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Noyer M, Bernard M, Verneau O, Palacios C. Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49685-49702. [PMID: 36780079 DOI: 10.1007/s11356-023-25637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/14/2023]
Abstract
Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.
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Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.,Unit. for Environmental Sciences and Management, North-West University, Potchefstroom, ZA-2520, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France. .,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.
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Shen J, Liu H, Zhou H, Chen R. Specific characteristics of the microbial community in the groundwater fluctuation zone. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:76066-76077. [PMID: 35665458 DOI: 10.1007/s11356-022-21166-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Groundwater level fluctuation is a common natural phenomenon that causes alternate changes in oxygen, moisture, and biogeochemical processes in sediments. Microbes are sensitive to these environmental changes. Therefore, a specific microbial community is proposed to form in the groundwater fluctuation zone (GFZ). The vertical distributions of microbial abundance, diversity, and functional microbes and genes in sediment profiles were investigated, focusing on the GFZ, using high-throughput 16S rRNA gene sequencing, qPCR, and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) approach. The relationships between chemical variables and microbial community structure were investigated by redundancy analysis (RDA). Results showed that the microbial abundance and microbial community richness and diversity were higher in the sediments of the GFZ. The nitrate reducers prefer to stay just below the groundwater level in the GFZ. The predominant microbes in the GFZ functioned as nitrifiers and Fe-oxidizers. The specific community in the GFZ is mainly related to NO3- and Fe(III) in the sediment. Consequently, the biochemical processes nitrification and Fe- and Mn-oxidation sequentially happen above the nitrate-reduction zone near the groundwater level in the GFZ. These results provide new knowledge in the biogeochemistry cycle of the GFZ and its disturbance on the vertical distribution and transport of biogenic elements and contaminants.
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Affiliation(s)
- Junhao Shen
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Hui Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China.
| | - Huazhong Zhou
- Plant Protection Station of Hubei Province, Wuhan, 430070, People's Republic of China
| | - Rong Chen
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
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3
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Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station. Int Microbiol 2022; 25:571-586. [DOI: 10.1007/s10123-022-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
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Zhang W, Liu W, He S, Chen Q, Han J, Zhang Q. Mixed plantations of Metasequoia glyptostroboides and Bischofia polycarpa change soil fungal and archaeal communities and enhance soil phosphorus availability in Shanghai, China. Ecol Evol 2021; 11:7239-7249. [PMID: 34188809 PMCID: PMC8216939 DOI: 10.1002/ece3.7532] [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: 10/29/2020] [Revised: 02/19/2021] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
Soil degradation has been found in urban forests in Shanghai, especially in the pure plantations. Mixed plantations are considered to improve soil quality because they can stimulate organic matter cycling and increase soil carbon and nutrient content. Although soil microbes play crucial roles in regulating soil biogeochemical processes, little is known about how mixed plantations affect soil microbial communities, including bacteria, archaea, and fungi. Here, we evaluated soil chemical properties, abundances and compositions of soil bacterial, archaeal, and fungal communities, and enzyme activities in pure and mixed Metasequoia glyptostroboides and Bischofia polycarpa plantations, located in Shanghai, China. The results showed that soil available phosphorus content in the mixed plantation of M. glyptostroboides and B. polycarpa was significantly higher than that in pure plantations, while no significant difference was observed in the content of soil organic carbon, total and available nitrogen, total and available potassium among the three studied plantations. We found higher fungal abundance in the mixed plantation, when compared to both pure plantations. Moreover, fungal abundance was positively correlated with the content of soil available phosphorus. No significant difference was found in the abundance and diversity of bacterial and archaeal community among the three studied plantations. A similarity analysis (ANOSIM) showed that mixed plantation significantly altered the community composition of archaea and fungi, accompanied with an increase of alkaline phosphatase activity. However, ANOSIM analysis of bacterial communities showed that there was no significant group separation among different plantations. Overall, results from this study indicated that fungal and archaeal communities were more sensitive to aboveground tree species than bacterial community. Moreover, mixed plantations significantly increased the activity of alkaline phosphatase and the content of soil available phosphorus, suggesting that afforestation with M. glyptostroboides and B. polycarpa is an effective way to alleviate phosphorus deficiency in urban forests in Shanghai, China.
