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Zheng H, Yin Z, Chen L, He H, Li Z, Lv X, Chen J, Du W, Lin X. Effects of salinity on nitrogen reduction pathways in estuarine wetland sediments. MARINE POLLUTION BULLETIN 2024; 207:116834. [PMID: 39142052 DOI: 10.1016/j.marpolbul.2024.116834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/24/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024]
Abstract
Denitrification, anammox, and DNRA are three important nitrogen (N) reduction pathways in estuarine sediments. Although salinity is an important variables controlling microbial growth and activities, knowledge about the effects of changing salinity on those three processes in estuarine and coastal wetland sediments are not well understood. Herein, we performed a 60-d microcosms experiment with different salinities (0, 5, 15, 25 and 35 ‰) to explore the vital role of salinity in controlling N-loss and N retention in estuarine wetland sediments. The results showed that sediment organic matter, sulfide, and nitrate (NO3-) were profoundly decreased with increasing salinity, while sediment ammonium (NH4+) and ferrous (Fe2+) varied in reverse patterns. Meanwhile, N-loss and N retention rates and associated gene abundances were differentially inhibited with increasing salinity, while the contributions of denitrification, anammox, and DNRA to total nitrate reduction were apparently unaffected. Moreover, denitrification rate was the most sensitive to salinity, and then followed by DNRA, while anammox was the weakest among these three processes. In other words, anammox bacteria showed a wide range of salinity tolerance, while both denitrification and DNRA reflected a relatively limited dynamic range of it. Our findings could provide insights into temporal interactive effects of salinity on sediment physico-chemical properties, N reduction rates and associated gene abundances. Our findings can improve understanding of the effects of saltwater incursion on the N fate and N balance in estuarine and coastal sediments.
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Affiliation(s)
- Hao Zheng
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Zhengxin Yin
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China.
| | - Liang Chen
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Huizhong He
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Zhengyuan Li
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Xiuya Lv
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Jiyu Chen
- Key Laboratory of Marine Environmental Survey Technology and Application, South China Sea Marine Survey Center, Ministry of Natural Resources, Guangzhou 510300, China
| | - Wei Du
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming 650500, China
| | - Xianbiao Lin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
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Deng Y, Li F, Shang L, Hu Z, Yue C, Tang YZ. The resting cyst of dinoflagellate Scrippsiella acuminata host bacterial microbiomes with more diverse trophic strategies under conditions typically observed in marine sediments. Front Microbiol 2024; 15:1407459. [PMID: 39104580 PMCID: PMC11298437 DOI: 10.3389/fmicb.2024.1407459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Variation in the condition of marine sediments provides selective preservation milieus, which act as a key determinant for the abundance and distribution of dinoflagellate resting cysts in natural sediments. Microbial degradation is an understudied biological factor of potential importance in the processes. However, gaps remain in our knowledge about the fundamental information of the bacterial consortia associated with dinoflagellate resting cysts both in laboratory cultures and in the field. Here we used Scrippsiella acuminata as a representative of cyst-producing dinoflagellates to delineate the diversity and composition of bacterial microbiomes co-existing with the laboratory-cultured resting cysts, and to explore possible impacts of low temperature, darkness, and anoxia (the mock conditions commonly observed in marine sediments) on the associated bacterial consortia. Bacterial microbiome with high diversity were revealed associated with S. acuminata at resting stage. The mock conditions could significantly shift bacterial community structure and exert notably inhibitory effects on growth-promoting bacteria. Resting cysts under conditions typically observed in marine sediments fostered bacterial microbiomes with more diverse trophic strategies, characteristic of prominently enriched anaerobic chemotrophic bacteria generating energy via respiration with several different terminal electron acceptors, which yielded more acidic milieu unfavorable for the preservation of calcareous resting cysts. Our findings suggest that there is complex and dynamic interaction between dinoflagellates resting cysts and the associated bacterial consortia in natural sediments. This intrinsic interaction may influence the maintenance and/or accumulation of dinoflagellate resting cysts with potential of germination and initiation blooms in the field.
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Affiliation(s)
- Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fengting Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Caixia Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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3
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Sun Y, Du P, Li H, Zhou K, Shou L, Chen J, Meng Li. Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column. ENVIRONMENTAL RESEARCH 2024; 252:119011. [PMID: 38670213 DOI: 10.1016/j.envres.2024.119011] [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: 02/21/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO43-, and distance offshore (p < 0.05). Water depth, NH4+, and PO43- were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3- (or NO2-) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.
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Affiliation(s)
- Yihua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Konglin Zhou
- Institute of Oceanography, Minjiang University, No. 200 xiyuangong Road, 350108 Fuzhou, Fujian, PR China
| | - Lu Shou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, China, No. 36 Baochubei Road, 310012 Hangzhou, Zhejiang, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China; Synthetic Biology Research Center, Shenzhen University, No. 3688 Nanhai Avenue, 518060 Shenzhen, Guangdong, PR China.
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4
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Alegbeleye O, Alegbeleye I, Oroyinka MO, Daramola OB, Ajibola AT, Alegbeleye WO, Adetunji AT, Afolabi WA, Oyedeji O, Awe A, Badmus A, Oyeboade JT. Microbiological quality of ready to eat coleslaw marketed in Ibadan, Oyo-State, Nigeria. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2023. [DOI: 10.1080/10942912.2023.2173775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, Brazil
| | - Ithamar Alegbeleye
- Department of Computer Science, Faculty of Science, University of Ibadan, Oyo-state, Nigeria
| | - Moses O. Oroyinka
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Oyo-State, Nigeria
| | | | - Abiola Tosin Ajibola
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Adewole Tomiwa Adetunji
- Department of Agriculture, Faculty of Applied Sciences, Cape Peninsula University of Technology, Wellington, South Africa
| | - Wasiu Akinloye Afolabi
- Department of Nutrition and Dietetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Olayinka Oyedeji
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AL, Canada
| | - Adetunji Awe
- Department of Conservation and Marine Sciences, Faculty of Applied Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Aminat Badmus
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Joshua Temiloluwa Oyeboade
- Department of Aquaculture and Fisheries Management, Federal University of Agriculture, Abeokuta, Nigeria
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5
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Ye F, Duan L, Sun Y, Yang F, Liu R, Gao F, Wang Y, Xu Y. Nitrogen removal in freshwater sediments of riparian zone: N-loss pathways and environmental controls. Front Microbiol 2023; 14:1239055. [PMID: 37664113 PMCID: PMC10469909 DOI: 10.3389/fmicb.2023.1239055] [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: 06/12/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The riparian zone is an important location of nitrogen removal in the terrestrial and aquatic ecosystems. Many studies have focused on the nitrogen removal efficiency and one or two nitrogen removal processes in the riparian zone, and less attention has been paid to the interaction of different nitrogen transformation processes and the impact of in situ environmental conditions. The molecular biotechnology, microcosm culture experiments and 15N stable isotope tracing techniques were used in this research at the riparian zone in Weinan section of the Wei River, to reveal the nitrogen removal mechanism of riparian zone with multi-layer lithologic structure. The results showed that the nitrogen removal rate in the riparian zone was 4.14-35.19 μmol·N·kg-1·h-1. Denitrification, dissimilatory reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox) jointly achieved the natural attenuation process of nitrogen in the riparian zone, and denitrification was the dominant process (accounting for 59.6%). High dissolved organic nitrogen and nitrate ratio (DOC:NO3-) would promote denitrification, but when the NO3- content was less than 0.06 mg/kg, DNRA would occur in preference to denitrification. Furthermore, the abundances of functional genes (norB, nirS, nrfA) and anammox bacterial 16S rRNA gene showed similar distribution patterns with the corresponding nitrogen transformation rates. Sedimentary NOX-, Fe(II), dissolved organic carbon (DOC) and the nitrogen transformation functional microbial abundance were the main factors affecting nitrogen removal in the riparian zone. Fe (II) promoted NO3- attenuation through nitrate dependent ferrous oxidation process under microbial mediation, and DOC promotes NO3- attenuation through enhancing DNRA effect. The results of this study can be used for the management of the riparian zone and the prevention and control of global nitrogen pollution.
