Alice Dove
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Kenneth G. Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Cluster Nature & Society, HAS University of Applied Sciences, s-Hertogenbosch, Netherlands
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada,Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - Arthur Zastepa
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, Quebec City, QC, Canada,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université de Montréal, Montreal, QC, Canada
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16
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Castañeda-Gómez L, Lajtha K, Bowden R, Mohammed Jauhar FN, Jia J, Feng X, Simpson MJ. Soil organic matter molecular composition with long-term detrital alterations is controlled by site-specific forest properties. GLOBAL CHANGE BIOLOGY 2023; 29:243-259. [PMID: 36169977 DOI: 10.1111/gcb.16456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Forest ecosystems are important global soil carbon (C) reservoirs, but their capacity to sequester C is susceptible to climate change factors that alter the quantity and quality of C inputs. To better understand forest soil C responses to altered C inputs, we integrated three molecular composition published data sets of soil organic matter (SOM) and soil microbial communities for mineral soils after 20 years of detrital input and removal treatments in two deciduous forests: Bousson Forest (BF), Harvard Forest (HF), and a coniferous forest: H.J. Andrews Forest (HJA). Soil C turnover times were estimated from radiocarbon measurements and compared with the molecular-level data (based on nuclear magnetic resonance and specific analysis of plant- and microbial-derived compounds) to better understand how ecosystem properties control soil C biogeochemistry and dynamics. Doubled aboveground litter additions did not increase soil C for any of the forests studied likely due to long-term soil priming. The degree of SOM decomposition was higher for bacteria-dominated sites with higher nitrogen (N) availability while lower for the N-poor coniferous forest. Litter exclusions significantly decreased soil C, increased SOM decomposition state, and led to the adaptation of the microbial communities to changes in available substrates. Finally, although aboveground litter determined soil C dynamics and its molecular composition in the coniferous forest (HJA), belowground litter appeared to be more influential in broadleaf deciduous forests (BH and HF). This synthesis demonstrates that inherent ecosystem properties regulate how soil C dynamics change with litter manipulations at the molecular-level. Across the forests studied, 20 years of litter additions did not enhance soil C content, whereas litter reductions negatively impacted soil C concentrations. These results indicate that soil C biogeochemistry at these temperate forests is highly sensitive to changes in litter deposition, which are a product of environmental change drivers.
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Affiliation(s)
- Laura Castañeda-Gómez
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Kate Lajtha
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Bowden
- Department of Environmental Science and Sustainability, Allegheny College, Meadville, Pennsylvania, USA
| | | | - Juan Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Myrna J Simpson
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
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17
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Iniesto M, Moreira D, Benzerara K, Reboul G, Bertolino P, Tavera R, López‐García P. Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient. LIMNOLOGY AND OCEANOGRAPHY 2022; 67:2718-2733. [PMID: 37064594 PMCID: PMC10087431 DOI: 10.1002/lno.12233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/12/2022] [Accepted: 09/04/2022] [Indexed: 06/19/2023]
Abstract
Continental freshwater systems are particularly vulnerable to environmental variation. Climate change-induced desertification and the anthropogenic exploitation of hydric resources result in the progressive evaporation and salinization of inland water bodies in many areas of the globe. However, how this process impacts microbial communities and their activities in biogeochemical cycles is poorly known. Here, we take a space-for-time substitution approach and characterize the prokaryotic and eukaryotic microbial communities of two planktonic cell-size fractions (0.2-5 μm and 5-30 μm) from lakes of diverse trophic levels sampled along a salinity-alkalinity gradient located in the Trans-Mexican Volcanic Belt (TMVB). We applied a 16S/18S rRNA gene metabarcoding strategy to determine the microbial community composition of 54 samples from 12 different lakes, from the low-salinity lake Zirahuén to the hypersaline residual ponds of Rincón de Parangueo. Except for systems at both extremes of the salinity gradient, most lakes along the evaporation trend bear actively forming microbialites, which harbor microbial communities clearly distinct from those of plankton. Several lakes were sampled in winter and late spring and the crater lakes Alchichica and Atexcac were sampled across the water column. Physicochemical parameters related to salinity-alkalinity were the most influential drivers of microbial community structure whereas trophic status, depth, or season were less important. Our results suggest that climate change and anthropogenic-induced hydric deficit could significantly affect microbial communities, potentially altering ecosystem functioning.
