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Fortune J, van de Kamp J, Holmes B, Bodrossy L, Gibb K, Kaestli M. Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106500. [PMID: 38626627 DOI: 10.1016/j.marenvres.2024.106500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.
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Affiliation(s)
- Julia Fortune
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Environment, Parks and Water Security, Northern Territory Government, Australia.
| | | | | | | | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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2
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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2024; 69:595-612. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [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: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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Chen J, Zhao S, Gan Y, Wu J, Dai J, Chao HJ, Yan D. Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122063. [PMID: 37330184 DOI: 10.1016/j.envpol.2023.122063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0-6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3--N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3--N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3--N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.
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Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Shuo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yating Gan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jing Wu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jingcheng Dai
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hong-Jun Chao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Dazhong Yan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
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Wang H, Li P, Liu X, Zhang J, Stein LY, Gu JD. An overlooked influence of reactive oxygen species on ammonia-oxidizing microbial communities in redox-fluctuating aquifers. WATER RESEARCH 2023; 233:119734. [PMID: 36804337 DOI: 10.1016/j.watres.2023.119734] [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: 11/30/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Reactive oxygen species (ROS) are ubiquitous in O2-perturbed aquifers, but their role in shaping ammonia-oxidizing microbial communities is not clear. This study examined the dynamic responses of ammonia-oxidizing microorganisms (AOMs) in redox-fluctuating aquifers to ROS via field investigation and in-lab verification using transcriptomes/ metatranscriptome and RT-qPCR. Ammonia-oxidizing archaea (AOA) dominated recharge aquifers with lower ROS levels, whereas ammonia-oxidizing bacteria (AOB) and heterotrophic nitrifying aerobic bacteria (HNB) predominated in discharge areas with higher ROS levels. Similar succession in AOM enrichments was found in that the dominant AOMs changed from AOA Nitrosopumilus to AOB Nitrosomonas with increasing ROS. Ammonia oxidation and antioxidant capacity differed significantly among three AOM isolates exposed to ROS. ROS decreased the amoA gene expression of AOA strain Nitrososphaera viennensis PLX03, accompanied by inhibited ammonia oxidation capacity. By contrast, the catalase and superoxide dismutase activities of the AOB strain Nitrosomonas oligotropha PLL12 and HNB strain Pseudomonas aeruginosa PLL01 increased, and the antioxidant genes katG, sodA, ahpC, and ahpF were significantly upregulated. These results demonstrate that ROS exert an important influence on AOMs in redox-fluctuating aquifers. This study improves our understanding of the ecological niches of AOMs in surface/subsurface environments.
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Affiliation(s)
- Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, Wuhan, 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, 430074, PR China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, Wuhan, 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, 430074, PR China.
| | - Xiaohan Liu
- State Key Laboratory of Biogeology and Environmental Geology, Wuhan, 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, 430074, PR China
| | - Jing Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Wuhan, 430074, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, 430074, PR China
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ji-Dong Gu
- Environmental Science and Engineering, Guangdong Technion Israel Institute of Technology, Guangdong, 515063, PR China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, Guangdong, 515063, PR China
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de Chaves MG, Merloti LF, de Souza LF, Américo-Pinheiro JHP, Kozusny-Andreani DI, de Souza Moreira FM, Tsai SM, Navarrete AA. Ecological co-occurrence and soil physicochemical factors drive the archaeal community in Amazonian soils. Arch Microbiol 2023; 205:31. [DOI: 10.1007/s00203-022-03372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/18/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
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Ai J, Li Y, Lv Y, Zhong X, Li J, Yang A. Study on microbes and antibiotic resistance genes in karst primitive mountain marshes - A case study of Niangniang Mountain in Guizhou, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114210. [PMID: 36306620 DOI: 10.1016/j.ecoenv.2022.114210] [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: 04/20/2022] [Revised: 09/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Previous research on antibiotic resistance genes and microorganisms centered on those in urban sewage treatment plants, breeding farms, hospitals and others with serious antibiotic pollution. However, at present, there are evident proofs that antibiotic resistance genes (ARGs) indeed exist in a primitive environment hardly without any human's footprints. Accordingly, an original karst mountain swamp ecosystem in Niangniang Mountain, Guizhou, China, including herbaceous swamp, shrub swamp, sphagnum bog and forest swamp, was selected to analyze the physical and chemical parameters of sediments. Moreover, microbial compositions, functions, as well as their connections with ARGs were assayed and analyzed using metagenomic technology. The results showed that there was no significant difference in the dominant microorganisms and ARGs in the four marshes, in which the dominant bacteria phyla were Proteobacteria (37.82 %), Acidobacteriota (22.17 %) and Actinobacteriota (20.64 %); the dominant archaea Euryarchaeota. (1.00 %); and the dominant eukaryotes Ascomycota (0.07 %), with metabolism as their major functions. Based on the ARDB database, the number of ARGs annotated reached 209 including 30 subtypes, and the dominant ARGs were all Bacitracin resistance genes (bacA, 84.77 %). In terms of the diversity of microorganisms and ARGs, the herbaceous swamp ranked the top, and the shrub swamp were at the bottom. Correlation analysis between microorganisms and resistance genes showed that, apart from aac2ic, macB, smeE, tetQ, and tetL, other ARGs were positively correlated with microorganisms. Among them, baca coexisted with microorganisms. Pearson correlation analysis results showed that contrary to ARGs, microorganisms were more affected by environmental factors.
