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McKnight MM, Neufeld JD. Comammox Nitrospira among dominant ammonia oxidizers within aquarium biofilter microbial communities. Appl Environ Microbiol 2024; 90:e0010424. [PMID: 38899882 PMCID: PMC11267875 DOI: 10.1128/aem.00104-24] [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: 01/19/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Nitrification by aquarium biofilters transforms ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Prior to the discovery of complete ammonia-oxidizing ("comammox" or CMX) Nitrospira, previous research revealed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Here, we profiled aquarium biofilter microbial communities and quantified the abundance of all three known ammonia oxidizers using 16S rRNA gene sequencing and quantitative PCR (qPCR), respectively. Biofilter and water samples were each collected from representative residential and commercial freshwater and saltwater aquaria. Distinct biofilter microbial communities were associated with freshwater and saltwater biofilters. Comammox Nitrospira amoA genes were detected in all 38 freshwater biofilter samples (average CMX amoA genes: 2.2 × 103 ± 1.5 × 103 copies/ng) and dominant in 30, whereas AOA were present in 35 freshwater biofilter samples (average AOA amoA genes: 1.1 × 103 ± 2.7 × 103 copies/ng) and only dominant in 7 of them. The AOB were at relatively low abundance within biofilters (average of 3.2 × 101 ± 1.1 × 102 copies of AOB amoA genes/ng of DNA), except for the aquarium with the highest ammonia concentration. For saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. Additional sequencing of Nitrospira amoA genes revealed differential distributions, suggesting niche adaptation based on water chemistry (e.g., ammonia, carbonate hardness, and alkalinity). Network analysis of freshwater microbial communities demonstrated positive correlations between nitrifiers and heterotrophs, suggesting metabolic and ecological interactions within biofilters. These results demonstrate that comammox Nitrospira plays a previously overlooked, but important role in home aquarium biofilter nitrification. IMPORTANCE Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) Nitrospira were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox Nitrospira, and highlights the value of aquaria as microcosms for studying nitrifier ecology.
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Affiliation(s)
| | - Josh D. Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Tan Q, Wu H, Zheng L, Wang X, Xing Y, Tian Q, Zhang Y. Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum. WATER RESEARCH 2024; 255:121480. [PMID: 38518415 DOI: 10.1016/j.watres.2024.121480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Haoming Wu
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing 100875, PR China.
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Qi Tian
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yaoxin Zhang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
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Ma J, Niu A, Liao Z, Qin J, Xu S, Lin C. Factors affecting N 2O fluxes from heavy metal-contaminated mangrove soils in a subtropical estuary. MARINE POLLUTION BULLETIN 2023; 186:114425. [PMID: 36462424 DOI: 10.1016/j.marpolbul.2022.114425] [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: 06/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
A 1-year field monitoring program was carried out to observe seasonal variation in N2O fluxes at two typical mangrove wetlands in a subtropical estuary. The soils in the island-type mangrove wetland had a higher level of heavy metal(loid) contamination and a lower level of salinity compared to the small bay-type mangrove wetland. While there was a high level of similarity in the seasonal variation pattern of N2O fluxes between the two investigated sites with both being significantly higher in summer than in other seasons, the average of N2O fluxes in the island-type mangrove wetland was 7.19 μg·m-2·h-1, which tended to be lower compared to the small bay-type mangrove wetland (15.63 μg·m-2·h-1). Overall, N2O flux was closely related to soil-borne heavy metal(loid)s, showing a trend to decrease with increasing concentration of these heavy metal(loid)s. The N2O fluxes increased with decreasing abundance of either denitrifiers or nitrifiers. But the opposite was observed for the anammox bacteria present in the soils. The anammox bacteria were more sensitive to heavy metal(loid) stress but more tolerated high salinity encountered in the investigated soils compared to the denitrifiers or nitrifiers. It appears that anammox reactions mediated by anammox bacteria played a key role in affecting the spatial variation in N2O fluxes from the mangrove soils in the study area. And an increased level of ammonium in soils tended to promote the activity of anammox bacteria and consequently enhanced N2O emission from the mangrove soils.
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Affiliation(s)
- Jiaojiao Ma
- School of Geography, South China Normal University, Guangzhou 510631, China; Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Anyi Niu
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Zhenni Liao
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Junhao Qin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Songjun Xu
- School of Geography, South China Normal University, Guangzhou 510631, China.
| | - Chuxia Lin
- Faculty of Science, Engineering and Built Environment, Deakin University, Burwood, VIC 3125, Australia.