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Affiliation(s)
- Miguel Iniesto
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - David Moreira
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Karim Benzerara
- Institut de Minéralogie de Physique des Matériaux et de Cosmochimie, CNRSSorbonne Université, Muséum National d'Histoire NaturelleParisFrance
| | - Guillaume Reboul
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRSUniversité Paris‐Saclay, AgroParisTechOrsayFrance
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos NaturalesUniversidad Nacional Autónoma de MéxicoMexico CityMexico
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18
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Chaudhary A, Dunn ST, Kelly J, Hoellein TJ. Plastic microbiome development in a freshwater ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157697. [PMID: 35914595 DOI: 10.1016/j.scitotenv.2022.157697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/21/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
To understand biological interactions of plastic litter in freshwater ecosystems, as well the potential effects of plastics on ecosystem processes, studies of the activity and composition of plastic-associated microbial communities are needed. The physical properties and chemical composition of plastic polymers are key components of plastic product design, and may also select for distinct microbial biofilms colonizing plastic litter. We monitored growth and succession of biofilm communities on plastic substrates of common morphotypes (i.e., hard, soft, foam, and film) and a natural surface (i.e., an unglazed ceramic tile) incubated in an urban stream. We measured biofilm biomass, metabolism, extracellular enzyme activity, and bacterial, fungal and algal community composition over four weeks during primary succession. Results demonstrated a general increase in biofilm biomass and enzymatic activity corresponding to carbon, nitrogen and phosphorus metabolism during biofilm development for all substrate types. We observed higher respiration rates and negative net ecosystem productivity on foam and tile surfaces in comparison to hard, soft and film plastic surfaces. Biofilm bacterial, fungal and algal assemblages showed few significant differences in composition among substrates. However, all microbial communities changed significantly in composition over time. While substrate type was not the major factor driving biofilm composition and activity, these data show plastic litter in streams is well colonized by an active and dynamic biofilm community. As plastic litter is increasing across all types of aquatic ecosystems, it should be considered a medium for biologically active organisms that contribute to key ecosystem processes.
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Affiliation(s)
- Adit Chaudhary
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America.
| | - Samuel T Dunn
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - John Kelly
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Timothy J Hoellein
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
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19
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Pearman JK, Thomson-Laing G, Thompson L, Waters S, Vandergoes MJ, Howarth JD, Duggan IC, Hogg ID, Wood SA. Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes. PeerJ 2022; 10:e14378. [PMID: 36389411 PMCID: PMC9661969 DOI: 10.7717/peerj.14378] [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: 07/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.
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Affiliation(s)
| | | | | | | | | | | | | | - Ian D. Hogg
- University of Waikato, Hamilton, New Zealand,Canadian High Arctic Research Station, Nunavut, Canada
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20
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Abstract
Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.
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21
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Cabello-Yeves PJ, Scanlan DJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Millard AD, Camacho A, Rodriguez-Valera F, Puxty RJ. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. THE ISME JOURNAL 2022; 16:2421-2432. [PMID: 35851323 PMCID: PMC9477826 DOI: 10.1038/s41396-022-01282-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain.
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET., Av. Intendente Marino Km 8,200, 7130, Chascomús, Buenos Aires, Argentina
- Instituto Nacional de Limnología (INALI), CONICET-UNL., Ciudad Universitaria-Paraje el Pozo s/n, 3000, Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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22
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Gao N, Liang Y, Li J, Cui K, Lu W. Bacterial community composition and indicators of water quality in Caizi lake, a typical Yangtze-connected freshwater lake. FEMS Microbiol Lett 2022; 369:6674759. [PMID: 36001998 DOI: 10.1093/femsle/fnac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022] Open
Abstract
Caizi Lake is an important lake connected to the Yangtze River in Anhui Province and a crucial connection for the Yangtze-to-Huaihe Water Diversion Project (YHWD). There were marked differences in trophic status of the six sampling sites based on the physicochemical characterization. The Bacterial Eutrophic Index (BEI), used to quantify water quality, was well related to Carlson's trophic state index (TSI) (Spearman's ρ = 0.829, P < 0.05). Mean TSI and BEI were 54 and 0.58, respectively, indicating that Caizi Lake was slightly eutrophic. Actinobacteriota were the predominant bacterial phylum in the water and Acidobacteriota in sediments. The diversity and composition of the bacterial community was markedly different between sites for water but not sediment samples. Unlike other Yangtze-connected freshwater lakes, the distance-based redundancy analysis (db-RDA) revealed that dissolved oxygen (DO) affected the composition of the planktonic bacterial community (P < 0.001) while total phosphorus (TP) was the major factor in the sediments (P < 0.05). Water quality of Caizi Lake significantly improved since a few years ago. These results contribute to the long-term monitoring of the ecological quality of the water environment along the Yangtze River to the Huaihe River.
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Affiliation(s)
- Na Gao
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yangyang Liang
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jing Li
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Kai Cui
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wenxuan Lu
- Key Laboratory of Freshwater Aquaculture and Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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23
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Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081280. [PMID: 36013459 PMCID: PMC9409723 DOI: 10.3390/life12081280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.