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Affiliation(s)
- Fei Ye
- School of Water and Environment, Chang’an University, Xi’an, China
- Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang’an University, Xi’an, China
| | - Lei Duan
- School of Water and Environment, Chang’an University, Xi’an, China
- Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang’an University, Xi’an, China
| | - Yaqiao Sun
- School of Water and Environment, Chang’an University, Xi’an, China
- Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang’an University, Xi’an, China
| | - Fan Yang
- Power China Northwest Engineering Corporation Limited, Xi’an, Shaanxi, China
- Shaanxi Union Research Center of University and Enterprise for River and Lake Ecosystems Protection and Restoration, Xi’an, Shaanxi, China
| | - Rui Liu
- Power China Northwest Engineering Corporation Limited, Xi’an, Shaanxi, China
- Shaanxi Union Research Center of University and Enterprise for River and Lake Ecosystems Protection and Restoration, Xi’an, Shaanxi, China
| | - Fan Gao
- Power China Northwest Engineering Corporation Limited, Xi’an, Shaanxi, China
- Shaanxi Union Research Center of University and Enterprise for River and Lake Ecosystems Protection and Restoration, Xi’an, Shaanxi, China
| | - Yike Wang
- School of Water and Environment, Chang’an University, Xi’an, China
- Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang’an University, Xi’an, China
| | - Yirong Xu
- School of Water and Environment, Chang’an University, Xi’an, China
- Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang’an University, Xi’an, China
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6
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Jia F, Lei X, Yan Y, Su Y, Zhou H, Wei H, Yuan Y, Zou C, Shi X, Yang C. Sulphate-reducing bacteria-mediated pyrite formation in the Dachang Tongkeng tin polymetallic deposit, Guangxi, China. Sci Rep 2023; 13:11650. [PMID: 37468706 DOI: 10.1038/s41598-023-38827-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 07/15/2023] [Indexed: 07/21/2023] Open
Abstract
Mediation by sulphate-reducing bacteria (SRB) is responsible for pyrite (FeS2) formation. The origin of the Dachang tin polymetallic ore field is related to the mineralisation of submarine hydrothermal vent sediments. Here, we investigated SRB in these ores via morphological, chemical, and isotopic analyses. Polarised and scanning electron microscopy indicated that trace SRB fossils in the metal sulphide ore were present in the form of tubular, beaded, and coccoidal bodies comprising FeS2 and were enclosed within a pyrrhotite (FeS) matrix in the vicinity of micro-hydrothermal vents. The carbon (C), nitrogen (N), and oxygen (O) contents in the FeS2 synthesised by SRB were high, and a clear biological Raman signal was detected. No such signals were discerned in the peripheral FeS. This co-occurrence of FeS, FeS2, and the remains of bacteria (probably chemoautotrophic bacteria) was interpreted as the coprecipitation process of SRB-mediated FeS2 formation, which has, to the best of our knowledge, not been reported before. Our study also illustrates that combined energy-dispersive X-ray spectroscopy, Raman spectroscopy, and isotopic analysis can be used as a novel methodology to document microbial-mediated processes of mineral deposition in submarine hydrothermal vent ecology on geological time scales.
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Affiliation(s)
- Fuju Jia
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, 650093, Yunnan, China
| | - Xiangtong Lei
- Yunnan Key Laboratory for Paleobiology & MEC International Joint Laboratory for Paleobiology and Paleoenvironment, Institute of Paleontology, Yunnan University, Kunming, 650500, China.
| | - Yongfeng Yan
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, 650093, Yunnan, China
| | - Yaru Su
- Guangxi 215 Geological Team Co., Ltd., Liuzhou, 545006, Guangxi, China
| | - Hongjun Zhou
- Guangxi 215 Geological Team Co., Ltd., Liuzhou, 545006, Guangxi, China
| | - Honglian Wei
- Guangxi China-Tin Group Tongkeng Co., Ltd., Nandan, 547205, Guangxi, China
| | - Yuan Yuan
- Guangxi 215 Geological Team Co., Ltd., Liuzhou, 545006, Guangxi, China
| | - Chao Zou
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, 650093, Yunnan, China
| | - Xianwen Shi
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, 650093, Yunnan, China
| | - Ceting Yang
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, 650093, Yunnan, China
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Xiong G, Zhu X, Wu J, Liu M, Yang Y, Zeng X. Seawater intrusion alters nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions: Based on Bayesian isotope mixing model and microbial functional network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161368. [PMID: 36621512 DOI: 10.1016/j.scitotenv.2022.161368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/07/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Seawater intrusion is a global coastal environmental issue of great concern and significantly impacts the regional biogeochemical environment and material cycles, including nitrogen cycling. To reveal the mechanism of seawater intrusion altering nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions, the Bayesian mixing model (δ15N-NO3- and δ18O-NO3-) and 16S rDNA gene amplicon sequencing are used to establish nitrogen cycling pathways and microbial functional network. The results show that the nitrate in the coastal groundwater is from manure and septic waste (M&S, over 44 %), soil organic nitrogen (SON, over 20 %), and nitrogen fertilizer (FN, over 16 %). The hydrological interaction has promoted the coupling between material cycling and microbial community in the coastal groundwater systems. Among them, precipitation infiltration has caused the gradual decrease of specific microbes along the flow direction, such as Lactobacillus, Acinetobacter, Bifidobacterium, etc. And seawater intrusion has caused the mutations of specific microbes (Planktomarina, Clade_Ia, Wenyingzhuangia, Glaciecola, etc.) and convergence of microbial community at the salt-freshwater interface in the aquifer. In the coastal intruded aquifer systems, the nitrogen cycling pattern can be divided into oxidation and reduction processes. The oxidation process involves the enhancement of nitrification while the weakening of denitrification and anammox with the increase of aquifer depth. The reduction process consists of the enhancement of denitrification and anammox while the erosion of nitrification and ammonification with increased seawater intrusion. In addition, seawater intrusion can mitigate nitrate contamination by promoting denitrification and anammox in coastal areas.
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Affiliation(s)
- Guiyao Xiong
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaobin Zhu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Mengwen Liu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Yun Yang
- School of Earth Sciences and Engineering, Hohai University, Nanjing 211100, China
| | - Xiankui Zeng
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
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8
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Shan X, Goyal A, Gregor R, Cordero OX. Annotation-free discovery of functional groups in microbial communities. Nat Ecol Evol 2023; 7:716-724. [PMID: 36997739 DOI: 10.1038/s41559-023-02021-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/16/2023] [Indexed: 04/01/2023]
Abstract
Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa whose abundance is more stable and better-associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent of error-prone functional gene annotations remains a major open problem. Here we tackle this structure-function problem by developing a novel unsupervised approach that coarse-grains taxa into functional groups, solely on the basis of the patterns of statistical variation in species abundances and functional read-outs. We demonstrate the power of this approach on three distinct datasets. On data of replicate microcosms with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labour and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are probably responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis-generating tool for mechanistic studies. Overall, this work advances our understanding of structure-function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Zhao R, Babbin AR, Roerdink DL, Thorseth IH, Jørgensen SL. Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments. ISME COMMUNICATIONS 2023; 3:26. [PMID: 36991114 PMCID: PMC10060263 DOI: 10.1038/s43705-023-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Desiree L Roerdink
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Ingunn H Thorseth
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway.