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Xie C, Ma X, Zhao Y, Dai T, Song W, Qi Q, Feng J, Cui X, Zhou J, Huang X, Qi F, Zeng Y, Zhou J, Lin G, Yang Y. Nitrogen addition and warming rapidly alter microbial community compositions in the mangrove sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157992. [PMID: 35970461 DOI: 10.1016/j.scitotenv.2022.157992] [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: 04/19/2022] [Revised: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The mangrove ecosystem is an important CO2 sink with an extraordinarily high primary productivity. However, it is vulnerable to the impact of climate warming and eutrophication. While there has been extensive research on plant growth and greenhouse gas emission in mangrove ecosystems, microbial communities, the primary biogeochemical cycling drivers, are much less understood. Here, we examined whether short-term experimental treatments: (1) eutrophication with a supplement of 185 g N m-2·year-1 (N), (2) 3°C warming (W), and (3) the dual treatment of N and W (NW) were sufficient to alter microbial communities in the sediment. After 4 months of experiments, most environmental factors remained unchanged. However, N had significant, strong effects on bacterial, fungal, and functional community compositions, while the effects of W on microbial communities were weaker. N increased bacterial richness, phylogenetic diversity, and evenness, owing to stronger stochastic processes induced by eutrophication. There were no interactive effects of N and W on bacterial, fungal, and functional community compositions, suggesting that joint effects of N and W were additive. Concomitant with higher N2O efflux induced by N, the relative abundances of most bacterial nitrogen cycling genes were increased or remained changed by N. In contrast, N decreased or did not change those of most bacterial carbon degradation genes, while W increased or did not change the relative abundances of most of bacterial and fungal carbon degradation genes, implying higher carbon degradation potentials. As the most abundant inorganic nitrogenous species in mangrove sediment, ammonium was a key factor in shaping microbial functional communities. Collectively, our findings showed that microbial community compositions in the mangrove sediment were highly sensitive to short-term N and W treatments, giving rise to ecological consequences such as higher N2O efflux.
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Affiliation(s)
- Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yan Zhao
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Tianjiao Dai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weimin Song
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; The Yellow River Delta Ecology Research Station of Coastal Wetland, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianxiang Feng
- Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China; School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaowei Cui
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Jian Zhou
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Fei Qi
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guanghui Lin
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Mu S, Chen X, Song B, Wu C, Li Q. Enhanced performance and mechanism of the combined process of ozonation and a semiaerobic aged refuse biofilter for mature landfill leachate treatment. CHEMOSPHERE 2022; 308:136432. [PMID: 36115471 DOI: 10.1016/j.chemosphere.2022.136432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
A semiaerobic aged refuse biofilter (SAARB) can effectively treat mature landfill leachate (ML), but prolonged operation can lead to the enrichment of pollutants in the biofilter, resulting in severely degraded treatment performance. In this study, we constructed a combination process of ozonation and a SAARB to treat ML based on the principles of selective oxidation of aromatic organics by ozone and the preference of microorganisms for ozonation products. The results showed that the removal of organic and nitrogen pollutants became extremely poor after long-term treatment of ML using the SAARB alone. The decrease of chemical oxygen demand (COD), light absorbance at 254 nm (UV254), NH4+, and total nitrogen (TN) improved significantly after recirculating the ozonated ML effluent (OLE) into the SAARB, and the removal extents increased significantly to 63.59% (COD), 26.14% (UV254), 92.85% (NH4+), and 52.04% (TN), respectively. In addition, the recirculation of OLE enhanced the complete denitrification and tolerance to high NH4+ loading by the SAARB. An analysis of the community composition of 16S_bacteria and ammonia oxidation bacteria (AOB) showed that long-term treatment of ML using the SAARB alone had difficulty enriching the dominant functional bacteria. In the OLE recirculation stage, environmental factors-such as influent organic matter species and concentration, nitrogen pollutant concentration, and pH-were changed to influence the community composition of 16S_bacteria and AOB and enrich functional bacteria (e.g., Truepera, Luteibacter, and Nitrosospira). Therefore, ozonation combined with a SAARB can remove organic and nitrogen pollutants more effectively. In particular, this can be used to solve the problem of inefficient total nitrogen removal using the SAARB alone. This study provides a theoretical reference for the efficient and stable operation of biological processes when treating ML.
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Affiliation(s)
- Shiqi Mu
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Xinglong Chen
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Bowen Song
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Chuanwei Wu
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Qibin Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China.
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6
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Chen J, Zhou Z, Gu JD. Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments. MARINE ENVIRONMENTAL RESEARCH 2022; 181:105739. [PMID: 36084374 DOI: 10.1016/j.marenvres.2022.105739] [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: 07/23/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.
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Affiliation(s)
- Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China; Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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Changes in Temporal Dynamics and Factors Influencing the Environment of the Bacterial Community in Mangrove Rhizosphere Sediments in Hainan. SUSTAINABILITY 2022. [DOI: 10.3390/su14127415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural characteristics of the rhizosphere soil’s microbial community is crucial to understanding the ecological function of mangroves. However, the mechanism influencing mangrove plants in soil microbial communities has yet to be determined. Here, the mangrove ecosystem of Xinying Mangrove National Wetland Park in Hainan Province was taken as the research object. The microbial communities, external regulatory factors, and the relationship between communities were analyzed using 16S rRNA high-throughput sequencing in the rhizosphere and non-rhizosphere sediments of mangrove forests under different spatiotemporal conditions. The results showed that there was no significant difference in the α-diversity of the bacterial community between the rhizosphere and non-rhizosphere sediments. However, β-diversity was significantly different. Redundancy analysis (RDA) showed that other environmental factors besides sulfide and Fe2+ affected the bacterial community structure in sediments. The co-occurrence pattern analysis of bacteria in the mangrove ecosystem indicates that the bacteria in rhizosphere sediments were more closely related than those in non-rhizosphere sediments. The results reveal significant differences between the rhizosphere and non-rhizosphere bacterial community diversity, structure, and their interaction in the mangrove ecosystem. Therefore, the ecological system of the mangrove wetland needs to be preserved and rehabilitated, which would have a tremendous impact on the sustainable development.