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24
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Mikhailov IS, Galachyants YP, Bukin YS, Petrova DP, Bashenkhaeva MV, Sakirko MV, Blinov VV, Titova LA, Zakharova YR, Likhoshway YV. Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal. MICROBIAL ECOLOGY 2022; 84:404-422. [PMID: 34510242 DOI: 10.1007/s00248-021-01860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov A Titova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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25
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Huang X, Li M, Huang Y, Yang H, Geng Y, Ouyang P, Chen D, Yin L, Yang S, Jiang J, Luo W, He Z. Microbiome analysis reveals microecological advantages of emerging ditchless rice-crayfish co-culture mode. Front Microbiol 2022; 13:892026. [PMID: 35935240 PMCID: PMC9355531 DOI: 10.3389/fmicb.2022.892026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Ditchless rice-crayfish co-culture is an emerging model of rice-crayfish farming that circumvents the potential hazards of digging ditches in traditional rice-crayfish farming. However, due to the complex interactions among crayfish, ambient microbiota, and environmental variables, it is necessary to assess the differences in bacterial structure between ditchless and traditional rice-crayfish culture. In this study, the crayfish culture area in the Sichuan basin was selected as the study area, and the bacterial communities of two rice-crayfish culture systems were compared by high-throughput sequencing of 16S rDNA. The results showed that the ditchless system had lower water depth, higher dissolved oxygen, lower total ammonia nitrogen and lower morbidity. There are intuitive differences in the composition of environmental bacterial communities due to environmental changes, even if they are similar in composition at the phylum level. Microbiota in sediments from ditchless systems appear to produce less ammonia nitrogen. The abundance of the pathogens colonizing the intestine of ditchless crayfish was lower than ditched one, and the composition was similar to water. Ditch-farmed crayfish appear to be more susceptible to environmental microbes and have a more fragile intestinal structure. Water depth and dissolved oxygen are the main environmental factors that determine the distribution of microbiota. This study is the first to investigate the bacterial ecology of a ditchless rice- crayfish farming system. The results show that the ditchless rice-crayfish culture model has a more superior bacterial system than the traditional rice-crayfish culture.
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Affiliation(s)
- Xiaoli Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghao Li
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ya Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hai Yang
- Haide Aquatic Technology Co., Ltd, Yibin, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yi Geng,
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lizi Yin
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shiyong Yang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jun Jiang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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26
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Zhang Y, Huo Y, Zhang Z, Zhu S, Fan W, Wang X, Huo M. Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39973-39984. [PMID: 35112248 DOI: 10.1007/s11356-021-18386-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH3-N as well as NO3--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.
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Affiliation(s)
- Ying Zhang
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Yang Huo
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
- School of Physics, Northeast Normal University, Changchun, 130024, China.
| | - Zhiruo Zhang
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, China
| | - Suiyi Zhu
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Wei Fan
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Xianze Wang
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Mingxin Huo
- School of Environment, Northeast Normal University, Changchun, 130117, China.
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
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27
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Song X, Zhao Y, Zhang L, Xie X, Wu J, Wei Z, Yang H, Zhang S, Song C, Jia L. Photodegradation, bacterial metabolism, and photosynthesis drive the dissolved organic matter cycle in the Heilongjiang River. CHEMOSPHERE 2022; 295:133923. [PMID: 35143859 DOI: 10.1016/j.chemosphere.2022.133923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/23/2021] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Dissolved organic matter (DOM) plays a vital role in the biogeochemistry of aquatic ecosystems. However, the mechanisms of DOM cycling in the water column during different seasons have not been fully elucidated to date. The differences in DOM degradation in summer, autumn, and winter water columns were evaluated in this study. The results showed that bacteria played an essential role in the degradation of DOM in the summer water column. Photochemical degradation was the primary degradation pathway of DOM in the autumn and winter water columns. Notably, while DOM is degraded, photosynthetic bacteria produce organic matter through photosynthesis to replenish the water column. EEM-PARAFAC analysis indicated more tryptophan component C1 in summer, but the contents of humic substance component C2 and terrestrial substance C3 were higher in autumn and winter. In summer, more tryptophan-like components were consumed by bacteria, and Cyanobacteria produced more organic matter through photosynthesis to replenish the water column. Moreover, a similar bacterial community structure and a more active tryptophan biosynthesis pathway were found in autumn and winter. Random forest models identified representative bacteria involved in the DOM transformation process in different seasons. The above findings may be helpful to explore the degradation characteristics of DOM in different seasons and predict the fate of DOM in the water column in the future.