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Affiliation(s)
- Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Qiannan Ecological Environment Monitoring Center, Duyun 558000, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China.
| | - Yang Lv
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Xiong Zhong
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
| | - Aijiang Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
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Meng S, Peng T, Wang H, Huang T, Gu JD, Hu Z. Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments. Appl Microbiol Biotechnol 2022; 106:5811-5822. [PMID: 35941255 DOI: 10.1007/s00253-022-12104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China.,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China.
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DeCastro ME, Escuder-Rodríguez JJ, Becerra M, Rodríguez-Belmonte E, González-Siso MI. Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide. Front Microbiol 2021; 12:769065. [PMID: 34899652 PMCID: PMC8661477 DOI: 10.3389/fmicb.2021.769065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.
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Affiliation(s)
| | | | | | | | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
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Semanti P, Robin RS, Purvaja R, Ramesh R. Fatty acid signatures of sediment microbial community in the chronically polluted mangrove ecosystem. MARINE POLLUTION BULLETIN 2021; 172:112885. [PMID: 34461371 DOI: 10.1016/j.marpolbul.2021.112885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Phospholipid fatty acid (PLFA) analysis was used to examine variation in the distribution of microbial communities in heavily polluted mangrove sediments of Thane creek, west coast of India. A total of 40 individual PLFAs representing 11 functional groups were identified in the sediment and were mainly dominated by saturated fatty acids (anaerobic prokaryotes) >50%. Significant dominance of PUFA, 16:3 ω6c (34.2%) indicators of micro-eukaryotes, in subsurface depth (p < 0.05) suggests input from the remnants of marine microalgae. Declined mean relative abundance of fungi (<6%) and actinomycetes (<1%) were detected in the sediment indicating their sensitivity to anthropic stressors. Homogenous profile of microbial diversity indicating active bioturbation. Cumulative metabolic stress evident from SAT/MUFA (>1), B/F (>1) and G+/G- (<1) ratio and prolonged hypoxia to be prevalent in the creek during the study. In conclusion, PLFA signatures can thus be used as potential biomarkers of environmental monitoring and proxy for interpreting ecosystem health.
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Affiliation(s)
- P Semanti
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R S Robin
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Purvaja
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India.
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11
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Chen X, Xu P, Yang C, Wang S, Lu Q, Sun X. Study of enhanced nitrogen removal efficiency and microbial characteristics of an improved two-stage A/O process. ENVIRONMENTAL TECHNOLOGY 2021; 42:4306-4316. [PMID: 32419659 DOI: 10.1080/09593330.2020.1754924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
During the cold winter in northern China, the temperature is generally below 8°C, and low water temperature significantly inhibits biological treatment processes, especially the biological denitrification process. To solve this problem, this study proposed an improved two-stage A/O process with built-in submerged biofilm modules. Experimental water was acquired from the Sanbaotun Wastewater Treatment Plant, which is situated in the city of Fushun, Liaoning Province. After one year of experimental research, the improved two-stage A/O process proved to be significantly better than the traditional two-stage A/O process, especially in winter. In the one-year experiment, the average removal rates of COD, TN, and NH4+-N in the improved two-stage A/O process were 85.2%, 77.6%, and 96.9%, respectively. Microbial properties of the process were studied by means of high-throughput sequencing. High-throughput sequencing was conducted on the biofilm of the improved two-stage A/O terminal aerobic tank and the activated sludge of the conventional two-stage A/O aerobic tank. The result showed that the microbial diversity and abundance of the biofilms were considerably higher than those of the activated sludge during stable operation in winter. Under low-temperature conditions, the main denitrifying bacteria of the improved two-stage A/O process was Terrimonas, belonging to the sphingolipid class of Bacteroides, and the main genus of nitrifying bacteria was Nitrospira, belonging to the nitrite oxidizing bacteria.