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Lai X, Li X, Song J, Yuan H, Duan L, Li N, Wang Y. Nitrogen loss from the coastal shelf of the East China Sea: Implications of the organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158805. [PMID: 36113798 DOI: 10.1016/j.scitotenv.2022.158805] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Organic matter is a critical factor which regulates nitrogen loss pathways of denitrification and anammox for microbes in marine ecosystems. However, only a little attention has been paid to contrasting studies on denitrification and anammox in sandy and muddy sediments, especially in the coastal continental shelf dominated by sandy sediments. This study determined the bulk properties and associated microbial nitrogen transformation processes of surface sediments in the East China Sea coastal shelf, with the aim of gaining insight into the interaction of nitrogen loss with organic matter at the molecular level. The results illustrate that nitrogen loss dominates in organic-rich muddy sediments, and its denitrification rate (14.39 nmol N g-1 h-1) and anammox rate (2.73 nmol N g-1 h-1) are greater than those of sandy sediments (denitrification rate = 5.55 nmol N g-1 h-1, anammox rate = 1.57 nmol N g-1 h-1). Furthermore, determination of the mean summed ladderanes shows higher anammox generated in the muddy sediments with a value of 167.78 ng g-1dw. Quantitative analysis demonstrated that organic-rich muddy sediments enhanced the copy number of the denitrifying functional gene nosZ and anammox functional gene hzsB. We inferred that the greater rate of nitrogen loss in muddy sediments was due to the coupling relationship between anammox and denitrification. Overall, the community distribution and abundance of denitrifying bacteria and anammox bacteria changed intricately under the influence of organic matter. Moreover, this study further improves the understanding of nitrogen loss pathways and mechanistic factors from sediments.
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Affiliation(s)
- Xiaoshuang Lai
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Jinming Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Huamao Yuan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Liqin Duan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ning Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yingxia Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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11
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Howe KL, Seitz KW, Campbell LG, Baker BJ, Thrash JC, Rabalais NN, Rogener MK, Joye SB, Mason OU. Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column. FEMS Microbiol Ecol 2022; 99:6909064. [PMID: 36520069 PMCID: PMC9874027 DOI: 10.1093/femsec/fiac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 12/20/2022] [Indexed: 12/23/2022] Open
Abstract
The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.
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Affiliation(s)
- Kathryn L Howe
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States
| | - Lauren G Campbell
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States,Department of Integrative Biology, University of Texas at Austin, 78712, Austin, United States
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, 90089, Los Angeles, United States
| | - Nancy N Rabalais
- Department of Oceanography and Coastal Sciences, Louisiana State University, 70803, Baton Rouge, United States,Louisiana Universities Marine Consortium, 70344, Chauvin, United States
| | - Mary-Kate Rogener
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Olivia U Mason
- Corresponding author: Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States. E-mail:
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12
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Li J, Li J, Zhang Y, Lu H. The responses of marine anammox bacteria-based microbiome to multi-antibiotic stress in mariculture wastewater treatment. WATER RESEARCH 2022; 224:119050. [PMID: 36084441 DOI: 10.1016/j.watres.2022.119050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Saline mariculture wastewater containing multi-antibiotics poses a challenge to anaerobic ammonia oxidation (anammox) process. Herein, the halophilic marine anammox bacteria (MAB)-based microbiome was used for treating mariculture wastewater (35‰ salinity) under multi-antibiotics (enrofloxacin + oxytetracycline + sulfamethoxazole, EOS) stress. And the main focus of this study lies in the response of MAB-based microbiome against multi-antibiotics stress. It is found that MAB-based microbiome shows stable community structure and contributes high nitrogen removal efficiency (>90%) even under high stress of EOS (up to 4 mg·L-1). The relative abundance of main functional genus Candidatus Scalindua, responsible for anammox, had little change while controlling the influent EOS concentration within 4 mg·L-1, whereas, significantly decreased to 2.23% at EOS concentration of as high as 24 mg·L-1. As an alternative, antibiotic resistance bacteria (ARB) species Rheinheimera dominated the microbial community of MAB-based biological reactor under extremely high EOS stress (e.g. 24 mg·L-1 in influent). The response mechanism of MAB-based microbiome consists of extracellular and intracellular defenses with dependence of EOS concentration. For example, while EOS within 4 mg·L-1 in this study, most of the antibiotics were retained by extracellular polymeric substances (EPS) via adsorption; If increasing the EOS concentration to 8 and even 24 mg·L-1, part of antibiotics could intrude into the cells and cause the intracellular accumulation of antibiotic resistance genes (ARGs) (total abundance up to 2.44 × 10-1 copies/16S rRNA) for EOS response. These new understandings will facilitate the practical implementation of MAB-based bioprocess for saline nitrogen- and antibiotics-laden wastewater treatment.
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Affiliation(s)
- Jialu Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
| | - Yulong Zhang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China.
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13
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A Universal Biofilm Reactor Sensor for the Determination of Biochemical Oxygen Demand of Different Water Areas. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27155046. [PMID: 35956996 PMCID: PMC9370119 DOI: 10.3390/molecules27155046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
Abstract
In this study, we developed a simple strategy to prepare a biofilm reactor (BFR) sensor for the universal biochemical oxygen demand (BOD) determination. The microorganisms in fresh water were domesticated by artificial seawater with different salinity gradients successively to prepare the BFR sensor. The prepared BFR sensor exhibits an efficient ability to degrade a variety of organic substances. The linear range of BOD determination by the BFR sensor is 1.0–10.0 mg/L−1 with a correlation coefficient of 0.9951. The detection limit is 0.30 mg/L according to three times of signal-to-noise ratio. What is more, the BFR sensor displayed excellent performances for the BOD determination of different water samples, including both fresh water and seawater. The 16S-rRNA gene sequencing technology was used to analyze the microbial species before and after the domestication. The results show that it is a general approach for the rapid BOD determination in different water samples.
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14
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Zhou Z, Meng H, Gu W, Li J, Deng M, Gu JD. High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea. MARINE ENVIRONMENTAL RESEARCH 2022; 178:105641. [PMID: 35594805 DOI: 10.1016/j.marenvres.2022.105641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 05/16/2023]
Abstract
Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Meng
- School of Environment, Nanjing Normal University, 122 Ninghai Road, Nanjing, Jiangsu, 210023, China
| | - Wenjie Gu
- Insitute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences/Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, 66 Jinying Road, Guangzhou, Guangdong, 510640, China
| | - Jing Li
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Maocheng Deng
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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15
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Zhao R, Biddle JF, Jørgensen SL. Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments. ISME COMMUNICATIONS 2022; 2:42. [PMID: 37938673 PMCID: PMC9723696 DOI: 10.1038/s43705-022-00125-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 07/21/2023]
Abstract
Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presence of Ca. Bathyanammoxibiaceae was confined within the nitrate-ammonium transition zones with the counter gradients of nitrate and ammonium, coinciding with the predicted occurrence of the anammox process. Ca. Bathyanammoxibiaceae genomes encode the core genetic machinery for the anammox metabolism, including hydrazine synthase for converting nitric oxide and ammonium to hydrazine, and hydrazine dehydrogenase for hydrazine oxidation to dinitrogen gas, and hydroxylamine oxidoreductase for nitrite reduction to nitric oxide. Their occurrences assessed by genomes and 16S rRNA gene sequencings surveys indicate that they are present in both marine and terrestrial environments. By introducing the anammox potential of Ca. Bathyanammoxibiaceae and charactering their ideal niche in marine sediments, our findings suggest that the diversity and abundance of anammox bacteria may be higher than previously thought, and provide important insights on cultivating them in the future to not only assess their biogeochemical impacts but also constrain the emergence and evolutionary history of this functional guild on Earth.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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16
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Liu L, Lv AP, Narsing Rao MP, Ming YZ, Salam N, Li MM, Liu ZT, Zhang XT, Zhang JY, Xian WD, Jiao JY, Li WJ. Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China. Front Microbiol 2022; 12:739234. [PMID: 35145488 PMCID: PMC8822059 DOI: 10.3389/fmicb.2021.739234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.