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Affiliation(s)
- Xinyu Song
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Linyuan Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xinyu Xie
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Hongyu Yang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Shubo Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Caihong Song
- College of Life Science, Liaocheng University, Liaocheng, 252000, China
| | - Liming Jia
- Environmental Monitoring Center of Heilongjiang Province, Harbin, 150056, China
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28
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Sanseverino I, Pretto P, António DC, Lahm A, Facca C, Loos R, Skejo H, Beghi A, Pandolfi F, Genoni P, Lettieri T. Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese. MICROBIAL ECOLOGY 2022; 83:850-868. [PMID: 34766210 PMCID: PMC9016052 DOI: 10.1007/s00248-021-01914-5] [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: 04/26/2021] [Accepted: 10/26/2021] [Indexed: 05/09/2023]
Abstract
Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.
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Affiliation(s)
- Isabella Sanseverino
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Patrizia Pretto
- Biosearch Ambiente Srl, Via Tetti Gai 59, 10091, Alpignano, TO, Italy
| | - Diana Conduto António
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Armin Lahm
- Bioinformatics Project Support, P.za S.M. Liberatrice 18, 00153, Roma, Italy
| | - Chiara Facca
- Department of Environmental Science, Informatics and Statistics, University Ca' Foscari Venezia, Via Torino 155, 301702, Mestre, VE, Italy
| | - Robert Loos
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Helle Skejo
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy
| | - Andrea Beghi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Franca Pandolfi
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Pietro Genoni
- ARPA, Agenzia Regionale Per La Protezione Dell'Ambiente Della Lombardia, Via Ippolito Rosellini 17, 20124, Milano, Italy
| | - Teresa Lettieri
- European Commission, Joint Research Centre (JRC), Via E. Fermi 2749, 21027, Ispra, VA, Italy.
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29
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Pearman JK, Thomson-Laing G, Thomson-Laing J, Thompson L, Waters S, Reyes L, Howarth JD, Vandergoes MJ, Wood SA. The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes. Front Microbiol 2022; 12:793441. [PMID: 35250905 PMCID: PMC8888906 DOI: 10.3389/fmicb.2021.793441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.
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Affiliation(s)
- John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Lucy Thompson
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Sean Waters
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Jamie D Howarth
- School of Geography, Environment and Earth Sciences, University of Victoria, Wellington, New Zealand
| | | | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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Gao FZ, He LY, Hu LX, Chen J, Yang YY, Zou HY, He LX, Bai H, Liu YS, Zhao JL, Ying GG. Anthropogenic activities and seasonal properties jointly drive the assemblage of bacterial communities in subtropical river basins. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151476. [PMID: 34742952 DOI: 10.1016/j.scitotenv.2021.151476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic activities have inevitably impacted riverine ecosystems, yet their overall contribution to the assemblage of bacterial communities at a large river basin scale remains unclear. In this study, 16S amplicon sequencing was implemented to investigate the bacterial ecosystems in paired water and sediment of North River and West River basins in South China., which contains various anthropogenic environments (e.g., rural/urban area, mining area and livestock area). Subsequently, the links between bacterial community and various types of emerging pollutants in river water were analyzed. The results show that the bacterial assemblage of water and sediment had their own properties that the bacterial community of sediment were mainly affected by seasonal properties, while the bacterial community of water were affected by both seasons and anthropogenic activities. Therein, the aquatic bacterial compositions and abundances were driven by changes in temperature, dissolved oxygen and the emerging pollutants. The dominant phyla Proteobacteria and Firmicutes exhibited adaptability to the mining-affected regions, therein many clades (e.g., Beijerinckiaceae, Acetobacteraceae and Mycobacteriaceae) were also prevalent in the livestock-affected and densely-populated regions. In addition, these two phyla presented associations to the antibiotic resistance in water. The levels of antibiotics, relative antibiotic resistance gens (ARGs) and non-antibiotic pharmaceuticals (NAPs) were closely related to bacterial community composition, diversity and functional diversity, indicating their drive in shifting bacterial communities. Collectively, this work provides a basis for understanding the contribution of anthropogenic activities in shifting bacterial community at a large river basin scale. Further, the results provide new insights for expansion of ecological assessment.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Li-Xin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jun Chen
- Pearl River Water Resource Research Institute, Guangzhou 510611, China
| | - Yuan-Yuan Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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31
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Shang Y, Wu X, Wang X, Wei Q, Ma S, Sun G, Zhang H, Wang L, Dou H, Zhang H. Factors affecting seasonal variation of microbial community structure in Hulun Lake, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150294. [PMID: 34536882 DOI: 10.1016/j.scitotenv.2021.150294] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there is a lack of research on the seasonal variation in lake water microorganisms in cold environments. In this study, 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors in Hulun Lake water during different seasons. The results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most important phyla in the microbial community of Hulun Lake, but they had significant seasonal differences in their distribution. In addition, significant seasonal differences were observed in the α diversity of microorganisms, with bacterial diversity being higher in winter than in summer. Changes in environmental variables were significantly correlated with changes in the microbial community, and the rapid changes in temperature, pH, and dissolved oxygen are potentially the major factors influencing seasonal bacterial diversity trends. The findings of the present study enhance our understanding of the microbial communities in alpine lake ecosystems and are of great significance for the management and protection of lake ecosystems.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Shengchao Ma
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Guolei Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China.