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. WATER RESEARCH X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses. Arch Microbiol 2022; 204:109. [PMID: 34978623 DOI: 10.1007/s00203-021-02661-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 09/28/2021] [Accepted: 10/13/2021] [Indexed: 11/02/2022]
Abstract
Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.
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Kasak K, Espenberg M, Anthony TL, Tringe SG, Valach AC, Hemes KS, Silver WL, Mander Ü, Kill K, McNicol G, Szutu D, Verfaillie J, Baldocchi DD. Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N 2O production potential. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113562. [PMID: 34425499 DOI: 10.1016/j.jenvman.2021.113562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/03/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
The concentration of nitrous oxide (N2O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N2O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N2O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N2O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N2O emissions.
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Affiliation(s)
- Kuno Kasak
- University of Tartu, Institute of Ecology and Earth Sciences, Department of Geography, Tartu, Estonia.
| | - Mikk Espenberg
- University of Tartu, Institute of Ecology and Earth Sciences, Department of Geography, Tartu, Estonia
| | - Tyler L Anthony
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Berkeley, CA, USA
| | | | - Alex C Valach
- Climate and Agriculture Group, Agroscope, Switzerland
| | | | - Whendee L Silver
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Berkeley, CA, USA
| | - Ülo Mander
- University of Tartu, Institute of Ecology and Earth Sciences, Department of Geography, Tartu, Estonia
| | - Keit Kill
- University of Tartu, Institute of Ecology and Earth Sciences, Department of Geography, Tartu, Estonia
| | - Gavin McNicol
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Daphne Szutu
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Berkeley, CA, USA
| | - Joseph Verfaillie
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Berkeley, CA, USA
| | - Dennis D Baldocchi
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Berkeley, CA, USA
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11
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Lin G, He Y, Lu J, Chen H, Feng J. Seasonal variations in soil physicochemical properties and microbial community structure influenced by Spartina alterniflora invasion and Kandelia obovata restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149213. [PMID: 34311375 DOI: 10.1016/j.scitotenv.2021.149213] [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: 04/10/2021] [Revised: 06/05/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Spartina alterniflora invasion has initiated one of the greatest changes to occur in coastal wetlands in China, and ecological replacement using mangrove species such as Kandelia obovata is an effective method for controlling these invasions. The effects of S. alterniflora invasions and subsequent K. obovata restorations on soil microbial community structures in different seasons are still not fully understood. In this study, soil samples were collected from six vegetation types (unvegetated mudflat, invasive S. alterniflora stands, one-/eight-/ten-year K. obovata restoration areas, and native mature K. obovata forests) in summer and winter. The variations in the soil microbial community structure between the vegetation types across two seasons were then characterized based on 16S rRNA gene sequencing, and the physicochemical properties that shaped the microbial communities were also determined. The invasion and restoration processes significantly influenced microbial community diversity, composition, and putative functions in different seasonal patterns. Microbial communities from a ten-year restoration area and a native mature K. obovata area shared more similarities than other areas. In both seasons, the key environmental factors driving microbial community included total carbon and nitrogen content, the ratio of carbon to nitrogen, and the soil pH. In addition, total sulfur and total phosphorus contents significantly contributed to structuring microbial communities in summer and winter, respectively. This study provides insights into microbial diversity, composition, and functional profiles in association with physicochemical impacts, with the aim of understanding microbial ecological functions during the invasion and restoration processes in wetland ecosystems.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Yongni He
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Hui Chen
- College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Jianxiang Feng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China.
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12
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Puthusseri RM, Nair HP, Johny TK, Bhat SG. Insights into the response of mangrove sediment microbiomes to heavy metal pollution: Ecological risk assessment and metagenomics perspectives. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113492. [PMID: 34385112 DOI: 10.1016/j.jenvman.2021.113492] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Rapid urbanisation and ensuing anthropogenic pollution lead to an escalated occurrence of heavy metals and metal-resistant bacteria in the soil ecosystem. Mangrove ecosystems are particularly vulnerable to heavy metal bioaccumulation and often act as metal sinks of the coastal areas. As a consequence, the microbial population in mangrove sediments develop multifarious metal tolerance mechanisms to combat metal toxicity. In this context, metagenomic investigation of two mangroves, viz. Mangalavanam and Puthuvypin from the heavily populated metropolitan city, Cochin (Central Kerala, India) was undertaken to discern the metal resistance functions and taxonomic diversity of the microbial consortia. Estimation of heavy metal content using Inductively Coupled Plasma Atomic Emission Spectrometer (ICP-MS) identified the abundance of zinc, chromium, nickel copper, lead, arsenic, and cadmium in the mangrove sediments. Ecological risk index values indicated high cadmium contamination of the two estuarine samples. Whole metagenome shotgun sequencing of the Central Kerala mangroves and comparative analysis with mangrove metal resistomes from other geographical regions revealed the prevalence of cobalt-zinc-cadmium resistance and preponderance of Proteobacteria in all the datasets. Cation efflux system protein CusA constituted the majority of the reads at the function level. Comparative analysis of taxonomy identified the dominance of Anaeromyxobacter, Geobacter, Pseudomonas, Candidatus Solibacter, and Pelobacter in the mangrove datasets. Non-metric multidimensional scaling analysis of the metal resistance genes depicted strong geographical clustering of the function and composition of metal resistant bacteria, suggesting a strong innate resilience of microbiome towards anthropogenic perturbations. More robust studies with intensive sampling will enhance our understanding of the occurrence, interactions, and functions of microbial heavy metal resistome in mangrove ecosystems.