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Affiliation(s)
- Xiurong Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Peng Xu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Chenchen Yang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Shanshan Wang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Quanling Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
| | - Xiaoli Sun
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, East China University of Science and Technology, Shanghai, PR People's Republic of China
- National Engineering Laboratory for High-concentration Refractory Organic Wastewater Treatment Technologies (NELHROWTT), East China University of Science and Technology, Shanghai, People's Republic of China
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12
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Yan W, Wang N, Wei D, Liang C, Chen X, Liu L, Shi J. Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40895-40907. [PMID: 33772473 DOI: 10.1007/s11356-021-13570-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.
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Affiliation(s)
- Weizhi Yan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Chengyu Liang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaomiao Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Li Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China.
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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13
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Dai Y, Lin X, Luo Y, Sun J, Tian Y. Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145632. [PMID: 33940741 DOI: 10.1016/j.scitotenv.2021.145632] [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: 11/09/2020] [Revised: 01/28/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.
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Affiliation(s)
- Yujie Dai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yi Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jing Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen 361102, China.
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14
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Zhang CJ, Chen YL, Sun YH, Pan J, Cai MW, Li M. Diversity, metabolism and cultivation of archaea in mangrove ecosystems. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:252-262. [PMID: 37073347 PMCID: PMC10077227 DOI: 10.1007/s42995-020-00081-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.
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Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yu-Lian Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yi-Hua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Ming-Wei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
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15
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Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.
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16
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Cai F, Luo P, Yang J, Irfan M, Zhang S, An N, Dai J, Han X. Effect of Long-Term Fertilization on Ammonia-Oxidizing Microorganisms and Nitrification in Brown Soil of Northeast China. Front Microbiol 2021; 11:622454. [PMID: 33613469 PMCID: PMC7890093 DOI: 10.3389/fmicb.2020.622454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to find out changes in ammonia oxidation microorganisms with respect to fertilizer as investigated by real-time polymerase chain reaction and high-throughput sequencing. The treatments included control (CK); chemical fertilizer nitrogen low (N) and high (N2); nitrogen and phosphorus (NP); nitrogen phosphorus and potassium (NPK) and organic manure fertilizer (M); MN; MN2; MNPK. The results showed that long-term fertilization influenced soil fertility and affected the abundance and community of ammonia-oxidizing microorganisms by changing the physical and chemical properties of the soil. The abundance and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was influenced by soil organic carbon, total nitrogen, total soil phosphorus, available phosphorus, available potassium, and soil nitrate. Soil environmental factors affected the nitrification potential by affecting the structure of ammonia-oxidizing microorganisms; specific and rare AOA and AOB rather than the whole AOA or AOB community played dominant role in nitrification.
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Affiliation(s)
- Fangfang Cai
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Peiyu Luo
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Jinfeng Yang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Muhammad Irfan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Shiyu Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Ning An
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Jian Dai
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
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17
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Wang C, Wu R, Song Y, Guo J, Liu R, Cui Y. Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:136-144. [PMID: 33259261 DOI: 10.1080/10934529.2020.1852845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) are ammonium oxidising prokaryotes that can drive soil nitrification in wetlands. During the restoration of wetlands, different types of land use soils (agricultural soil [AS], restored wetland soil [RS], and natural wetland soil [NWS]) are present. However, studies on the effects of changes in the types of land use in wetlands during restoration on nitrification and the community composition of AOA and AOB are still not well understood. In this study, the differences in the potential nitrification rate (PNR) and community composition of AOA and AOB in AS, RS, and NWS were compared and discussed. The results indicated that the PNRs in the AS, RS, and NWS were on the same order of magnitude. Nitrification was mainly driven by AOB. High-throughput sequencing results showed that the genus Nitrososphaera of AOA and unclassified_o_Nitrosomonadales of AOB were only detected in the AS. Redundancy analysis (RDA) results indicated that the community composition of AOA was mostly influenced by pH, while TC was the most influential variable on the community composition of AOB. Our study provides a basis for distinguishing the roles of ammonium-oxidising prokaryotes in nitrification and further understanding the changes in nitrifying activity in wetlands during restoration.