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Affiliation(s)
- Weiwei Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Wen Liu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Shanwen He
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Qingchu Chen
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Jigang Han
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
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5
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Lin J, Chen N, Yuan X, Tian Q, Hu A, Zheng Y. Impacts of human disturbance on the biogeochemical nitrogen cycle in a subtropical river system revealed by nitrifier and denitrifier genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141139. [PMID: 32745858 DOI: 10.1016/j.scitotenv.2020.141139] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Human activities have largely modified nitrogen (N) sources supply, cycling and export from land to ocean. Nitrification and denitrification are vital processes alleviating N pollution in aquatic ecosystems but the diverse responses and niche of microbial N retention to human disturbance are still understudied. Here we investigated the changes in N species and functional genes in the urban, agriculture and reservoir river sections of the Jiulong River (southeast China). Our results show that ammonia-oxidizing bacteria (AOB) (Nitrosomonas) were dominant in the urban river section receiving ammonium-rich sewage that enhanced nitrification and subsequent denitrification, while ammonia-oxidizing archaea (AOA) was more abundant than AOB in the river section flowing through areas of pomelo (Citrus maxima) agriculture with low pH, low ammonium and very high nitrate input. Warm temperatures and large total suspended matter (TSM) in the wet season promoted growth of nitrifiers and denitrifiers, which were mostly particle-attached. The potential river N retention through gaseous N removal (PRN2O and PRN2) in the agriculture section with huge N loading was among the lowest. Strong nitrification and denitrification were suspected to occur in the agricultural acid soil system rather than in the river network. In addition, the decreased TSM and N concentration promoted free-living microbes in the reservoir. The highest PRN2 and N2 production observed in the reservoir in the dry season implied that denitrification and anammox occurring in sediments was likely to increase N retention. This study suggests the diverse factors involved in processing of N pollution among diverse landscapes.
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Affiliation(s)
- Jingjie Lin
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, China.
| | - Xin Yuan
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qing Tian
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yi Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
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6
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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7
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Wang H, Yang X, Chen Q, Su JQ, Mulla SI, Rashid A, Hu A, Yu CP. Response of prokaryotic communities to extreme precipitation events in an urban coastal lagoon: A case study of Yundang lagoon, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135937. [PMID: 31841847 DOI: 10.1016/j.scitotenv.2019.135937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Increasing extreme precipitation events (EPEs) can induce biogeochemical disturbances in the coastal lagoon ecosystems. Very little is known about the response of prokaryotic communities to such influences, which are the key components mediating the biogeochemical cycling in lagoons. Here 16S rRNA gene amplicon sequencing and high-through quantitative PCR (HT-qPCR) were employed to investigate the distribution of prokaryotic communities and fecal indicator genes in the surface waters of Yundang lagoon, Xiamen, China during EPEs, respectively. Prokaryotic communities from rainwaters, influents (IFs) and effluents (EFs) from a nearby wastewater treatment plant were also characterised. The results indicated a significant variation in the composition of lagoon prokaryotic communities compared with rainwaters, IFs and EFs. Multivariate and phylogenetic signal analyses revealed that environmental filtering, mainly controlled by salinity, was the major ecological process responsible for the temporal succession of lagoon prokaryotic communities during EPEs. Moreover, the pollution indicator taxa (based on amplicon sequencing) and fecal indicator genes (based on HT-qPCR) demonstrated that EPEs may induce sewage overflows and fecal pollution (mainly from humans and dogs), resulting in an increase in the relative abundance of pollution indicator taxa and genes in Yundang lagoon. Network analysis illustrated that the number of network edges and keystone species decreased along the sampling times, implying that EPEs-induced disturbances may affect prokaryotic species associations. Taken together, this study provides an enhanced understanding of the responses of lagoon prokaryotic communities to EPEs-induced disturbances.