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Affiliation(s)
- Lan Liu
- 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, China
| | - Ai-Ping Lv
- 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, China
| | - Manik Prabhu Narsing Rao
- 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, China
| | - Yu-Zhen Ming
- 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, China
| | - Nimaichand Salam
- 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, China
| | - Meng-Meng 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, China
| | - Ze-Tao Liu
- 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, China
| | - Xiao-Tong Zhang
- 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, China
| | - Jing-Yi Zhang
- 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, China
| | - Wen-Dong Xian
- 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, China
| | - Jian-Yu Jiao
- 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, China
- Jian-Yu Jiao,
| | - 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, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- *Correspondence: Wen-Jun Li,
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17
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Pashaei R, Zahedipour-Sheshglani P, Dzingelevičienė R, Abbasi S, Rees RM. Effects of pharmaceuticals on the nitrogen cycle in water and soil: a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:105. [PMID: 35044585 PMCID: PMC8766359 DOI: 10.1007/s10661-022-09754-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
The effects of pharmaceuticals on the nitrogen cycle in water and soil have recently become an increasingly important issue for environmental research. However, a few studies have investigated the direct effects of pharmaceuticals on the nitrogen cycle in water and soil. Pharmaceuticals can contribute to inhibition and stimulation of nitrogen cycle processes in the environment. Some pharmaceuticals have no observable effect on the nitrogen cycle in water and soil while others appeared to inhibit or stimulate for it. This review reports on the most recent evidence of effects of pharmaceuticals on the nitrogen cycle processes by examination of the potential impact of pharmaceuticals on nitrogen fixation, nitrification, ammonification, denitrification, and anammox. Research studies have identified pharmaceuticals that can either inhibit or stimulate nitrification, ammonification, denitrification, and anammox. Among these, amoxicillin, chlortetracycline, ciprofloxacin, clarithromycin, enrofloxacin, erythromycin, narasin, norfloxacin, and sulfamethazine had the most significant effects on nitrogen cycle processes. This review also clearly demonstrates that some nitrogen transformation processes such as nitrification show much higher sensitivity to the presence of pharmaceuticals than other nitrogen transformations or flows such as mineralization or ammonia volatilization. We conclude by suggesting that future studies take a more comprehensive approach to report on pharmaceuticals' impact on the nitrogen cycle process.
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Affiliation(s)
- Reza Pashaei
- Marine Research Institute of Klaipeda University, Klaipeda, Lithuania
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Torun, Poland
| | | | | | - Sajjad Abbasi
- Department of Earth Sciences, College of Science, Shiraz University, Shiraz, Iran
- Department of Radiochemistry and Environmental Chemistry, Maria Curie-Skłodowska University, Lublin, Poland
| | - Robert M. Rees
- Scotland’s Rural College (SRUC), West Mains Rd. Edinburgh, Scotland, EH9 3JG UK
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18
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Lv H, Yang Q, Chen Y, Xu X, Liu C, Jia J. Determination of seawater biochemical oxygen demand based on in situ cultured biofilm reactor. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Okabe S, Kamigaito A, Kobayashi K. Maintenance power requirements of anammox bacteria "Candidatus Brocadia sinica" and "Candidatus Scalindua sp.". THE ISME JOURNAL 2021; 15:3566-3575. [PMID: 34145389 PMCID: PMC8629980 DOI: 10.1038/s41396-021-01031-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023]
Abstract
Little is known about the cell physiology of anammox bacteria growing at extremely low growth rates. Here, "Candidatus Brocadia sinica" and "Candidatus Scalindua sp." were grown in continuous anaerobic membrane bioreactors (MBRs) with complete biomass retention to determine maintenance energy (i.e., power) requirements at near-zero growth rates. After prolonged retentostat cultivations, the specific growth rates (μ) of "Ca. B. sinica" and "Ca. Scalindua sp." decreased to 0.000023 h-1 (doubling time of 1255 days) and 0.000157 h-1 (184 days), respectively. Under these near-zero growth conditions, substrate was continuously utilized to meet maintenance energy demands (me) of 6.7 ± 0.7 and 4.3 ± 0.7 kJ mole of biomass-C-1 h-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which accorded with the theoretically predicted values of all anaerobic microorganisms (9.7 and 4.4 kJ mole of biomass-C-1 h-1at 37 °C and 28 °C, respectively). These me values correspond to 13.4 × 10-15 and 8.6 × 10-15 watts cell-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which were five orders of magnitude higher than the basal power limit for natural settings (1.9 × 10-19 watts cells-1). Furthermore, the minimum substrate concentrations required for growth (Smin) were calculated to be 3.69 ± 0.21 and 0.09 ± 0.05 μM NO2- for "Ca. B. sinica" and "Ca. Scalindua sp.", respectively. These results match the evidence that "Ca. Scalindua sp." with lower maintenance power requirement and Smin are better adapted to energy-limited natural environments than "Ca. B. sinica", suggesting the importance of these parameters on ecological niche differentiation in natural environments.
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Affiliation(s)
- Satoshi Okabe
- grid.39158.360000 0001 2173 7691Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628 Japan
| | - Atsushi Kamigaito
- grid.39158.360000 0001 2173 7691Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628 Japan
| | - Kanae Kobayashi
- grid.39158.360000 0001 2173 7691Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628 Japan
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20
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Zhang X, Meng H, Yang Y, Lan W, Wang W, Lam PKS, Li XY, Gu JD. Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1705-1718. [PMID: 33433766 DOI: 10.1007/s10646-020-02332-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 105 to 1.28 × 106 gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH4+-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH4+-N, (NO3- + NO2-)-N, and NH4+/NOX were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.
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Affiliation(s)
- Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu, 210023, The People's Republic of China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, The People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Inspection and Quarantine, Food Inspection and Quarantine Center of Shenzhen Customs, 1011 Fuqiang Road, Shenzhen, 518045, The People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, 163319, People's Republic of China
| | - Paul K S Lam
- Department of Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, The People's Republic of China
| | - Xiao-Yan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, The People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, The People's Republic of China.
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21
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Wu J, Hong Y, Liu X, Hu Y. Variations in nitrogen removal rates and microbial communities over sediment depth in Daya Bay, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117267. [PMID: 33965803 DOI: 10.1016/j.envpol.2021.117267] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Depth-related variations in the activities, abundances, and community composition of denitrification and anaerobic ammonia oxidation (anammox) bacteria in coastal sediment cores remain poorly understood. In this study, we used 15N-labelled incubation, quantitative polymerase chain reaction (qPCR), and high-throughput sequencing techniques to reveal the structure and function of denitrifiers and anammox bacteria in sediment cores (almost 100 cm depth) collected in winter and summer from four locations in Daya Bay. The results indicated that the activities and abundances of both denitrifiers and anammox bacteria were detected even in deeper sediments with low concentrations of dissolved inorganic nitrogen (DIN). The potential rates, abundances, and community compositions of denitrifiers and anammox bacteria only varied spatially. In the surface sediment (top 2 cm), denitrifiers had significantly higher activities and abundances than anammox bacteria, but the relative contribution of anammox bacteria to nitrogen loss increased to >60% in the subsurface sediments. Phylogenetic analysis revealed that nirS-type denitrifiers were affiliated to 10 different clusters and Candidatus Scalindua dominated the anammox community in the whole sediments. Furthermore, both denitrification and anammox bacterial communities in the subsurface sediments were distinct from those in the surface sediments. Coupled nitrification and denitrification or anammox may play significant roles in removing fixed N, and the availability of electronic acceptors (e.g. nitrite and nitrate) strongly influenced the N loss activities in the subsurface sediment, emphasising its role as a sink for buried N.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yaohao Hu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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22
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Li Y, Hong Y, Wu J, Wang Y, Ye F. Spatial variability pattern of the anaerobic ammonia-oxidizing bacterial community across a salinity gradient from river to ocean. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1743-1753. [PMID: 32951159 DOI: 10.1007/s10646-020-02282-5] [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] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
In natural habitats, the diversity of anaerobic ammonia-oxidizing (anammox) bacteria could be affected by multiple environmental variables. In this study, we investigated the distribution of the anammox bacterial community in surface sediment from the Dongjiang River (riverine sediment, DJ) to the Pearl River Estuary (estuarine sediment, PRE) and then to the South China Sea (coastal sediment, SCS). The results revealed evident differences in the structural diversity of anammox bacteria in three different habitats. Candidatus Brocadia accounted for approximately 90% of the total anammox bacteria in DJ, conversely, Ca. Scalindua dominated in the SCS. Nevertheless, Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia coexisted in the PRE. The qPCR results indicated that anammox bacterial 16S rRNA gene abundance ranged from 2.23 × 105 to 1.19 × 107 copies g-1 of wet weight, but no significant correlation was found between the abundances and environmental variables (p > 0.05). The relative abundances of Ca. Brocadia gradually decreased with increasing salinity, and Ca. Scalindua showed the opposite trend, suggesting that salinity was a crucial factor in sculpturing the community composition of anammox bacteria in natural environments. Ca. Brocadia should be able to live in freshwater ecosystems, but it can also tolerate a certain level of salinity. Ca. Scalindua was halophilic anammox bacterium and exists only in saline environments. Ca. Kuenenia could adapt to a wide range of salinity and preferred to live in high DIN level conditions according to our search. The distribution pattern of anammox bacteria may be the result of microbial migration and long-term adaptation to salinity.