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Affiliation(s)
- Chunyong Wang
- School of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, PR China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Rui Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Jianbo Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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18
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Monthly distribution of ammonia-oxidizing microbes in a tropical bay. J Microbiol 2020; 59:10-19. [PMID: 33201437 DOI: 10.1007/s12275-021-0287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
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19
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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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20
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Li T, Zhou Q. The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115135. [PMID: 32650301 DOI: 10.1016/j.envpol.2020.115135] [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: 04/20/2020] [Revised: 06/11/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
In the past two decades, more and more attentions have been paid to soil-derived greenhouse gases (GHGs) including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) because there are signs that they have rising negative impacts on the sustainability of the earth surface system. Farmlands, particularly paddy soils, have been regarded as the most important emitter of GHGs (nearly 17%) due to a large influx of fertilization and the abundance in animals, plants and microorganisms. Geobacter, as an electroactive microorganism widely occurred in soil, has been well studied on electron transport mechanisms and the direct interspecies electron transfer. These studies on Geobacter illustrate that it has the ability to be involved in the pathways of soil GHG emissions through redox reactions under anaerobic conditions. In this review, production mechanisms of soil-derived GHGs and the amount of these GHGs produced had been first summarized. The cycling process of CH4 and N2O was described from the view of microorganisms and discussed the co-culture relationships between Geobacter and other microorganisms. Furthermore, the role of Geobacter in the production of soil-derived GHGs is defined by biogeochemical cycling. The complete view on the effect of Geobacter on the emission of soil-derived GHGs has been shed light on, and appeals further investigation.
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Affiliation(s)
- Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Qixing Zhou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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21
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Huang YT, Chen SS, Jetten MSM, Lin JG. Nanoarchitectured structure and population dynamics of anaerobic ammonium oxidizing (anammox) bacteria in a wastewater treatment plant. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122714. [PMID: 32413666 DOI: 10.1016/j.jhazmat.2020.122714] [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: 02/21/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Studies on microbial community and population dynamics are essential for the successful development, monitoring and operation of biological wastewater treatment systems. Especially for novel or sustainable systems such as the anaerobic ammonium oxidizing (anammox) process that are not yet well explored. Here we collected granular microbial sludge samples and investigated a community of anammox bacteria over a period of four years, divided into eight stages in a full scale simultaneous partial nitrification, anammox and denitrification (SNAD) process for treating landfill leachate. Specific qPCR primers were designed to target and quantify the two most abundant anammox species, Candidatus Kuenenia stuttgartiensis (KS) and Candidatus Brocadia anammoxidans (BA). The two species were monitored and could explain the dynamic shift of the anammox community corresponding to the operating conditions. Using the newly designed KS-specific primer (KSqF3/KSqR3) and BA-specific primer (BAqF/BAqR), we estimated the amounts of KS and BA to be in the range of 6.2 × 106 to 5.9 × 108 and 1.1 × 105 to 4.1 × 107 copies μg-1 DNA, respectively. KS was found to be the dominant species in all anammox granules studied and played an important role in the formation of granules. The KS/BA ratio was positively correlated to the size of granules in the reactor and ammonia nitrogen removal efficiency of the treatment plant.
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Affiliation(s)
- Yu-Tzu Huang
- Department of Chemical Engineering and Research Center for Circular Economy, Chung Yuan Christian University, No. 200, Chung-Pei Road, Taoyuan 32023, Taiwan; R&D Center for Membrane Technology and Research Center for Analysis and Identification, Chung Yuan Christian University, No. 200, Chung-Pei Road, Taoyuan 32023, Taiwan; Department of Environmental Engineering, Chung Yuan Christian University, No. 200, Chung-Pei Road, Taoyuan 32023, Taiwan.
| | - Shiou-Shiou Chen
- Department of Environmental Engineering, Chung Yuan Christian University, No. 200, Chung-Pei Road, Taoyuan 32023, Taiwan
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegenm the Netherlands
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City 30010, Taiwan
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22
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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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Zhou W, Jiang X, Ouyang J, Lu B, Liu W, Liu G. Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau. Microorganisms 2020; 8:E933. [PMID: 32575850 PMCID: PMC7355592 DOI: 10.3390/microorganisms8060933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.