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Affiliation(s)
- Rinu Madhu Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
| | - Harisree Paramel Nair
- School of Life Science, Faculty of Science and Engineering, Anglia Ruskin University, East Road, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK.
| | - Tina Kollannoor Johny
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
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13
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Lv J, Yuan R, Wang S. Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112876. [PMID: 34098351 DOI: 10.1016/j.jenvman.2021.112876] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.
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Affiliation(s)
- Jiali Lv
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China; Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101408, China; Sino-Danish Centre for Education and Research, Beijing, 101408, China
| | - Ruiqiang Yuan
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China.
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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14
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Wang H, Bagnoud A, Ponce-Toledo RI, Kerou M, Weil M, Schleper C, Urich T. Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils. mSystems 2021; 6:e0054621. [PMID: 34463572 DOI: 10.1128/msystems.00546-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Alexandre Bagnoud
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Micha Weil
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
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15
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Chen W, Wen D. Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion. ENVIRONMENTAL MICROBIOME 2021; 16:10. [PMID: 33941277 PMCID: PMC8091715 DOI: 10.1186/s40793-021-00377-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/02/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora (S. alterniflora) invasion in China. However, little is known about mangrove sediment microbial community assembly processes and interactions under S. alterniflora invasion. Here, we investigated the assembly processes and co-occurrence networks of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China. RESULTS Assembly of overall archaeal and bacterial communities was driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analyses showed that the network structure of bacteria was more complex than that of the archaea. The keystone taxa often had low relative abundances (conditionally rare taxa), suggesting low abundance taxa may significantly contribute to network stability. Moreover, S. alterniflora invasion increased bacterial and archaeal drift process (part of stochastic processes), and improved archaeal network complexity and stability, but decreased the network complexity and stability of bacteria. This could be attributed to S. alterniflora invasion influenced microbial communities diversity and dispersal ability, as well as soil environmental conditions. CONCLUSIONS This study fills a gap in the community assembly and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem under S. alterniflora invasion. Thereby provides new insights of the plant invasion on mangrove microbial biogeographic distribution and co-occurrence network patterns.
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Affiliation(s)
- Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871 China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871 China
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16
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Lv J, Niu Y, Yuan R, Wang S. Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes. Microorganisms 2021; 9:microorganisms9040782. [PMID: 33917984 PMCID: PMC8068392 DOI: 10.3390/microorganisms9040782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years, different responses of archaea and bacteria to environmental changes have attracted increasing scientific interest. In the mid-latitude region, Fen River receives water transferred from the Yellow River, electrical conductivity (EC), concentrations of Cl- and Na+ in water, total phosphorus (TP), and Olsen phosphorus (OP) in sediments were significantly affected by water transfer. Meanwhile, temperature and oxidation-reduction potential (ORP) of water showed significant seasonal variations. Based on 16S rRNA high-throughput sequencing technology, the composition of bacteria and archaea in sediments was determined in winter and summer, respectively. Results showed that the dominance of bacterial core flora decreased and that of archaeal core flora increased after water diversion. The abundance and diversity of bacterial communities in river sediments were more sensitive to anthropogenic and naturally induced environmental changes than that of archaeal communities. Bacterial communities showed greater resistance than archaeal communities under long-term external disturbances, such as seasonal changes, because of rich species composition and complex community structure. Archaea were more stable than bacteria, especially under short-term drastic environmental disturbances, such as water transfer, due to their insensitivity to environmental changes. These results have important implications for understanding the responses of bacterial and archaeal communities to environmental changes in river ecosystems affected by water diversion.
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Affiliation(s)
- Jiali Lv
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yangdan Niu
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
| | - Ruiqiang Yuan
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Correspondence:
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
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17
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Ma J, Ullah S, Niu A, Liao Z, Qin Q, Xu S, Lin C. Heavy metal pollution increases CH 4 and decreases CO 2 emissions due to soil microbial changes in a mangrove wetland: Microcosm experiment and field examination. CHEMOSPHERE 2021; 269:128735. [PMID: 33127108 DOI: 10.1016/j.chemosphere.2020.128735] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Mangrove plays an important role in modulating global warming through substantial blue carbon storage relative to their greenhouse gas emission potential. The presence of heavy metals in mangrove wetlands can influence soil microbial communities with implications for decomposition of soil organic matter and emission of greenhouse gases. In this study, field monitoring and a microcosm experiment were conducted to examine the impacts of heavy metal pollution on soil microbial communities and greenhouse gas fluxes. The results show that heavy metal pollution decreased the richness and diversity of the overall soil microbial functional groups (heterotrophs and lithotrophs); however, it did not inhibit the activities of the methanogenic communities, possibly due to their stronger tolerance to heavy metal toxicity compared to the broader soil microbial communities. Consequently, the presence of heavy metals in the mangrove soils significantly increased the emission of CH4 while the emission of CO2 as a proxy of soil microbial respiration was decreased. The soil organic carbon content could also buffer the effect of heavy metal pollution and influence CO2 emissions due to reduced toxicity to microbes. The findings have implications for understanding the complication of greenhouse gas emissions by heavy metal pollution in mangrove wetlands.