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Affiliation(s)
- Yiben Li
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
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23
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Zheng Y, Hou L, Zhang Z, Ge J, Li M, Yin G, Han P, Dong H, Liang X, Gao J, Gao D, Liu M. Overlooked contribution of water column to nitrogen removal in estuarine turbidity maximum zone (TMZ). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147736. [PMID: 34020087 DOI: 10.1016/j.scitotenv.2021.147736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Estuarine systems are important sites of eliminating reactive nitrogen (N) delivered from land to sea. Numerous studies have focused on N cycling in estuarine sediment. However, the N elimination role of suspended sediments in estuarine turbid water column, which might provide anaerobic microenvironment for N loss, is rarely considered. This study examined the community dynamics and activities of denitrifying and anaerobic ammonium oxidation (anammox) bacteria in the water column of the turbidity maximum zone (TMZ) of the Yangtze Estuary, using molecular and 15N isotope-tracing techniques. Results showed that the anammox bacterial community was dominated by Candidatus Kuenenia and Candidatus Brocadia in the TMZ water column, while the main nirS-harboring denitrifiers were affiliated with Rhodobacterales. The denitrifying nirS gene was two orders of magnitude more abundant than anammox bacterial 16S rRNA gene, ranging from 1.77 × 105 to 1.42 × 108 copies l-1 and from 7.68 × 104 to 4.27 × 106 copies l-1, respectively. Compared with anammox, denitrification, with rates of 0.88 to 20.83 μmol N l-1 d-1, overwhelmingly dominated the N removal in the TMZ water column and was significantly correlated to suspended sediment concentrations (SSC). Based on the measured N removal rates, it was estimated that about 2.5 × 105 ton N was annually removed from the TMZ water column, accounting for approximately 18.5% of the total inorganic N (TIN) discharged from the Yangtze River. Overall, this study implies the importance of estuarine turbid water column in controlling N budget, and also improves the understanding of N loss mechanisms in estuarine TMZ systems.
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Affiliation(s)
- Yanling Zheng
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Jianzhong Ge
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Maotian Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Juan Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
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24
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Chen X, Li J, Zhang Y, Liu W. Unraveling nitrogen removal and microbial response of marine anammox bacteria-dominated consortia to Mo(VI) addition in nitrogen-laden saline wastewater treatment. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Akram M, Dietl A, Müller M, Barends TRM. Purification of the key enzyme complexes of the anammox pathway from DEMON sludge. Biopolymers 2021; 112:e23428. [PMID: 33798263 DOI: 10.1002/bip.23428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.
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Affiliation(s)
- Mohd Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Melanie Müller
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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26
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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27
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Liu X, Wu J, Hong Y, Li Y, Hu Y, Wang L, Wang Y, Long A. Wide distribution of anaerobic ammonium‐oxidizing bacteria in the water column of the South China Sea: Implications for their survival strategies. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Yaohao Hu
- State Key Laboratory of Tropical Oceanography (LTO) South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Limei Wang
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area Key Laboratory for Water Quality and Conservation of the Pearl River Delta Ministry of Education Guangzhou University Guangzhou China
- School of Environmental Science and Engineering Guangzhou University Guangzhou China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO) South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
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28
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Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord. World J Microbiol Biotechnol 2020; 36:107. [PMID: 32638161 DOI: 10.1007/s11274-020-02886-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.
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29
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Zhang L, Okabe S. Ecological niche differentiation among anammox bacteria. WATER RESEARCH 2020; 171:115468. [PMID: 31926373 DOI: 10.1016/j.watres.2020.115468] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/03/2019] [Accepted: 01/02/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μmax) and the half-saturation constant for nitrite (KNO2-) and ammonium (KNH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.
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Affiliation(s)
- Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan.
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30
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Bagnoud A, Guye-Humbert S, Schloter-Hai B, Schloter M, Zopfi J. Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils. FEMS Microbiol Ecol 2020; 96:5647352. [PMID: 31782780 DOI: 10.1093/femsec/fiz191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/26/2019] [Indexed: 11/13/2022] Open
Abstract
In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using 15N-labeled substrates revealed that anammox processes contributed about <2% to total N2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs.
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Affiliation(s)
- Alexandre Bagnoud
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland.,Institut de Génie Thermique, Haute École d'Ingénierie et de Gestion du Canton de Vaud, Avenue des Sports 20, CH-1400 Yverdon-les-Bains, Switzerland
| | - Sylvia Guye-Humbert
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
| | - Brigitte Schloter-Hai
- Research Unit for Comparative Microbiome Analysis; Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis; Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Jakob Zopfi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland.,Aquatic and Stable Isotope Biogeochemistry, University of Basel, Bernoullistrasse 30, CH-4056 Basel, Switzerland
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31
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Affiliation(s)
- J. Gijs Kuenen
- Environmental Biotechnology Section, Department of BiotechnologyDelft University of Technology The Netherlands
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32
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Wang Y, Xu L, Wang S, Ye F, Zhu G. Global Distribution of Anaerobic Ammonia Oxidation (Anammox) Bacteria - Field Surveys in Wetland, Dryland, Groundwater Aquifer and Snow. Front Microbiol 2019; 10:2583. [PMID: 31798550 PMCID: PMC6861858 DOI: 10.3389/fmicb.2019.02583] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/24/2019] [Indexed: 11/26/2022] Open
Abstract
The discovery of anaerobic ammonia oxidation (anammox) expanded our knowledge on the microbial nitrogen cycle. Previous studies report that anammox bacteria are distributed in a wide range of habitats and plays significant roles in the global nitrogen cycle. However, most studies focus only on individual ecosystems or datasets from public databases. To date, our understanding of how anammox bacteria respond to environmental properties and are distributed in different habitats on a global scale, remain unclear. To explore the global distribution of anammox bacteria, samples were collected from different habitats at different locations globally, including wetlands, drylands, groundwater aquifers and snow from 10 countries across six continents. We then used high-throughput amplicon sequencing targeting the functional gene hydrazine synthase (HZS) and generated community profiles. Results showed that Candidatus Brocadia is detected as the dominant genus on a global scale, accounting for 80.0% to 99.9% of the retrieved sequences in different habitats. The Jettenia-like sequences were the second most abundant group, accounting for no more than 19.9% of the retrieved sequences in all sites. The samples in drylands, wetlands and groundwater aquifers showed similar community composition and diversity, with the snow samples being the most different. Deterministic processes seem stronger in regulating the community composition of anammox bacteria, which is supported by the higher proportion explained by local-scale factors. Groundwater aquifers showed high gene abundance and the most complex co-occurrence network among the four habitat types, suggesting that it might be the preferred habitat of anammox bacteria. There is little competition between anammox bacterial species based on co-occurrence analysis. Hence, we could infer that environmental factors such as anaerobic and stable conditions, instead of substrate limitations, may be vital factors determining the anammox bacteria community. These results provide a better understanding of the global distribution of anammox bacteria and the ecological factors that affect their community structuring in diverse habitats.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Guangzhou University, Guangzhou, China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Guangzhou University, Guangzhou, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Zheng Y, Hou L, Liu M, Yin G. Dynamics and environmental importance of anaerobic ammonium oxidation (anammox) bacteria in urban river networks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112998. [PMID: 31422342 DOI: 10.1016/j.envpol.2019.112998] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 106 to 3.9 × 107 copies g-1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH4+) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.