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Affiliation(s)
- Wen Zhou
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Ouyang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Research Center for Ecology and Environment of Qinghai–Tibetan Plateau, Tibet University, Lhasa 850000, China
- College of Science, Tibet University, Lhasa 850000, China
| | - Bei Lu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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24
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Xu L, Zhang B, Peng X, Zhang X, Sun B, Sun H, Jiang C, Zhou S, Zeng X, Bai Z, Xu S, Zhuang X. Dynamic variations of microbial community structure in Myriophyllum aquaticum constructed wetlands in response to different NH4+-N concentrations. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Fu G, Zhao L, Huangshen L, Wu J. Isolation and identification of a salt-tolerant aerobic denitrifying bacterial strain and its application to saline wastewater treatment in constructed wetlands. BIORESOURCE TECHNOLOGY 2019; 290:121725. [PMID: 31301568 DOI: 10.1016/j.biortech.2019.121725] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 06/10/2023]
Abstract
A salt-tolerant aerobic denitrifying bacterium, Zobellella denitrificans strain A63, was isolated, and its effects on the efficiency of denitrification of saline wastewater and the denitrifying microbial community structure in the matrix were studied in vertical-flow constructed wetlands (VFCWs). In a VFCW system with strain A63, the removal efficiencies of NH4+-N, NO3--N, and total nitrogen reached 79.2%, 95.7%, and 89.9%, respectively. Quantitative PCR analysis indicated that the amoA gene from ammonia-oxidizing archaea (AOA) was highly abundant, whereas amoA from ammonia-oxidizing bacteria and nxrA from nitrite-oxidizing bacteria were lowly abundant because of the influent salinity, irrespective of whether strain A63 was added. However, the addition of strain A63 significantly increased the abundance of nirK in the top layer of the VFCW. Therefore, AOA-driven partial nitrification and aerobic denitrification by strain A63 occurred in VFCWs. Our findings suggest that adding salt-tolerant denitrifying strains to constructed wetlands can enhance denitrification for saline wastewater treatment.
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Affiliation(s)
- Guiping Fu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Lin Zhao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Linkun Huangshen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jinfa Wu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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26
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Wang W, Su Y, Wang B, Wang Y, Zhuang L, Zhu G. Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:629-640. [PMID: 31170597 DOI: 10.1016/j.scitotenv.2019.04.415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.
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Affiliation(s)
- Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Baoling Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
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27
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Liu H, Khan MY, Carvalhais LC, Delgado-Baquerizo M, Yan L, Crawford M, Dennis PG, Singh B, Schenk PM. Soil amendments with ethylene precursor alleviate negative impacts of salinity on soil microbial properties and productivity. Sci Rep 2019; 9:6892. [PMID: 31053834 PMCID: PMC6499801 DOI: 10.1038/s41598-019-43305-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/12/2019] [Indexed: 12/04/2022] Open
Abstract
Some microbes enhance stress tolerance in plants by minimizing plant ethylene levels via degradation of its immediate precursor, 1-aminocyclopropane-1-carboxylate (ACC), in the rhizosphere. In return, ACC is used by these microbes as a source of nitrogen. This mutualistic relationship between plants and microbes may be used to promote soil properties in stressful environments. In this study, we tested the hypothesis that amendments of ACC in soils reshape the structure of soil microbiome and alleviate the negative impacts of salinity on soil properties. We treated non-saline and artificially-developed saline soils with ACC in different concentrations for 14 days. The structure of soil microbiome, soil microbial properties and productivity were examined. Our results revealed that microbial composition of bacteria, archaea and fungi in saline soils was affected by ACC amendments; whereas community composition in non-saline soils was not affected. The amendments of ACC could not fully counteract the negative effects of salinity on soil microbial activities and productivity, but increased the abundance of ACC deaminase-encoding gene (acdS), enhanced soil microbial respiration, enzymatic activity, nitrogen and carbon cycling potentials and Arabidopsis biomass in saline soils. Collectively, our study indicates that ACC amendments in soils could efficiently ameliorate salinity impacts on soil properties and plant biomass production.