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Affiliation(s)
- Jiaojiao Ma
- School of Geography, South China Normal University, Guangzhou, 510631, China; School of Geography, Earth and Environmental Sciences, And Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Sciences, And Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Anyi Niu
- School of Geography, South China Normal University, Guangzhou, 510631, China
| | - Zhenni Liao
- School of Geography, South China Normal University, Guangzhou, 510631, China
| | - Qunhao Qin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Songjun Xu
- School of Geography, South China Normal University, Guangzhou, 510631, China.
| | - Chuxia Lin
- Faculty of Science, Engineering and Built Environment, Deakin University, Burwood, VIC, 3125, Australia.
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18
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Liu Z, Zhang C, Wei Q, Zhang S, Quan Z, Li M. Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140456. [PMID: 32629251 DOI: 10.1016/j.scitotenv.2020.140456] [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: 04/21/2020] [Revised: 06/21/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.
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Affiliation(s)
- Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Cuijing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Qiaoyan Wei
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, PR China
| | - Siyu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China.
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19
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Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
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20
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Mukherji S, Ghosh A, Bhattacharyya C, Mallick I, Bhattacharyya A, Mitra S, Ghosh A. Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110481. [PMID: 32203775 DOI: 10.1016/j.ecoenv.2020.110481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anandita Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Chandrima Bhattacharyya
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Ivy Mallick
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anish Bhattacharyya
- Department of Biochemistry, 35 Ballygunge Circular Road, University of Calcutta, Kolkata, 700019, India
| | - Suparna Mitra
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Thoresby Place, Leeds, LS1 3EX, W. Yorkshire, United Kingdom
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India.
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21
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Cao L, Yu X, Liu C, Liu M, Chen J, Qin H, Liang C, Xu Q, Penttinen P. Alteration of soil nitrifiers and denitrifiers and their driving factors during intensive management of Moso bamboo (Phyllostachys pubescens). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135236. [PMID: 31841899 DOI: 10.1016/j.scitotenv.2019.135236] [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: 07/17/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Long-term intensive management, such as inorganic fertilization and soil tillage, have been reported to decrease soil organic carbon content (SOC) and diversity of soil bacterial communities, as well as increase N2O emissions in moso bamboo forests. However, the response of the N-cycling soil microbial community to intensive management remains unclear. To address this, we examined the effects of intensive moso bamboo management on nitrifying and denitrifying microorganisms. Soils receiving non-management (NM) and 10, 15, 20, and 25 years of intensive management (IM10, IM15, IM20, IM25) were characterized using quantitative real-time PCR (qPCR) and high-through sequencing methods. Our results showed that abundances of ammonia monooxygenase (amoA) from ammonia-oxidizing archaea (AOA) significantly increased (P < 0.05) and were greatest in IM15 (8.37 × 107 copies/g dry soils) and IM25 (5.42 × 107 copies/g dry soils) in top- and subsoils, respectively, while nitrous oxide reductase (nosZ) abundance significantly decreased by 59.1% (topsoil) and 36.4% (subsoil) in IM20 (P < 0.05). GroupI.1a-associated affiliating to AOA, and Bradyrhizobium affiliating to nosZ, were keys groups for nitrifiers and denitrifiers, respectively, and showed the greatest variations in response to long-term intensive management. Abundances of ammonia-oxidizing bacteria (AOB) and the nitrite reductase gene nirS were less affected, as were the dominant Nitrosospira species belonging to the AOB community. Except the AOB amoA abundance, soil nitrogen was found to be the main factor influencing the abundance, diversity, and composition of nitrifying genes, while denitrifying genes were mainly affected by SOC and available potassium, indicating that different factors control populations of nitrifiers and denitrifiers. Collectively, our study revealed that groupings of nitrifying and denitrifying microorganisms responded differently to intensive management. This information is of potential value towards identifying strategies to minimize nitrogen loss in moso bamboo plantations.
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Affiliation(s)
- Linhua Cao
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xiao Yu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Caixia Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Ming Liu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Junhui Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Hua Qin
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Chenfei Liang
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Qiufang Xu
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
| | - Petri Penttinen
- College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
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22
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Wang S, Zheng X, Xia H, Shi D, Fan J, Wang P, Yan Z. Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing. PLoS One 2019; 14:e0218611. [PMID: 31226149 PMCID: PMC6588238 DOI: 10.1371/journal.pone.0218611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Huijuan Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Di Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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23
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Feng W, Yan X, Le XC. Editorial: Effects of metal contamination on ammonia-oxidizing microorganisms in a freshwater reservoir. J Environ Sci (China) 2019; 79:364-366. [PMID: 30784461 DOI: 10.1016/j.jes.2019.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 06/09/2023]
Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2G3, Canada
| | - Xiaowen Yan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2G3, Canada.