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Affiliation(s)
- Yanling Zheng
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
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Bulseco AN, Giblin AE, Tucker J, Murphy AE, Sanderman J, Hiller-Bittrolff K, Bowen JL. Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments. GLOBAL CHANGE BIOLOGY 2019; 25:3224-3241. [PMID: 31317634 DOI: 10.1111/gcb.14726] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 06/10/2023]
Abstract
Salt marshes sequester carbon at rates more than an order of magnitude greater than their terrestrial counterparts, helping to mitigate climate change. As nitrogen loading to coastal waters continues, primarily in the form of nitrate, it is unclear what effect it will have on carbon storage capacity of these highly productive systems. This uncertainty is largely driven by the dual role nitrate can play in biological processes, where it can serve as a nutrient-stimulating primary production or a thermodynamically favorable electron acceptor fueling heterotrophic metabolism. Here, we used a controlled flow-through reactor experiment to test the role of nitrate as an electron acceptor, and its effect on organic matter decomposition and the associated microbial community in salt marsh sediments. Organic matter decomposition significantly increased in response to nitrate, even at sediment depths typically considered resistant to decomposition. The use of isotope tracers suggests that this pattern was largely driven by stimulated denitrification. Nitrate addition also significantly altered the microbial community and decreased alpha diversity, selecting for taxa belonging to groups known to reduce nitrate and oxidize more complex forms of organic matter. Fourier Transform-Infrared Spectroscopy further supported these results, suggesting that nitrate facilitated decomposition of complex organic matter compounds into more bioavailable forms. Taken together, these results suggest the existence of organic matter pools that only become accessible with nitrate and would otherwise remain stabilized in the sediment. The existence of such pools could have important implications for carbon storage, since greater decomposition rates as N loading increases may result in less overall burial of organic-rich sediment. Given the extent of nitrogen loading along our coastlines, it is imperative that we better understand the resilience of salt marsh systems to nutrient enrichment, especially if we hope to rely on salt marshes, and other blue carbon systems, for long-term carbon storage.
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Affiliation(s)
- Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Jane Tucker
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Anna E Murphy
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| | | | | | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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Wang J, Kan J, Qian G, Chen J, Xia Z, Zhang X, Liu H, Sun J. Denitrification and anammox: Understanding nitrogen loss from Yangtze Estuary to the east China sea (ECS). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1659-1670. [PMID: 31284208 DOI: 10.1016/j.envpol.2019.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/18/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.
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Affiliation(s)
- Jing Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Jinjun Kan
- Stroud Water Research Center, 970 Spencer Road, Avondale, PA, 19311, USA
| | - Gang Qian
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jianfang Chen
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Zhiqiang Xia
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaodong Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
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Yin S, Li J, Dong H, Qiang Z. Enhanced nitrogen removal through marine anammox bacteria (MAB) treating nitrogen-rich saline wastewater with Fe(III) addition: Nitrogen shock loading and community structure. BIORESOURCE TECHNOLOGY 2019; 287:121405. [PMID: 31085055 DOI: 10.1016/j.biortech.2019.121405] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Marine anammox bacteria (MAB) were used to treat nitrogen-rich saline wastewater with Fe(III) addition under nitrogen shock loading. Ammonia loading rate (ALR) and nitrite loading rate (NLR) gradually increased from 0.033 and 0.039 to 0.68 and 0.89 kg/(m3·d), respectively. With 5 mg/L Fe(III) addition, ammonia removal rate (ARR) and nitrite removal rate (NRR) reached maximal values of 0.56 and 0.60 kg/(m3·d), respectively. The value of ΔNO2--N/ΔNH4+-N was lower than theoretical ratio due to existing marine Feammox process. The growth rate of MAB was accelerated by Fe(III) and it dominated the reactor (27.70%). Besides, MAB were synergized with Marinicella and Caldithrix to achieve higher total nitrogen removal. Haldane model was proper to analyze and predict the effect resulting from nitrite on the activity of MAB under nitrogen shock loading. Overall, this study provides novel insights into the effect of Fe(III) on MAB treating nitrogen-rich wastewater.
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Affiliation(s)
- Shuyan Yin
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
| | - Huiyu Dong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY, Zhang T. Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. MICROBIOME 2019; 7:122. [PMID: 31462278 PMCID: PMC6714388 DOI: 10.1186/s40168-019-0730-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The metabolic capacities of anammox bacteria and associated microbial community interactions in partial-nitritation anammox (PNA) reactors have received considerable attention for their crucial roles in energy-efficient nitrogen removal from wastewater. However, a comprehensive understanding of how abiotic and biotic factors shape bacterial community assembly in PNA reactors is not well reported. RESULTS Here, we used integrated multi-omics (i.e., high-throughput 16S rRNA gene, metagenomic, metatranscriptomic, and metaproteomic sequencing) to reveal how abiotic and biotic factors shape the bacterial community assembly in a lab-scale one-stage PNA reactor treating synthetic wastewater. Analysis results of amplicon sequences (16S rRNA gene) from a time-series revealed distinct relative abundance patterns of the key autotrophic bacteria, i.e., anammox bacteria and ammonia-oxidizing bacteria (AOB), and the associated heterotrophic populations in the seed sludge and the sludge at the new stable state after deterioration. Using shotgun metagenomic sequences of anammox sludge, we recovered 58 metagenome-assembled genomes (MAGs), including 3 MAGs of anammox bacteria and 3 MAGs of AOB. The integrated metagenomic, metatranscriptomic, and metaproteomic data revealed that nitrogen metabolism is the most active process in the studied PNA reactor. The abundant heterotrophs contribute to the reduction of nitrate to nitrite/ammonium for autotrophic bacteria (anammox bacteria and AOB). Genomic and transcriptomic data revealed that the preference for electron donors of the dominant heterotrophs in different bacterial assemblages (seed and new stable state) varied along with the shift in anammox bacteria that have different metabolic features in terms of EPS composition. Notably, the most abundant heterotrophic bacteria in the reactor were more auxotrophic than the less abundant heterotrophs, regarding the syntheses of amino acids and vitamins. In addition, one of the abundant bacteria observed in the bacterial community exhibited highly transcribed secretion systems (type VI). CONCLUSIONS These findings provide the first insight that the bacterial communities in the PNA reactor are defined by not only abiotic factors (operating mode) but also metabolic interactions, such as nitrogen metabolism, exchange of electron donors, and auxotrophies.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Qigui Niu
- School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, 266237 Shandong Province People’s Republic of China
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Mishty Negi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579 Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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Lau E, Frame CH, Nolan EJ, Stewart FJ, Dillard ZW, Lukich DP, Mihalik NE, Yauch KE, Kinker MA, Waychoff SL. Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone. PLoS One 2019; 14:e0217136. [PMID: 31112557 PMCID: PMC6529010 DOI: 10.1371/journal.pone.0217136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2-) and NO2- to nitrate (NO3-), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). We characterized the distribution of nitrifiers at 5 depths spanning the oxic to hypoxic zone of the offshore Benguela upwelling system above the continental slope off Namibia. Based on 16S rRNA gene amplicon sequencing, the proportional abundance of nitrifiers (ammonia and nitrite oxidizers) increased with depth, driven by an increase in ammonia-oxidizing archaea (AOA; Thaumarchaeota) to up to 33% of the community at hypoxic depths where O2 concentrations fell to ~25 μM. The AOA community transitioned from being dominated by a few members at oxic depths to a more even representation of taxa in the hypoxic zone. In comparison, the community of NO2--oxidizing bacteria (NOB), composed primarily of Nitrospinae, was far less abundant and exhibited higher evenness at all depths. The AOA:NOB ratio declined with depth from 41:1 in the oxic zone to 27:1 under hypoxia, suggesting potential variation in the balance between NO2- production and consumption via nitrification. Indeed, in contrast to prior observations from more O2-depleted sites closer to shore, NO2- did not accumulate at hypoxic depths near this offshore site, potentially due in part to a tightened coupling between AOA and NOB.