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China.
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32
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Zhang C, Jiao S, Shu D, Wei G. Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization. STRESS BIOLOGY 2021; 1:15. [PMID: 37676329 PMCID: PMC10441860 DOI: 10.1007/s44154-021-00015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/14/2021] [Indexed: 09/08/2023]
Abstract
Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.
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Affiliation(s)
- Chunfang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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33
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Hempel PP, Keffer JL, Maresca JA. RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria. Front Microbiol 2021; 12:739005. [PMID: 34790178 PMCID: PMC8591293 DOI: 10.3389/fmicb.2021.739005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/11/2021] [Indexed: 01/20/2023] Open
Abstract
Light is a ubiquitous source of both energy and information in surface environments, and regulates gene expression not only in photosynthetic microorganisms, but in a broad range of photoheterotrophic and heterotrophic microbes as well. Actinobacteria are keystone species in surface freshwater environments, where the ability to sense light could allow them to coordinate periods of nutrient uptake and metabolic activity with primary production. The model freshwater Actinobacteria Rhodoluna (R.) lacicola strain MWH-Ta8 and Aurantimicrobium (A.) photophilum strain MWH-Mo1 grow faster in the light than in the dark, but do not use light energy to support growth. Here, we characterize transcription throughout a light-dark cycle in R. lacicola and A. photophilum. In both species, some genes encoding carbohydrate metabolism and storage are upregulated in the light. However, expression of genes of the TCA cycle is only coordinated with light availability in R. lacicola. In fact, the majority of genes that respond to light and darkness in these two species are different, even though their light-responsive phenotypes are similar. The ability to respond to light and darkness may be widespread in freshwater Actinobacteria, but the genetic networks controlled by these two stimuli may vary significantly.
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Affiliation(s)
- Priscilla P. Hempel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Jessica L. Keffer
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, United States
| | - Julia A. Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, United States
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34
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Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure. SUSTAINABILITY 2021. [DOI: 10.3390/su132011518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacteria, an integral part of aquatic ecosystems, are responsible for the circulation of matter and flow of energy. Since bacterioplankton rapidly responds to any natural and human-induced disturbances in the environment, it can serve as a bioindicator of these changes. Knowing factors that shape the microbial community structure may help the sustainable management of the water environment. However, the identification of environmental signals affecting the structure and function of bacterioplankton is still a challenge. The study analyses the impact of environmental variables on basic microbial parameters, which determines the effectiveness of ecological processes in rivers. Measurements of bacterioplankton abundance (BA) and extracellular enzyme activity (EEA) were based on fluorescent markers. The bacterial community structure was determined by 16S rRNA gene amplicon sequencing (Illumina). The results indicate spatial variation in bacterioplankton abundance. Temporal variation was not significant. Lipase and aminopeptidase had the highest level of activity. EEA was not correlated with bacterial abundance but was significantly correlated with temperature. Moreover, differences in lipase, α-glucosidase and β-glucosidase activity levels between spring and summer were noted. At the same time, the location of sampling site had a significant influence on aminopeptidase activity. The taxonomic analysis of bacterioplankton communities in the Brda River indicated that, although different numbers of OTUs were recorded in the studied river sections, bacterioplankton biodiversity did not change significantly along the river with distance downstream. Anthropogenically modified river sections were characterized by the dominance of Flavobacterium (Bacterioidetes) and hgcl clade (Actinobacteria) taxa, known for their ability to produce extracellular enzymes. PCoA analysis revealed that the sites located in the lower river course (urban area) had the most similar bacterial community structure (β-diversity). The study provides new insight into the changes in microbial communities along the river and emphasizes the potential impact of anthropogenization on these processes.