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Affiliation(s)
- Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Qingfu Chen
- Yundang Lake Management Center, Xiamen, Fujian 361004, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore 560 064, India
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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Chen S, Wang P, Liu H, Xie W, Wan XS, Kao SJ, Phelps TJ, Zhang C. Population dynamics of methanogens and methanotrophs along the salinity gradient in Pearl River Estuary: implications for methane metabolism. Appl Microbiol Biotechnol 2019; 104:1331-1346. [DOI: 10.1007/s00253-019-10221-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/11/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023]
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9
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Liao H, Yu K, Duan Y, Ning Z, Li B, He L, Liu C. Profiling microbial communities in a watershed undergoing intensive anthropogenic activities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1137-1147. [PMID: 30180322 DOI: 10.1016/j.scitotenv.2018.08.103] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
In lotic ecosystems highly susceptible to anthropogenic activities, the influences of environmental variables on microbial communities and their functions remain poorly understood, despite our rapidly increasing sequencing ability. In this study, we profiled the microbial communities in the hyporheic sediments of a watershed undergoing intensive anthropogenic activities via next-generation sequencing of 16S rRNA V4-V5 hypervariable regions on Illumina MiSeq platform. Tidal impacts on microbial communities were investigated via co-occurrence networks. In addition, the influences of physicochemical variables including salinity, and the concentrations of nutrients, organic matter and heavy metals on the microbial communities were explored via canonical correspondence analyses. The sediment samples were collected from 19 sites covering the whole main river stem of the target watershed (n = 19; Maozhou river watershed, Shenzhen, China). The samples were sub-divided in the field for microbiological analyses and measurements of physicochemical variables. The results indicated that core microbiome was associated with archaea methanogens and bacteria members from Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Synergistetes and Firmicutes, among which, gram-negative and anaerobic bacteria genera contributing to the cycling of carbon, nitrogen and sulfur were predominant. Site-specific microbiomes were revealed that may serve as indicators of local environmental conditions (e.g., members affiliated to Oceanospirillales were abundant at sites with salt intrusion). Distinct microbial co-occurrence networks were identified for non-tidal, inter-tidal and tidal sites. Major environmental factors influencing microbial community composition included the concentrations of nitrate and bicarbonate in river water, pore water concentrations of sulfate, dissolved organic carbon and electrical conductivity, as well as manganese concentrations associated with the solid sediment. Collectively, the results of this study provide fundamental insights into the influence of environmental perturbations on microbial community composition in a lotic system, which may aid in the design of effective remediation and/or restoration strategies in the target watershed and beyond.
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Affiliation(s)
- Hehuan Liao
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Kai Yu
- School of Environmental Studies, China University of Geoscience, Wuhan, Hubei 430074, China
| | - Yanhua Duan
- School of Environmental Studies, China University of Geoscience, Wuhan, Hubei 430074, China
| | - Zigong Ning
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Binrui Li
- School of Environmental Studies, China University of Geoscience, Wuhan, Hubei 430074, China
| | - Leiyu He
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chongxuan Liu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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10
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Liu X, Pan J, Liu Y, Li M, Gu JD. Diversity and distribution of Archaea in global estuarine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:349-358. [PMID: 29753224 DOI: 10.1016/j.scitotenv.2018.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 05/12/2023]
Abstract
Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.
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Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, People's Republic of China.
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11
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Isabwe A, Yang JR, Wang Y, Liu L, Chen H, Yang J. Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 630:658-667. [PMID: 29494974 DOI: 10.1016/j.scitotenv.2018.02.210] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 01/28/2018] [Accepted: 02/17/2018] [Indexed: 05/20/2023]
Abstract
Although the influence of microbial community assembly processes on aquatic ecosystem function and biodiversity is well known, the processes that govern planktonic communities in human-impacted rivers remain largely unstudied. Here, we used multivariate statistics and a null model approach to test the hypothesis that environmental conditions and obstructed dispersal opportunities, dictate a deterministic community assembly for phytoplankton and bacterioplankton across contrasting hydrographic conditions in a subtropical mid-sized river (Jiulong River, southeast China). Variation partitioning analysis showed that the explanatory power of local environmental variables was larger than that of the spatial variables for both plankton communities during the dry season. During the wet season, phytoplankton community variation was mainly explained by local environmental variables, whereas the variance in bacterioplankton was explained by both environmental and spatial predictors. The null model based on Raup-Crick coefficients for both planktonic groups suggested little evidences of the stochastic processes involving dispersal and random distribution. Our results showed that hydrological change and landscape structure act together to cause divergence in communities along the river channel, thereby dictating a deterministic assembly and that selection exceeds dispersal limitation during the dry season. Therefore, to protect the ecological integrity of human-impacted rivers, watershed managers should not only consider local environmental conditions but also dispersal routes to account for the effect of regional species pool on local communities.
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Affiliation(s)
- Alain Isabwe
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China; University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Jun R Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China; University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Yongming Wang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China
| | - Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, PR China.