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Affiliation(s)
- Evan Lau
- Department of Biology, Menlo College, Atherton, California, United States of America
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
- * E-mail:
| | - Caitlin H. Frame
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - E. Joseph Nolan
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zachary W. Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Daniel P. Lukich
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Nicole E. Mihalik
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Katelyn E. Yauch
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Marcus A. Kinker
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Samantha L. Waychoff
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
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Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria. mSphere 2019; 4:4/1/e00043-19. [PMID: 30787117 PMCID: PMC6382968 DOI: 10.1128/msphere.00043-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment. Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate the hypotheses that newly established aquaria show clear microbial successional patterns over time and that common marine aquarium-conditioning practices, such as the addition of ocean-derived “live rocks” (defined as any “dead coral skeleton covered with crustose coralline algae” transferred into an aquarium from open ocean habitats) impact the diversity of microbial populations as well as nitrogen cycling in aquaria. We collected water chemistry data alongside water and sediment samples from two independent and newly established saltwater aquaria over a 3-month period. Microbial communities in samples were assessed by DNA extraction, amplification of the 16S rRNA gene, and Illumina MiSeq sequencing. Our results showed clear and replicable patterns of community succession in both aquaria, with the existence of multiple stable states for aquarium microbial assemblages. Notably, our results show that changes in aquarium microbial communities do not always correlate with water chemistry measurements and that operational taxonomic unit (OTU)-level patterns relevant to nitrogen cycling were not reported as statistically significant. Overall, our results demonstrate that aquarium perturbations have a substantial impact on microbial community profiles of aquarium water and sediment and that the addition of live rocks improves nutrient cycling by shifting aquarium communities toward a more typical saltwater assemblage of microbial taxa. IMPORTANCE Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with “live rocks” through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment.
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Zhou X, Wang M, Wen C, Liu D. Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:604-615. [PMID: 30208346 DOI: 10.1016/j.scitotenv.2018.08.358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 07/03/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m2, J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m2, J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH4+-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO3--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH4+-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.
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Affiliation(s)
- Xiaohong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Mingyuan Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chunzi Wen
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dan Liu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Fu L, Chen Y, Li S, He H, Mi T, Zhen Y, Yu Z. Shifts in the anammox bacterial community structure and abundance in sediments from the Changjiang Estuary and its adjacent area. Syst Appl Microbiol 2019; 42:383-396. [PMID: 30679000 DOI: 10.1016/j.syapm.2018.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria. 16S rRNA and hzo gene fragments affiliating with known anammox bacterial lineages were recovered, and the two major phylotypes belonged to the Candidatus Scalindua (Ca. Scalindua) genus, with >90% sequence similarity. A phylogenetic analysis detected the Scalindua and Brocadia genera together with some anammox-like bacterial clusters, which suggested a higher diversity in the studied ecosystem than in open ocean environment, where only Scalindua genus was detected. A redundancy analysis (RDA) showed that total organic carbon (TOC) and total nitrogen (TN) content in sediments significantly influenced anammox bacterial abundance of. Spearman correlation analyses confirmed that the spatial variation in anammox bacterial abundance was highly correlated with TOC (P<0.01) and TN (P<0.01) contents in sediments.
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Affiliation(s)
- Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China
| | - Yangyang Chen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Siqi Li
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China
| | - Hui He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao 266100, PR China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China.
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao 266100, PR China
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Wu J, Hong Y, Chang X, Jiao L, Li Y, Liu X, Xie H, Gu JD. Unexpectedly high diversity of anammox bacteria detected in deep-sea surface sediments of the South China Sea. FEMS Microbiol Ecol 2019; 95:5298864. [DOI: 10.1093/femsec/fiz013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/21/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yiguo Hong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Xiangyang Chang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Lijing Jiao
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yiben Li
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Xiaohan Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Haitao Xie
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, P. R. China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P.R. China
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Karačić S, Wilén BM, Suarez C, Hagelia P, Persson F. Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities. BIOFOULING 2018; 34:1161-1174. [PMID: 30740996 DOI: 10.1080/08927014.2018.1556259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Deterioration of concrete is a large societal cost. In the Oslofjord subsea tunnel (Norway), deterioration of sprayed concrete and corrosion of reinforcing steel fibres occur under biofilm formed at sites with intrusion of saline groundwater. In this study, the microbial community structure, in situ environmental gradients and chemical composition of the biofilms were examined at three tunnel sites. Ammonia- and nitrite-oxidising microorganisms, in particular Nitrosopumilus sp., and iron-oxidising bacteria within Mariprofundus sp., were omnipresent, together with a diversity of presumably heterotrophic bacteria. Alpha- and beta diversity measures showed significant differences in richness and community structure between the sites as well as over time and null-models suggested that deterministic factors were important for the community assembly. The superficial flow of water over the biofilm had a strong effect on oxygen penetration in the biofilm and was identified as one major environmental gradient that varied between the sites, likely being important for shaping the microbial communities.
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Affiliation(s)
- Sabina Karačić
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Carolina Suarez
- b Department of Chemistry and Molecular Biology , University of Gothenburg , Göteborg , Göteborg , Sweden
| | - Per Hagelia
- c Tunnel and Concrete Division , The Norwegian Public Roads Administration , Oslo , Norway
| | - Frank Persson
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
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Ali M, Shaw DR, Zhang L, Haroon MF, Narita Y, Emwas AH, Saikaly PE, Okabe S. Aggregation ability of three phylogenetically distant anammox bacterial species. WATER RESEARCH 2018; 143:10-18. [PMID: 29933181 DOI: 10.1016/j.watres.2018.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/30/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are well known for their aggregation ability. However, very little is known about cell surface physicochemical properties of anammox bacteria and thus their aggregation abilities have not been quantitatively evaluated yet. Here, we investigated the aggregation abilities of three different anammox bacterial species: "Candidatus Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Brocadia sapporoensis". Planktonic free-living enrichment cultures of these three anammox species were harvested from the membrane bioreactors (MBRs). The physicochemical properties (e.g., contact angle, zeta potential, and surface thermodynamics) were analyzed for these anammox bacterial species and used in the extended DLVO theory to understand the force-distance relationship. In addition, their extracellular polymeric substances (EPSs) were characterized by X-ray photoelectron spectroscopy and nuclear magnetic resonance. The results revealed that the "Ca. B. sinica" cells have the most hydrophobic surface and less hydrophilic functional groups in EPS than other anammox strains, suggesting better aggregation capability. Furthermore, aggregate formation and anammox bacterial populations were monitored when planktonic free-living cells were cultured in up-flow column reactors under the same conditions. Rapid development of microbial aggregates was observed with the anammox bacterial population shifts to a dominance of "Ca. B. sinica" in all three reactors. The dominance of "Ca. B. sinica" could be explained by its better aggregation ability and the superior growth kinetic properties (higher growth rate and affinity to nitrite). The superior aggregation ability of "Ca. B. sinica" indicates significant advantages (efficient and rapid start-up of anammox reactors due to better biomass retention as granules and consequently stable performance) in wastewater treatment application.
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Affiliation(s)
- Muhammad Ali
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia; Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Dario Rangel Shaw
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia
| | - Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Mohamed Fauzi Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yuko Narita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology, Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Pascal E Saikaly
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Center, Thuwal, 23955-6900, Saudi Arabia.
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan.