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35
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Bioavailable Nutrients (N and P) and Precipitation Patterns Drive Cyanobacterial Blooms in Missisquoi Bay, Lake Champlain. Microorganisms 2021; 9:microorganisms9102097. [PMID: 34683418 PMCID: PMC8537112 DOI: 10.3390/microorganisms9102097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/04/2023] Open
Abstract
Anthropogenic activities release large amounts of nitrogen (N) and phosphorus (P) nutrients into the environment. Sources of nutrients include surface and sub-surface runoffs from agricultural practices with the application of chemical fertilizers and manure as well as combined sewer overflows (CSOs). Nutrient runoffs contribute to the eutrophication of aquatic ecosystems and enhance the growth of cyanobacteria. Precipitation is an important driving force behind the runoff of nutrients from agricultural fields into surrounding water bodies. To understand the dynamics between nutrient input, precipitation and cyanobacterial growth in Missisquoi Bay, Lake Champlain (Quebec), one location in Pike River (a major tributary into the bay) and four locations in Missisquoi Bay were monitored from April to November in 2017 and 2018. Biweekly water samples were analyzed using chemical methods and high-throughput sequencing of 16S rRNA gene amplicons. High concentrations of N and P were typically measured in April and May. Three major spikes in nutrient concentrations were observed in early and mid-summer as well as early fall, all of which were associated with intense cumulative precipitation events of 40 to 100 mm within 7 days prior to sampling. Despite the high concentrations of nutrients in the spring and early summer, the cyanobacterial blooms appeared in mid to late summer as the water temperature increased. Dolichospermum sp. was the major bloom-forming cyanobacterium during both summers. A second intense bloom event of Microcystis was also observed in the fall (October and November) for both years. Variation in the cyanobacteria population was strongly associated with inorganic and readily available fractions of N and P such as nitrites and nitrates (NOx), ammonia (NH3) and dissolved organic phosphorus (DOP). During blooms, total Kjeldahl nitrogen (TKN) and total particulate phosphorus (TPP) fractions had a substantial influence on total nitrogen (TN) and total phosphorus (TP) concentrations, respectively. The abundance of bacteria involved in the metabolism of nitrogen compared to that of phosphorus revealed the importance of nitrogen on overall microbial dynamics as well as CB formation in the bay. Our findings emphasize the combined influence of precipitation events, temperature and several bioavailable fractions of nitrogen and phosphorus on cyanobacterial bloom episodes.
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Tóth E, Toumi M, Farkas R, Takáts K, Somodi C, Ács É. Insight into the hidden bacterial diversity of Lake Balaton, Hungary. Biol Futur 2021; 71:383-391. [PMID: 34554460 DOI: 10.1007/s42977-020-00040-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/17/2020] [Indexed: 11/26/2022]
Abstract
In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.
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Affiliation(s)
- E Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary.
| | - M Toumi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - R Farkas
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - K Takáts
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Cs Somodi
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - É Ács
- MTA Centre for Ecological Research, Danube Research Institute, Budapest, Hungary
- National University of Public Service, Faculty of Water Sciences, Baja, Hungary
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37
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Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021; 22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
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Affiliation(s)
- Masood ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Wanqiu Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 200,000, China
| | - Ru Feng
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
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Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
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Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
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Reddy B, Dubey SK. Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26990-27005. [PMID: 33501578 DOI: 10.1007/s11356-021-12342-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.
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Affiliation(s)
- Bhaskar Reddy
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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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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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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Rasmussen AN, Damashek J, Eloe-Fadrosh EA, Francis CA. In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay. MICROBIAL ECOLOGY 2021; 81:601-616. [PMID: 33150499 DOI: 10.1007/s00248-020-01621-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA
| | - Julian Damashek
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA
- Department of Biology, Utica College, Utica, NY, 13502, USA
| | - Emiley A Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA.
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Gweon HS, Bowes MJ, Moorhouse HL, Oliver AE, Bailey MJ, Acreman MC, Read DS. Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environ Microbiol 2021; 23:484-498. [PMID: 33258525 PMCID: PMC7898806 DOI: 10.1111/1462-2920.15337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 01/26/2023]
Abstract
The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.
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Affiliation(s)
- Hyun S. Gweon
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- School of Biological SciencesUniversity of ReadingReadingRG6 6EXUK
| | - Michael J. Bowes
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Heather L. Moorhouse
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
- Lancaster Environment CentreLancaster UniversityLibrary Avenue, LancasterLA1 4YQUK
| | - Anna E. Oliver
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | - Mark J. Bailey
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
| | | | - Daniel S. Read
- UK Centre for Ecology & HydrologyWallingford, OxfordshireOX10 8BBUK
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Soldatova E, Dong Y, Li J, Liu Y, Zan J, Boeckx P, Sun Z. Nitrogen transformation and pathways in the shallow groundwater-soil system within agricultural landscapes. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:441-459. [PMID: 33000346 DOI: 10.1007/s10653-020-00733-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The present study considers the behavior of nitrogen compounds in the shallow groundwater-soil system as necessary for the functioning of the nitrogen cycle within agricultural landscapes and one of the first steps of the formation of groundwater chemical composition. Data were collected in 2011-2018 within the Poyang Lake area (Jiangxi Province, China), where agricultural landscapes prevail. The soil and groundwater samples were taken in different periods of an agricultural season at the beginning of the agricultural season (spring) and after harvesting (autumn). The combined geochemical data on the chemical and microbiological composition of the soils and shallow groundwater and isotopic data on dissolved nitrate allowed researchers to resolve that nitrogen enters the system in the form of organic compounds, particularly, due to the soil fertilization at the beginning of the agricultural season. Organic nitrogen compounds transform into nitrate under the influence of nitrifiers in the soil before getting the shallow aquifer, where the occurrence of denitrification is suggested. Within the Ganjiang and Xiushui interfluve, reducing conditions, together with the formation of clay minerals from the aqueous solution, may serve a geochemical barrier for the accumulation of nitrogen compounds preventing the transformation of ammonium to nitrate and providing its sorption. It also should be noted that bacterial diversity in the shallow groundwater has a strong relation with the amount of nitrate in the system, whereas in the soil, it is connected with sampling depth.