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12
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Liao K, Bai Y, Huo Y, Jian Z, Hu W, Zhao C, Qu J. Integrating microbial biomass, composition and function to discern the level of anthropogenic activity in a river ecosystem. ENVIRONMENT INTERNATIONAL 2018; 116:147-155. [PMID: 29679777 DOI: 10.1016/j.envint.2018.04.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/01/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
Anthropogenic activities (e.g., wastewater discharge and pesticide and fertilizer use) have considerable impact on the biotic properties of natural aquatic ecosystems, especially the microbial community and function. Microbes can respond to anthropogenic activities and are thus potential indicators of activity levels. Several reports have documented the impacts of anthropogenic activities on the variations in the microbial community, but the direct use of microbial community indices to discern anthropogenic activity levels remains limited. Here, we integrated flow cytometry, 16S rRNA sequencing, and natural organic matter metabolism determination to investigate microbial biomass, composition, and function in three areas along a gradient of anthropogenic disturbance (less-disturbed mountainous area, wastewater-discharge urban area, and pesticide and fertilizer used agricultural area) in a river ecosystem. Multiple statistical methods were used to explore the causal relationships between changes in environmental factors and microbial variation. Results showed that anthropogenic activities (e.g., wastewater discharge, pesticide and fertilizer use) facilitated bacterial production, affected dominant species distribution, and accelerated natural organic matter (NOM) metabolic rate by microbes. After screening the possible factors influencing the microbial community, we determined that cyanobacterial concentration could be a diagnostic indicator of nutrient levels. We also developed a NOM metabolic index to quantitatively reflect the holistic influence of nutrients and xenobiotics.
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Affiliation(s)
- Kailingli Liao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yang Huo
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Jian
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wanchao Hu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Archaeal community compositions in tilapia pond systems and their influencing factors. World J Microbiol Biotechnol 2018; 34:43. [PMID: 29492679 DOI: 10.1007/s11274-018-2412-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/12/2018] [Indexed: 10/17/2022]
Abstract
Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities' response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.
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Soliman T, Reimer JD, Yang SY, Villar-Briones A, Roy MC, Jenke-Kodama H. Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan. Front Microbiol 2017; 8:2451. [PMID: 29321767 PMCID: PMC5732179 DOI: 10.3389/fmicb.2017.02451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/27/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan “Kaichu-Doro” Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60–80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.
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Affiliation(s)
- Taha Soliman
- Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami, Japan.,Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan.,Genetics and Genetic Engineering Research Group, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Japan
| | - Sung-Yin Yang
- Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami, Japan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Alejandro Villar-Briones
- Imaging and Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami, Japan
| | - Michael C Roy
- Imaging and Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami, Japan
| | - Holger Jenke-Kodama
- Microbiology and Biochemistry of Secondary Metabolites Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami, Japan
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15
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Hu A, Ju F, Hou L, Li J, Yang X, Wang H, Mulla SI, Sun Q, Bürgmann H, Yu CP. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol 2017; 19:4993-5009. [DOI: 10.1111/1462-2920.13942] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Feng Ju
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Sikandar I. Mulla
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Helmut Bürgmann
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- Graduate Institute of Environmental Engineering; National Taiwan University; Taipei 106 Taiwan
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Hu A, Wang H, Yang X, Hou L, Li J, Li S, Yu CP. Seasonal and spatial variations of prokaryoplankton communities in a salinity-influenced watershed, China. FEMS Microbiol Ecol 2017; 93:3966710. [DOI: 10.1093/femsec/fix093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
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17
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Fan L, Song C, Meng S, Qiu L, Zheng Y, Wu W, Qu J, Li D, Zhang C, Hu G, Chen J. Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River. Sci Rep 2016; 6:39147. [PMID: 27966673 PMCID: PMC5155431 DOI: 10.1038/srep39147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/18/2016] [Indexed: 12/14/2022] Open
Abstract
Bacterioplankton and archaeaplankton communities play key roles in the biogeochemical processes of water, and they may be affected by many factors. In this study, we used high-throughput 16S rRNA gene sequencing to profile planktonic bacterial and archaeal community compositions in the upper section of the tidal reach in Yangtze River. We found that the predominant bacterial phyla in this river section were Proteobacteria, Firmicutes, and Actinobacteria, whereas the predominant archaeal classes were Halobacteria, Methanomicrobia, and unclassified Euryarchaeota. Additionally, the bacterial and archaeal community compositions, richnesses, functional profiles, and ordinations were affected by the spatial heterogeneity related to the concentration changes of sulphate or nitrate. Notably, the bacterial community was more sensitive than the archaeal community to changes in the spatial characteristics of this river section. These findings provide important insights into the distributions of bacterial and archaeal communities in natural water habitats.
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Affiliation(s)
- Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jianhong Qu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Cong Zhang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
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18
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Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China. Appl Microbiol Biotechnol 2016; 101:3379-3391. [PMID: 27942905 DOI: 10.1007/s00253-016-8019-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Abstract
Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH4+-N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.
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