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24
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Li Y, Zheng L, Zhang Y, Liu H, Jing H. Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments. Sci Rep 2019; 9:5739. [PMID: 30952929 PMCID: PMC6450915 DOI: 10.1038/s41598-019-42260-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/26/2019] [Indexed: 01/21/2023] Open
Abstract
Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.
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Affiliation(s)
- Yingdong Li
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Liping Zheng
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
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25
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Li N, Chen Y, Zhang Z, Chang S, Huang D, Chen S, Guo Q, Xie S, Bing Y. Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment. J Environ Sci (China) 2019; 77:392-399. [PMID: 30573104 DOI: 10.1016/j.jes.2018.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 06/09/2023]
Abstract
It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 102-1.35 × 107 copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.
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Affiliation(s)
- Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China..
| | - Yao Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Sha Chang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Dawei Huang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China..
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou 510655, China.
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26
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Capdeville C, Pommier T, Gervaix J, Fromard F, Rols JL, Leflaive J. Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance. Front Microbiol 2019; 9:3337. [PMID: 30697204 PMCID: PMC6340982 DOI: 10.3389/fmicb.2018.03337] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/24/2018] [Indexed: 11/13/2022] Open
Abstract
Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagal. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.
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Affiliation(s)
| | - Thomas Pommier
- Ecologie Microbienne, INRA, UMR 1418, CNRS, UMR 5557, Université Lyon 1, Villeurbanne, France
| | - Jonathan Gervaix
- Ecologie Microbienne, INRA, UMR 1418, CNRS, UMR 5557, Université Lyon 1, Villeurbanne, France
| | - François Fromard
- EcoLab, CNRS, INPT, UPS, Université de Toulouse, Toulouse, France
| | - Jean-Luc Rols
- EcoLab, CNRS, INPT, UPS, Université de Toulouse, Toulouse, France
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27
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Wang X, Wang S, Shi G, Wang W, Zhu G. Factors driving the distribution and role of AOA and AOB in Phragmites communis
rhizosphere in riparian zone. J Basic Microbiol 2019; 59:425-436. [DOI: 10.1002/jobm.201800581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/01/2018] [Accepted: 12/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guoshuai Shi
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
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28
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Luo L, Gu JD. Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment. MICROBIAL ECOLOGY 2018; 76:92-101. [PMID: 27623965 DOI: 10.1007/s00248-016-0844-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.
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Affiliation(s)
- Ling Luo
- College of Environmental Sciences, Sichuan Agricultural University, Huimin Road, Chengdu, Sichuan Province, People's Republic of China.
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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29
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Su Y, Wang W, Wu D, Huang W, Wang M, Zhu G. Stimulating ammonia oxidizing bacteria (AOB) activity drives the ammonium oxidation rate in a constructed wetland (CW). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:87-95. [PMID: 29248709 DOI: 10.1016/j.scitotenv.2017.12.084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 06/07/2023]
Abstract
An integrated approach to document high ammonium oxidation rate in Guanjinggang constructed wetland (GJG-CW) was performed and the results showed that the substantial ammonium oxidation rate could be obtained by enhancing Ammonia Oxidizing Bacteria (AOB) activity rather than Ammonia Oxidizing Archaea (AOA) activity. In the plant-bed/ditch system, ditch center and plant-bed fringe were two active zones for NH4+-N removal with ammonium oxidation rate peaking at 2.98±0.04 and 2.15±0.02mgNkg-1d-1, respectively. The enhanced AOB activity were achieved by increasing water level fluctuations, extending hydraulic retention time (HRT) and stimulating substrate availability, which subsequently enhanced NH4+-N removal by 34.06% in GJG-CW. However, the high AOB activity was not correlated with high AOB abundance, but was instead mostly determined by specific AOB taxa, particularly Nitrosomonas, which dominated in the active AOB. The increased cell-specific AOA activity and high AOA diversity were also achieved using those engineering measures. Although the AOA activity decreased overall with extended HRT and increased NH4+-N contents in GJG-CW, AOA still played a major role on ammonium oxidation in plant-bed soil. The study illustrated that artificially enhancing AOB activity and certain species in anthropogenically polluted water ecosystems would be an effective strategy to improve NH4+-N removal.
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Affiliation(s)
- Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Di Wu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wei Huang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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30
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Marcos MS, Barboza AD, Keijzer RM, Laanbroek HJ. Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle. MICROBIAL ECOLOGY 2018; 75:997-1008. [PMID: 29063148 PMCID: PMC5906487 DOI: 10.1007/s00248-017-1091-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/07/2017] [Indexed: 05/13/2023]
Abstract
Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.
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Affiliation(s)
- Magalí S Marcos
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CONICET), Puerto Madryn, Argentina
| | - Anthony D Barboza
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands.
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.
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31
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He H, Zhen Y, Mi T, Fu L, Yu Z. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China. Front Microbiol 2018; 9:116. [PMID: 29456526 PMCID: PMC5801408 DOI: 10.3389/fmicb.2018.00116] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.