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Affiliation(s)
- Hongwei Liu
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia. .,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.
| | - Muhammad Yahya Khan
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Institute of Soil and Environmental Science, The University of Agriculture, Faisalabad, 38000, Pakistan.,The University of Agriculture Faisalabad, Sub-Campus Burewala, Vehari, 61100, Pakistan
| | - Lilia C Carvalhais
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, Queensland, 4102, Australia
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
| | - Lijuan Yan
- Institute of Biodiversity, Friedrich Schiller University, Jena, 07749, Germany
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, QLD, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Peer M Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
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28
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Behera P, Mohapatra M, Kim JY, Adhya TK, Pattnaik AK, Rastogi G. Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:3893-3908. [PMID: 30547343 DOI: 10.1007/s11356-018-3927-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, Busan, 46241, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India.
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29
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Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis. Int J Syst Evol Microbiol 2018; 68:3316-3321. [DOI: 10.1099/ijsem.0.002990] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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30
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Wang H, Gilbert JA, Zhu Y, Yang X. Salinity is a key factor driving the nitrogen cycling in the mangrove sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1342-1349. [PMID: 29727958 DOI: 10.1016/j.scitotenv.2018.03.102] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.
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Affiliation(s)
- Haitao Wang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China; School of Life Sciences, Xiamen University, Xiamen, Fujian Province 361102, China; The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Yongguan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xiaoru Yang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China.
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31
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Li B, Yang Y, Chen J, Wu Z, Liu Y, Xie S. Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:310-318. [PMID: 29444483 DOI: 10.1016/j.scitotenv.2018.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/03/2018] [Accepted: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105-6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.
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Affiliation(s)
- Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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32
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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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33
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Huang S, Jaffé PR. Isolation and characterization of an ammonium-oxidizing iron reducer: Acidimicrobiaceae sp. A6. PLoS One 2018; 13:e0194007. [PMID: 29641534 PMCID: PMC5894979 DOI: 10.1371/journal.pone.0194007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/22/2018] [Indexed: 11/18/2022] Open
Abstract
Acidimicrobiaceae sp. A6 (ATCC, PTA-122488), a strain that has been previously reported to play a key role in the oxidation of ammonium (NH4+) under iron reducing conditions, has now been isolated from riparian wetland soils in New Jersey, USA. Incubations of this strain in a medium containing ferrihydrite as the ferric iron [Fe(III)] source, CO2 as the carbon source, under room temperature, and a pH of 4.5, resulted in 52% of NH4+ removal over a 20-day incubation period, while reducing Fe(III) in the expected stoichiometric ratio when NH4+ was oxidized to nitrite with Fe(III) as the electron acceptor. This study demonstrates that this new isolated strain is capable of oxidizing NH4+ while reducing iron under anaerobic conditions.
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Affiliation(s)
- Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Peter R. Jaffé
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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Chen J, Wang PF, Wang C, Wang X, Gao H. Effects of decabromodiphenyl ether and planting on the abundance and community composition of nitrogen-fixing bacteria and ammonia oxidizers in mangrove sediments: A laboratory microcosm study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:1045-1055. [PMID: 29100689 DOI: 10.1016/j.scitotenv.2017.10.214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/15/2017] [Accepted: 10/21/2017] [Indexed: 06/07/2023]
Abstract
While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Pei-Fang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
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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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Ling J, Lin X, Zhang Y, Zhou W, Yang Q, Lin L, Zeng S, Zhang Y, Wang C, Ahmad M, Long L, Dong J. Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems. Front Microbiol 2018; 9:7. [PMID: 29422885 PMCID: PMC5788956 DOI: 10.3389/fmicb.2018.00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/04/2018] [Indexed: 11/17/2022] Open
Abstract
Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.
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Affiliation(s)
- Juan Ling
- 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, China
| | - Xiancheng Lin
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Zhang
- 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, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
| | - Weiguo Zhou
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingsong Yang
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liyun Lin
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Siquan Zeng
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Wang
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manzoor Ahmad
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan Long
- 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, China
| | - Junde Dong
- 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, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
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Yao L, Chen C, Liu G, Li F, Liu W. Environmental factors, but not abundance and diversity of nitrifying microorganisms, explain sediment nitrification rates in Yangtze lakes. RSC Adv 2018; 8:1875-1883. [PMID: 35542587 PMCID: PMC9077250 DOI: 10.1039/c7ra11956a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/28/2017] [Indexed: 11/21/2022] Open
Abstract
Sediment nitrification plays a vital role in nitrogen (N) biogeochemical cycling and ecological function of an aquatic ecosystem.
