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Sampara P, Luo Y, Lin X, Ziels RM. Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11670-11682. [PMID: 35929783 PMCID: PMC9387530 DOI: 10.1021/acs.est.2c02081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.
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Xuan Y, Mai Y, Xu Y, Zheng J, He Z, Shu L, Cao Y. Enhanced microbial nitrification-denitrification processes in a subtropical metropolitan river network. WATER RESEARCH 2022; 222:118857. [PMID: 35868099 DOI: 10.1016/j.watres.2022.118857] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Urban rivers are hotspots of regional nitrogen (N) pollution and N transformations. Previous studies have reported that the microbial community of urban rivers was different from that of natural rivers. However, how microbial community affects N transformations in the urban rivers is still unclear. In this study, we employed N nutrients-related isotope technology (includes natural-abundance isotopes survey and isotope-labeling method) and bioinformatics methods (includes 16S rRNA high-throughput sequencing and quantitative PCR analysis) to investigate the major N transformations, microbial communities as well as functional gene abundances in a metropolitan river network. Our results suggested that the bacterial community structure in the highly urbanized rivers was characterized by higher richness, less complexity and increased abundances of nitrification and denitrifying bacterium compared to those in the suburban rivers. These differences were mainly caused by high sewage discharge and N loadings. In addition, the abundances of nitrifier gene (amoA) and denitrifier genes (nirK and nirS) were significantly higher in the highly urbanized rivers (2.36 × 103, 7.43 × 107 and 2.28 × 107 copies·mL-1) than that in the suburban rivers (0.43 × 103, 2.18 × 107 and 0.99 × 107 copies·mL-1). These changes in microbes have accelerated nitrification-denitrification processes in the highly urbanized rivers as compared to those in the suburban rivers, which was evidenced by environmental isotopes and the rates of nitrification (10.52 vs. 0.03 nmol·L-1·h-1) and denitrification (83.31 vs. 22.49 nmol·g-1·h-1). Overall, this study concluded that the excess exogenous N has significantly shaped the specific aquatic bacterial communities, which had a potential for enhancing nitrification-denitrification processes in the highly urbanized river network. This study provides a further understanding of microbial N cycling in urban river ecosystems and expands the combined application of isotopic technology and bioinformatics methods in studying biogeochemical cycling.
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Affiliation(s)
- Yingxue Xuan
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingwen Mai
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Yunqiu Xu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Jianyi Zheng
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China.
| | - Yingjie Cao
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China.
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53
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Patil MP, Woo HE, Lee IC, Nakashita S, Kim K, Kim JO, Kim K. A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115229. [PMID: 35544980 DOI: 10.1016/j.jenvman.2022.115229] [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: 01/19/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - In-Cheol Lee
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Shinya Nakashita
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan
| | - Kyeongmin Kim
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan; Coastal and Estuarine Sediment Dynamics Group, Port and Airport Research Institute, 3-1-1 Nagase, Yokosuka, 239-0826, Kanagawa, Japan
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
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54
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Xiong C, Li Q, Tam NF, Zhang X, Tai Y, Wu R, Huang L, Vymazal J, Dai Y, Yang Y. The combination sequence effect on nitrogen removal pathway in hybrid constructed wetlands treating raw sewage from multiple perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155200. [PMID: 35421456 DOI: 10.1016/j.scitotenv.2022.155200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
The combination sequence of traditional hybrid constructed wetlands (HCWs) affects the removal of nitrogen in raw sewage, but the effect of the combination sequence on nitrogen removal pathway have seldom been reported, especially the specific conditions allowing anammox to occur. Three-stage HCWs, namely vertical flow (VF), horizontal flow (HF) and surface flow (SF) constructed wetlands, were arranged in six different sequences to investigate nitrogen removal efficiencies and microbial removal pathways using metagenomic and stable isotope analyses. Results showed that the combination sequence significantly affected nitrogen removal pathways in HCWs. We found the best removal of total nitrogen (~50%) and ammonium (NH4+-N, ~99%) in HCWs with a VFCW in the 1st stage. Metagenomic results and stable isotope analyses further indicated that simultaneous nitrification and heterotrophic denitrification were the main pathways in unsaturated VFCW, which depended on the energy substance and electron donor supplied by chemical oxygen demand (CODCr) in raw sewage. Nitrifier, anammox bacteria and autotrophic denitrifies prevailed in the subsequent saturated CWs, which tend to nitrogen loss by partial nitrification and anammox in HFCW when fed with NH4+-N wastewater with low CODCr. Providing NH4+-N and oxygen in low CODCr wastewater was the essential step to facilitate anammox process in HFCW. It implied that the problem of poor nitrogen removal due to carbon limitation could be overcome by optimizing conditions in anammox's favor.
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Affiliation(s)
- Chunhui Xiong
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Qiwen Li
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Nora Fungyee Tam
- Department of Science, Open University of Hong Kong, Homantin, Kowloon, Hong Kong Special Administrative Region, China; Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region, China
| | - Xiaomeng Zhang
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Yiping Tai
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Ruitai Wu
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Lingjie Huang
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Jan Vymazal
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, 16521 Prague 6, Czech Republic
| | - Yunv Dai
- Department of Ecology, Jinan University, Guangzhou 510632, China.
| | - Yang Yang
- Department of Ecology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China.