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Affiliation(s)
- Hui He
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, China
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32
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Huang F, Xu Y, Tan Z, Wu Z, Xu H, Shen L, Xu X, Han Q, Guo H, Hu Z. Assessment of pollutions and identification of sources of heavy metals in sediments from west coast of Shenzhen, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:3647-3656. [PMID: 29164465 DOI: 10.1007/s11356-017-0362-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
The sediment samples were collected from eight sites located in the Pearl River Estuary and the Shenzhen Bay of the west coast of Shenzhen. The distributions of the seven elements Zn, Cr, Hg, Cu, Cd, Pb and As have been analyzed, and their pollution degrees, corresponding potential ecological risks and source identifications have been studied using geo-accumulation index, potential ecological risk index and integrated multivariate statistical methods, respectively. Based on the calculated geo-accumulation indices, the contamination levels of all elements in the Pearl River Estuary are similar to those in the Shenzhen Bay, reflecting that these elements in the study areas have similar sources because of the adequate seawater exchange. The calculated potential ecological risk indices suggest that Cd and Hg are at considerable and moderate risk, respectively. Multivariate statistical analyses further reveal that Zn, Hg, Cd and Pb originated from industrial wastewater, while Cr and Cu are mainly from both industrial wastewater and agricultural sources, and As is mainly from natural source. These research results provide baseline information for both the coastal environment management and the worldwide heavy metal distribution and assessment.
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Affiliation(s)
- Fengwen Huang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yang Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- Shenzhen High School, Shenzhen, 518001, China
| | - Zhenhao Tan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zhibing Wu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Hong Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Liangliang Shen
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xu Xu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Qingguo Han
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Hai Guo
- Air Quality Studies, Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Marine Bioresources and Ecology/Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China.
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Li X, Zhang M, Liu F, Chen L, Li Y, Li Y, Xiao R, Wu J. Seasonality distribution of the abundance and activity of nitrification and denitrification microorganisms in sediments of surface flow constructed wetlands planted with Myriophyllum elatinoides during swine wastewater treatment. BIORESOURCE TECHNOLOGY 2018; 248:89-97. [PMID: 28673518 DOI: 10.1016/j.biortech.2017.06.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Surface flow constructed wetlands (SFCWs) planted with Myriophyllum elatinoides for treatment of swine wastewater were examined to evaluate the effect of season, segment (site S1, S2, and S3), and treatment (100mgL-1 TN, T1; 300mgL-1 TN, T2; 500mgL-1 TN, T3) on the activity, and abundances of nitrifying and, denitrifying microorganisms, and on the abundance of sediment bacteria. The activity and abundances of nitrifiers, denitrifiers, and the abundance of bacteria were the highest in T3 samples, especially in S1 (P<0.05). The potential nitrification rate (PNR) was highest in the summer and potential denitrification rate (PDR) showed an increasing trend over seasons. The abundance of ammonia-oxidizing bacteria (AOB) was strongly correlated with PNR, while abundance of denitrifying gene (nirK) was strongly correlated with PDR. These results indicate that M. elatinoides SFCWs for swine wastewater treatment stimulate the growth of nitrifiers, denitrifiers and bacteria in sediments.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Miaomiao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China.
| | - Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan Province, PR China
| | - Yuyuan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Rulin Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
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Ramanathan B, Boddicker AM, Roane TM, Mosier AC. Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage. Front Microbiol 2017; 8:2136. [PMID: 29209281 PMCID: PMC5701628 DOI: 10.3389/fmicb.2017.02136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022] Open
Abstract
Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 104 – 4.9 × 107 archaeal amoA copies ∗ μg DNA-1, 1.5 × 103 – 5.3 × 105 AOB 16S rRNA copies ∗ μg DNA-1, and 1.3 × 106 – 7.7 × 107Nitrospira nxrB copies ∗ μg DNA-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.
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Affiliation(s)
- Bhargavi Ramanathan
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Timberley M Roane
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, United States
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Wu RN, Meng H, Wang YF, Lan W, Gu JD. A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils. MICROBIAL ECOLOGY 2017; 74:910-922. [PMID: 28808742 DOI: 10.1007/s00248-017-1045-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 05/20/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.
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Affiliation(s)
- Ruo-Nan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
- Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen, 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, SAR, People's Republic of China.
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Jiang X, Wu Y, Liu G, Liu W, Lu B. The effects of climate, catchment land use and local factors on the abundance and community structure of sediment ammonia-oxidizing microorganisms in Yangtze lakes. AMB Express 2017; 7:173. [PMID: 28905318 PMCID: PMC5597559 DOI: 10.1186/s13568-017-0479-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.
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Wang P, Di HJ, Cameron KC, Tan Q, Podolyan A, Zhao X, McLaren RG, Hu C. The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:2476-2483. [PMID: 27817146 DOI: 10.1007/s11356-016-8030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg-1), Zn (20 and 50 mg kg-1), and Cd (2 and 10 mg kg-1) were incubated for 14 days and then treated with 500 mg kg-1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.
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Affiliation(s)
- Pengcheng Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand.
| | - Keith C Cameron
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Qiling Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Ron G McLaren
- Centre for Soil and Environmental Research, Lincoln University, Christchurch, New Zealand
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
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New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria. Appl Microbiol Biotechnol 2016; 101:1267-1287. [PMID: 28032194 DOI: 10.1007/s00253-016-8013-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/13/2023]
Abstract
PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH4+ and NH4+/Σ(NO3- + NO2-) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.