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Affiliation(s)
- Evgeniya Soldatova
- Laboratory of Modeling Hydrogeochemical and Hydrothermal Processes, Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119991, Moscow, Russia.
| | - Yihui Dong
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Jiale Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Yajie Liu
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Jinjing Zan
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Pascal Boeckx
- Isotope Bioscience Laboratory (ISOFYS), Ghent University, 9000, Ghent, Belgium
| | - Zhanxue Sun
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
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46
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Genomes of the " Candidatus Actinomarinales" Order: Highly Streamlined Marine Epipelagic Actinobacteria. mSystems 2020; 5:5/6/e01041-20. [PMID: 33323418 PMCID: PMC7771536 DOI: 10.1128/msystems.01041-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge. “Candidatus Actinomarinales” was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial “Candidatus Nanopelagicales” or marine alphaproteobacterial Pelagibacterales. Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. “Ca. Actinomarinales” show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales. Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first “Ca. Actinomarinales” phages, including a prophage, with metaviromic islands related to sialic acid cleavage. IMPORTANCE Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge. Here, we study 182 genomes belonging to the only known exclusively marine pelagic group of the phylum Actinobacteria. The aquatic branch of this phylum is largely known from environmental sequencing studies (single-amplified genomes [SAGs] and metagenome-assembled genomes [MAGs]), and we have collected and analyzed the available information present in databases about the “Ca. Actinomarinales.” They are among the most streamlined microbes to live in the epipelagic zone of the ocean, and their study is critical to obtain a proper view of the diversity of Actinobacteria and their role in aquatic ecosystems.
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Matson PG, Boyer GL, Bridgeman TB, Bullerjahn GS, Kane DD, McKay RML, McKindles KM, Raymond HA, Snyder BK, Stumpf RP, Davis TW. Physical drivers facilitating a toxigenic cyanobacterial bloom in a major Great Lakes tributary. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:2866-2882. [PMID: 33707786 PMCID: PMC7942401 DOI: 10.1002/lno.11558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The Maumee River is the primary source for nutrients fueling seasonal Microcystis-dominated blooms in western Lake Erie's open waters though such blooms in the river are infrequent. The river also serves as source water for multiple public water systems and a large food services facility in northwest Ohio, USA. On 20 September 2017, an unprecedented bloom was reported in the Maumee River estuary within the Toledo metropolitan area, which triggered a recreational water advisory. Here we (1) explore physical drivers likely contributing to the bloom's occurrence, and (2) describe the toxin concentration and bacterioplankton taxonomic composition. A historical analysis using ten-years of seasonal river discharge, water level, and local wind data identified two instances when high-retention conditions occurred over ≥10 days in the Maumee River estuary: in 2016 and during the 2017 bloom. Observation by remote sensing imagery supported the advection of cyanobacterial cells into the estuary from the lake during 2017 and the lack of an estuary bloom in 2016 due to a weak cyanobacterial bloom in the lake. A rapid-response survey during the 2017 bloom determined levels of the cyanotoxins, specifically microcystins, in excess of recreational contact limits at sites within the lower 20 km of the river while amplicon sequencing found these sites were dominated by Microcystis. These results highlight the need to broaden our understanding of physical drivers of cyanobacterial blooms within the interface between riverine and lacustrine systems, particularly as such blooms are expected to become more prominent in response to a changing climate.