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Affiliation(s)
- Lu Yao
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
| | - Chengrong Chen
- Australian Rivers Institute and Griffith School of Environment
- Griffith University
- Nathan
- Australia
| | - Guihua Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
| | - Feng Li
- Dongting Lake Station for Wetland Ecosystem Research
- Institute of Subtropical Agriculture
- The Chinese Academy of Sciences
- Changsha 410125
- PR China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology
- Wuhan Botanical Garden
- Chinese Academy of Sciences
- Wuhan
- PR China
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38
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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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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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Chen J, Gu JD. Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments. MICROBIAL ECOLOGY 2017; 74:140-156. [PMID: 28130576 DOI: 10.1007/s00248-017-0939-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH4+ but lower concentrations of both NO2- and NO3-, and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH4+ and NO2- were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.
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Affiliation(s)
- Jing Chen
- 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
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - 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.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, SAR, People's Republic of China.
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Bao L, Wang X, Chen Y. Abundance and distribution of ammonia-oxidizing microorganisms in the sediments of Beiyun River, China. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1191-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Gu JD, Wang YS. Coastal and marine pollution and ecotoxicology. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1407-1410. [PMID: 26391368 DOI: 10.1007/s10646-015-1528-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China.
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, People's Republic of China.
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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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Wang S, Hong Y, Wu J, Xu XR, Bin L, Pan Y, Guan F, Wen J. Comparative analysis of two 16S rRNA gene-based PCR primer sets provides insight into the diversity distribution patterns of anammox bacteria in different environments. Appl Microbiol Biotechnol 2015; 99:8163-76. [PMID: 26231134 DOI: 10.1007/s00253-015-6814-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 08/02/2023]
Abstract
Due to the high divergence among 16S rRNA genes of anammox bacteria, different diversity pattern of the community could be resulted from using different primer set. In this study, the efficiencies and specificities of two commonly used sets, Amx368F/Amx820R and Brod541F/Amx820R, were evaluated by exploring the diversity characteristics of anammox bacteria in sediments from marine, estuary, and freshwater wetland. Statistical analysis indicated that the base mispairing rate between bases on 16S rRNA gene sequences retrieved by Amx368F/Amx820R and their corresponding ones on primer Brod541F was quite high, suggesting the different efficiency and specificity of Amx368F/Amx820R and Brod541F/Amx820R. Further experimental results demonstrated that multiple genera of anammox bacteria, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, were able to be detected by Amx368F/Amx820R, but only Ca. Scalindua could be retrieved by Brod541F/Amx820R. Moreover, the phylogenetic clusters of Ca. Scalindua by Amx368F/Amx820R were different completely from those by Brod541F/Amx820R, presenting a significant complementary effect. By joint application of these two primer sets, the diversity distribution patterns of anammox bacteria in different environments were analyzed. Almost all retrieved sequences from marine sediments belonged to Ca. Scalindua. Sequences from freshwater wetland were affiliated to Ca. Brocadia and two new clusters, while high diversity of anammox bacteria was found in estuary, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, corresponding to the river-sea intersection environmental feature. In total, these two prime sets have different characteristic for anammox bacteria detecting from environmental samples, and their combined application could achieve better diversity display of anammox community.
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Affiliation(s)
- Shuailong Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
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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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Li H, Weng BS, Huang FY, Su JQ, Yang XR. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China. Appl Microbiol Biotechnol 2015; 99:6113-23. [PMID: 25744648 DOI: 10.1007/s00253-015-6488-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 12/11/2022]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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Chen J, Zhou Z, Gu JD. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes. Appl Microbiol Biotechnol 2014; 99:1463-73. [DOI: 10.1007/s00253-014-6051-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 08/17/2014] [Accepted: 08/24/2014] [Indexed: 10/24/2022]
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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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Liu B, Li Y, Zhang J, Zhou X, Wu C. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake. Curr Microbiol 2014; 69:751-7. [PMID: 25008777 DOI: 10.1007/s00284-014-0646-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/12/2014] [Indexed: 11/25/2022]
Abstract
Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.
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Affiliation(s)
- Biao Liu
- Department of Environment Engineering, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China,
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Xu W, Li M, Ding JF, Gu JD, Luo ZH. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean. Appl Microbiol Biotechnol 2014; 98:7993-8004. [DOI: 10.1007/s00253-014-5833-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/29/2023]
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