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Mojiri A, Nishimoto K, Awata T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T. Effects of Salts on the Activity and Growth of "Candidatus Scalindua sp.", a Marine Anammox Bacterium. Microbes Environ 2018; 33:336-339. [PMID: 30146541 PMCID: PMC6167117 DOI: 10.1264/jsme2.me18068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/01/2018] [Indexed: 12/03/2022] Open
Abstract
Four salts, SEALIFE (a synthetic sea salt), NaCl, Na2SO4, and NaCl+KCl, were applied to monitor the effects of salinity on "Candidatus Scalindua sp.", a marine anaerobic ammonium oxidation (anammox) bacterium. The highest ammonium consumption of 10 μmol mg protein-1 d-1 was observed at 88 mmol L-1 of Na in the presence of NaCl. The highest inorganic carbon uptake of 0.6 μmol mg protein-1 d-1 was observed at 117 mmol L-1 of Na and at 16 mmol L-1 of K in the presence of NaCl+KCl. Thus, Na and K are both important for maintaining a high growth rate of "Candidatus Scalindua sp."
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Affiliation(s)
- Amin Mojiri
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University1–4–1, Kagamiyama, Higashihiroshima 739–8527Japan
| | - Kazuma Nishimoto
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University1–4–1, Kagamiyama, Higashihiroshima 739–8527Japan
| | - Takanori Awata
- Institute of Materials and Systems for Sustainability (IMaSS), Nagoya UniversityFuro-cho, Chikusa-ku, Nagoya 464–8601Japan
| | - Yoshiteru Aoi
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University1–3–1 Kagamiyama, Higashihiroshima 739–8530Japan
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University1–4–1, Kagamiyama, Higashihiroshima 739–8527Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University1–4–1, Kagamiyama, Higashihiroshima 739–8527Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University1–4–1, Kagamiyama, Higashihiroshima 739–8527Japan
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Wu J, Hong Y, He X, Jiao L, Wen X, Chen S, Chen G, Li Y, Huang T, Hu Y, Liu X. Anaerobic Ammonium Oxidation in Acidic Red Soils. Front Microbiol 2018; 9:2142. [PMID: 30233562 PMCID: PMC6134040 DOI: 10.3389/fmicb.2018.02142] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/21/2018] [Indexed: 01/29/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 106 to 1.81 × 109 and 4.81 × 106 to 4.54 × 108 copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a 15N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g−1 h−1, contributing 16.67–53.27% to N2 production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yiguo Hong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Xiang He
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Lijing Jiao
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Wen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Shuai Chen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Guangshi Chen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yiben Li
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Tianzheng Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yaohao Hu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohan Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
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Kamira B, Shi LL, Fan LM, Zhang C, Zheng Y, Song C, Meng SL, Hu GD, Bing XW, Chen ZJ, Xu P. Methane-generating ammonia oxidizing nitrifiers within bio-filters in aquaculture tanks. AMB Express 2018; 8:140. [PMID: 30155810 PMCID: PMC6113197 DOI: 10.1186/s13568-018-0668-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/17/2018] [Indexed: 11/10/2022] Open
Abstract
The discovery of aerobic and anammox bacteria capable of generating methane in bio-filters in freshwater aquaculture systems is generating interest in studies to understand the activity, diversity, distribution and roles of these environmental bacteria. In this study, we used microbial enrichment of bio-filters to assess their effect on water quality. Profiles of ammonia-oxidizing bacterial communities generated using nested PCR methods and DGGE were used to assess the expression of 16S rRNA genes using DNA sequencing. Five dominant ammonia-oxidizing bacterial strains-clones; KB.13, KB.15, KB.16, KB.17 and KB.18-were isolated and identified by phylogenetic analysis as environmental samples closely related to genera Methylobacillus, Stanieria, Nitrosomonas, and Heliorestis. The methyl ammonia-oxidizing microbes thereby found suggest a biochemical pathway involving electron donors and carbon sources, and all strains were functional in freshwater aquaculture systems. Environmental parameters including TN (2.69-20.43); COD (9.34-31.47); NH4+-N (0.44-11.78); NO2-N (0.00-3.67); NO3-N (0.05-1.82), mg/L and DO (1.47-10.31 µg/L) assessed varied in the ranges in the different tanks. Principal component analysis revealed that these water quality parameters significantly influenced the ammonia oxidizing microbial community composition. Temperature rises to about 40 °C significantly affected environmental characteristics-especially DO, TN and NH4+-N-and directly or indirectly affected the microbial communities. Although the nested PCR design was preferred due to its high sensitivity for amplifying specific DNA regions, a more concise method is recommended, as an equimolar mixture of degenerate PCR primer pairs, CTO189f-GC and CTO654r, never amplified only 16S rRNA of ammonia-oxidizing bacteria.
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Affiliation(s)
- Barry Kamira
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Present Address: Freshwater Fisheries Resources Center (FFRC), Chinese Academy of Fisheries Sciences (CAFs), Wuxi, People’s Republic of China
| | - Lei Lei Shi
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
| | - Li Min Fan
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Cong Zhang
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Yao Zheng
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Chao Song
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Shun Long Meng
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Geng Dong Hu
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Xu Wen Bing
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Zhang Jia Chen
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Pao Xu
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
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Kanders L, Beier M, Nogueira R, Nehrenheim E. Sinks and sources of anammox bacteria in a wastewater treatment plant - screening with qPCR. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2018; 78:441-451. [PMID: 30101779 DOI: 10.2166/wst.2018.318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The deammonification process, which includes nitritation and anammox bacteria, is an energy-efficient nitrogen removal process. Starting up an anammox process in a wastewater treatment plant (WWTP) is still widely believed to require external seeding of anammox bacteria. To demonstrate the principle of a non-seeded anammox start-up, anammox bacteria in potential sources must be quantified. In this study, seven digesters, their substrates and reject water were sampled and quantitative polymerase chain reaction (qPCR) was used to quantify both total and viable anammox bacteria. The results show that mesophilic digesters fed with nitrifying sludge (with high sludge ages) can be classified as a reliable source of anammox bacteria. Sludge hygienization and dewatering of digestate reduce the amount of anammox bacteria by one to two orders of magnitude and can be considered as a sink. The sampled reject waters contained on average >4.0 × 104 copies mL-1 and the majority of these cells (>87%) were viable cells. Furthermore, plants with side-stream anammox treatment appear to have higher overall quantities of anammox bacteria than those without such treatment. The present study contributes to the development of sustainable strategies for both start-up of anammox reactors and the possibility of improving microbial management in WWTPs.
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Affiliation(s)
- Linda Kanders
- Purac AB, Box 1146, SE-221 05 Lund, Sweden E-mail: ; School of Business, Society and Engineering, Mälardalen University, Box 883, SE-721 23 Västerås, Sweden
| | - Maike Beier
- Institute for Sanitary Engineering and Waste Management (ISAH), Leibniz Universitaet Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management (ISAH), Leibniz Universitaet Hannover, Welfengarten 1, 30167 Hannover, Germany
| | - Emma Nehrenheim
- School of Business, Society and Engineering, Mälardalen University, Box 883, SE-721 23 Västerås, Sweden
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Wang M, Keeley R, Zalivina N, Halfhide T, Scott K, Zhang Q, van der Steen P, Ergas SJ. Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:845-857. [PMID: 29660710 DOI: 10.1016/j.jenvman.2018.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 05/21/2023]
Abstract
The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes.
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Affiliation(s)
- Meng Wang
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Ryan Keeley
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, BSF 132, Tampa, FL 33620-5200, USA.
| | - Nadezhda Zalivina
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Trina Halfhide
- Department of Life Sciences, The University of The West Indies, Natural Sciences Building, New Wing, Room 225, St. Augustine, Trinidad and Tobago.
| | - Kathleen Scott
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, BSF 132, Tampa, FL 33620-5200, USA.
| | - Qiong Zhang
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Peter van der Steen
- Department of Environmental Engineering and Water Technology, IHE Institute for Water Education, PO Box 3015, 2601 DA, Delft, The Netherlands.
| | - Sarina J Ergas
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
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