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Affiliation(s)
- Paul G. Matson
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Present address: Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gregory L. Boyer
- Department of Chemistry, State University of New York–College of Environment Science and Forestry, Syracuse, NY 13210, USA
| | - Thomas B. Bridgeman
- Lake Erie Center and Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Douglas D. Kane
- Division of Natural Science, Applied Science, and Mathematics, Defiance College, Defiance, OH 43512, USA
- Present address: Biology and Environmental Sciences Department and National Center for Water Quality Research, Heidelberg University, Tiffin, OH 44883, USA
| | - R. Michael L. McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Katelyn M. McKindles
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Heather A. Raymond
- Division of Drinking and Ground Waters, Ohio Environmental Protection Agency, Columbus, OH 43216, USA
- Present address: College of Food, Agriculture, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Brenda K. Snyder
- Lake Erie Center and Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Richard P. Stumpf
- National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean Science, Silver Spring, MD 20910, USA
| | - Timothy W. Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
- Author of correspondence:
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Ferrera I, Reñé A, Funosas D, Camp J, Massana R, Gasol JM, Garcés E. Assessment of microbial plankton diversity as an ecological indicator in the NW Mediterranean coast. MARINE POLLUTION BULLETIN 2020; 160:111691. [PMID: 33181960 DOI: 10.1016/j.marpolbul.2020.111691] [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: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
High-throughput sequencing of microbial assemblages has been proposed as an alternative methodology to the traditional ones used in marine monitoring and environmental assessment. Here, we evaluated pico- and nanoplankton diversity as ecological indicators in NW Mediterranean coastal waters by comparing their diversity in samples subjected to varying degrees of continental pressures. Using metabarcoding of the 16S and 18S rRNA genes, we explored whether alphadiversity indices, abundance of Operational Taxonomic Units and taxonomic groups (and their ratios) provide information on the ecological quality of coastal waters. Our results revealed that only eukaryotic diversity metrics and a limited number of prokaryotic and eukaryotic taxa displayed potential in assessing continental influences in our surveyed area, resulting thus in a restrained potential of microbial plankton diversity as an ecological indicator. Therefore, incorporating microbial plankton diversity in environmental assessment could not always result in a significant improvement of current marine monitoring strategies.
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Affiliation(s)
- Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain; Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain.
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - David Funosas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Jordi Camp
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain.
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Pascual-Benito M, Ballesté E, Monleón-Getino T, Urmeneta J, Blanch AR, García-Aljaro C, Lucena F. Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115254. [PMID: 32721842 DOI: 10.1016/j.envpol.2020.115254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m3/s in winter to 0.006 m3/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.
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Affiliation(s)
- Miriam Pascual-Benito
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; The Water Research Institute, University of Barcelona, Montalegre 6, 08001, Barcelona, Spain
| | - Elisenda Ballesté
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; The Water Research Institute, University of Barcelona, Montalegre 6, 08001, Barcelona, Spain
| | - Toni Monleón-Getino
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; BIOST3 (Research Group in Biostatistics, Bioinformatics and Data Science), GRBIO (Research Group in Biostatistics and Bioinformatics), Spain
| | - Jordi Urmeneta
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; The Water Research Institute, University of Barcelona, Montalegre 6, 08001, Barcelona, Spain
| | - Cristina García-Aljaro
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; The Water Research Institute, University of Barcelona, Montalegre 6, 08001, Barcelona, Spain.
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain; The Water Research Institute, University of Barcelona, Montalegre 6, 08001, Barcelona, Spain
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50
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Shao Q, Lin Z, Zhou C, Yan X. Bacterioplankton assembly and interspecies interactions follow trajectories of Gymnodinium-diatom bloom. MARINE ENVIRONMENTAL RESEARCH 2020; 160:105010. [PMID: 32907730 DOI: 10.1016/j.marenvres.2020.105010] [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: 12/02/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
The underlying mechanisms of bacterioplankton community assembly and interspecies interactions during harmful algal blooms remain largely unclear. Using 16S rRNA gene amplicon sequencing, we analyzed the bacterioplankton communities over the continuous course of saxitoxin-producing Gymnodinium catenatum blooms and two diatom (i.e., Skeletonema costatum and Chaetoceros curvisetus) blooms in an anthropogenically controlled and eutrophic bay, East China Sea. The succession of bacterioplankton communities correlated with changes in the dynamics of algal species. Deterministic versus stochastic bacterioplankton community assemblage processes were quantified, demonstrating that stochastic processes increased when algal blooms happened. The occurrence of algal blooms caused weaker bacterioplankton interspecies interactions and higher degrees of cooperative activities, changed keystone taxa and diminished the stability of bacterial communities. These findings consequently have important implications for our understanding of bacterioplankton community ecology during algal blooms.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Zhongzhou Lin
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China; Ningbo Institute of Oceanography, Ningbo 315832, China
| | - Chengxu Zhou
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
| | - Xiaojun Yan
- Key Laboratory of Applied Marine Biotechnology, School of Marine Science, Ministry of Education, Ningbo University, Ningbo 315832, China.
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