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Wang L, Huang X, Zheng TL. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing. MARINE POLLUTION BULLETIN 2016; 109:281-289. [PMID: 27262497 DOI: 10.1016/j.marpolbul.2016.05.068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 06/05/2023]
Abstract
This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (p<0.05). Despite explaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361021, China
| | - Xu Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361021, China; Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Tian-Ling Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361021, China
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Bernhard AE, Sheffer R, Giblin AE, Marton JM, Roberts BJ. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill. Front Microbiol 2016; 7:854. [PMID: 27375576 PMCID: PMC4899434 DOI: 10.3389/fmicb.2016.00854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.
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Affiliation(s)
| | | | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA
| | - John M Marton
- Louisiana Universities Marine Consortium Chauvin, LA, USA
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Chen Q, Zhao Q, Li J, Jian S, Ren H. Mangrove succession enriches the sediment microbial community in South China. Sci Rep 2016; 6:27468. [PMID: 27265262 PMCID: PMC4893734 DOI: 10.1038/srep27468] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.
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Affiliation(s)
- Quan Chen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qian Zhao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jing Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Shuguang Jian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Hai Ren
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
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Zhang J, Zhou X, Chen L, Chen Z, Chu J, Li Y. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes. World J Microbiol Biotechnol 2016; 32:85. [DOI: 10.1007/s11274-016-2042-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/29/2016] [Indexed: 11/24/2022]
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Pyrosequencing-Based Seasonal Observation of Prokaryotic Diversity in Pneumatophore-Associated Soil of Avicennia marina. Curr Microbiol 2015; 72:68-74. [DOI: 10.1007/s00284-015-0920-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/09/2015] [Indexed: 02/02/2023]
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Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:968582. [PMID: 26346219 PMCID: PMC4543378 DOI: 10.1155/2015/968582] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/25/2015] [Accepted: 07/14/2015] [Indexed: 11/25/2022]
Abstract
Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.
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Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. ISME JOURNAL 2015; 10:85-96. [PMID: 26140533 PMCID: PMC4604658 DOI: 10.1038/ismej.2015.101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/13/2015] [Accepted: 05/08/2015] [Indexed: 11/09/2022]
Abstract
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.
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Affiliation(s)
- Eduard Vico Oton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | | | - Graeme W Nicol
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,Laboratoire Ampère UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, Ecully CEDEX, France
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
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Luo ZH, Xu W, Li M, Gu JD, Zhong TH. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean. Antonie van Leeuwenhoek 2015; 108:329-42. [PMID: 26014493 DOI: 10.1007/s10482-015-0485-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.
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Affiliation(s)
- Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen, 361005, People's Republic of China,
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Zhou Z, Chen J, Cao H, Han P, Gu JD. Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes. Front Microbiol 2015; 5:789. [PMID: 25774150 PMCID: PMC4343527 DOI: 10.3389/fmicb.2014.00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 106 copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 106 copies per gram dry weight) was observed, but higher abundance (6.9 × 106 to 1.02 × 108 copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 105 copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 105 copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 108 copies per gram dry weight) and pmoA gene (1.56 × 107 copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Jing Chen
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong China
| | - Ping Han
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Wen D. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China. Appl Microbiol Biotechnol 2015; 99:4495-507. [DOI: 10.1007/s00253-014-6352-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 12/11/2022]
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Liu J, Tian Y, Wang D, Lu Y, Zhang J, Zuo W. Quantitative analysis of ammonia-oxidizing bacteria in a combined system of MBR and worm reactors treating synthetic wastewater. BIORESOURCE TECHNOLOGY 2014; 174:294-301. [PMID: 25463811 DOI: 10.1016/j.biortech.2014.09.082] [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: 06/19/2014] [Revised: 09/12/2014] [Accepted: 09/17/2014] [Indexed: 06/04/2023]
Abstract
The Static Sequencing Batch Worm Reactor (SSBWR) followed by the MBR (S-MBR) is one of the advanced excess sludge treatments. In this paper, the control MBR (C-MBR) and the SSBWR-MBR were operated in parallel to study the changes of NH3-N removal and ammonia oxidizing bacteria (AOB). The results showed that the capacity of NH3-N removal of the S-MBR was improved by the worm reactors along with the operation. The S-MBR was favorable because it selected for the higher activity of the ammonia oxidization and better cells appearance of the sludge. The five species (Nitrosomonas, Betaproteobacteria, Clostridium, Dechloromonas and Bacteria) were found to be significantly correlate with the ammonia oxidization functions and performance of NH3-N removal in the C-MBR and S-MBR. The Nitrosomonas, Betaproteobacteria and Dechloromonas remained and eventually enriched in the S-MBR played a primary role in the NH3-N removal of the S-MBR.
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Affiliation(s)
- Jia Liu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Dezhen Wang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Yaobin Lu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Jun Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Zuo
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
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Wang HT, Su JQ, Zheng TL, Yang XR. Impacts of vegetation, tidal process, and depth on the activities, abundances, and community compositions of denitrifiers in mangrove sediment. Appl Microbiol Biotechnol 2014; 98:9375-87. [DOI: 10.1007/s00253-014-6017-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 07/30/2014] [Accepted: 08/05/2014] [Indexed: 12/18/2022]
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