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55
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Meng S, Peng T, Wang H, Huang T, Gu JD, Hu Z. Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments. Appl Microbiol Biotechnol 2022; 106:5811-5822. [PMID: 35941255 DOI: 10.1007/s00253-022-12104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China.,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China.
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56
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Rani V, Prasanna R, Kaushik R. Prospecting the significance of methane-utilizing bacteria in agriculture. World J Microbiol Biotechnol 2022; 38:176. [PMID: 35922575 DOI: 10.1007/s11274-022-03331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.
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Affiliation(s)
- Vijaya Rani
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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57
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Bai X, Hu X, Liu J, Gu H, Jin J, Liu X, Wang G. Evaluation of four primer sets for analysis of comammox communities in black soils. Front Microbiol 2022; 13:944373. [PMID: 35958136 PMCID: PMC9362984 DOI: 10.3389/fmicb.2022.944373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3–-N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.
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Affiliation(s)
- Xin Bai
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haidong Gu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- *Correspondence: Guanghua Wang,
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58
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Haryono MAS, Law YY, Arumugam K, Liew LCW, Nguyen TQN, Drautz-Moses DI, Schuster SC, Wuertz S, Williams RBH. Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling. Front Microbiol 2022; 13:869135. [PMID: 35756038 PMCID: PMC9230771 DOI: 10.3389/fmicb.2022.869135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
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Affiliation(s)
- Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Larry C-W Liew
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thi Quynh Ngoc Nguyen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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59
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Cao Y, Gao Y, Tian Y, Li J. Compost Addition Attenuates the Negative Impacts of High Soil Mineral Nitrogen Levels on Rhizosphere Microbial Characteristics and Enhances Cucumber Growth in Monoculture Systems. PLANTS (BASEL, SWITZERLAND) 2022; 11:1621. [PMID: 35807574 PMCID: PMC9269332 DOI: 10.3390/plants11131621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Due to the increase in the human population, it is necessary to seek efficient methods of increasing crop productivity and, simultaneously, sustaining the soil. One way is to grow high demand crops continuously without rotating with other crops. This practice is often accompanied by increased rates of fertilizer application that can affect efficient nitrogen (N) cycling in the plant rhizosphere soil which, in turn, affects both plant growth and environmental pollution. In the present study, twelve various cucumber soils were selected from monoculture systems presenting different cropping years and divided into two groups including soils with relatively high mineral N (HMN) content (N > 100 mg kg−1 soil) and those with a lower mineral N (LMN) content (N < 100 mg kg−1 soil). All soils were amended with the addition of compost alone or in combination with bacterial inoculation to evaluate their effects on plant growth, microbial numbers, N mineralization, and N cycling genes. In general, the HMN soils increased (p < 0.05) net N mineralization (NNM) but did not statistically (p > 0.05) affect plant biomass compared to the LMN soils; however, compost addition increased both NNM and plant biomass in the HMN soils. In addition, the HMN soils had higher fungal pathogen numbers (FPNs) but lower total microbial biomass (TMB) and bacterial numbers (BNs) compared to the LMN soils; however, compost addition decreased FPNs but increased TMB and BNs in the HMN soils (all p < 0.05). Plant biomass was positively related to TMB, BN and NNM but was negatively related to FPN (all p < 0.05). In summary, compost addition reduced the high mineral N levels’ adverse effects on the rhizosphere soil and plant growth.
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Affiliation(s)
- Yune Cao
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
| | - Yanming Gao
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
| | - Yongqiang Tian
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Jianshe Li
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
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60
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Patil MP, Woo HE, Kim JO, Kim K. Field study on short-term changes in benthic environment and benthic microbial communities using pyrolyzed oyster shells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153891. [PMID: 35182647 DOI: 10.1016/j.scitotenv.2022.153891] [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: 01/10/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To evaluate the effect of pyrolyzed crushed oyster shells (PCOS) on the remediation of sediments and microbial diversity, a field study was conducted in Buksin Bay, Tongyeong City, Republic of Korea. It was observed that after treatment with PCOS, the concentration of H2S in the sediment of the control site was 287 mg/L. Furthermore, it decreased up to 0 mg/L and remained so until the end of the field study, that is for a period of six months. Moreover, the concentrations of NO2-N + NO3-N, NH4-N, and PO4-P decreased sharply, and the oxidation-reduction potential (ORP) increased after PCOS treatment in pore water and overlying water. Regarding the diversity of microbial communities, the predominance of bacteria from phylum Chlorobi was observed in highly reduced (-410 mV; ORP) sediment, which is well known for the production of H2S. After PCOS treatment, the relative abundance of Chlorobi was sharply suppressed. On the other hand, the predominance of bacteria from the phyla Proteobacteria and Bacteroidetes was observed, and their relative abundance in the PCOS-treated sediment increased throughout the experiment, based on 16S rRNA sequencing. The results demonstrate that the abundance of bacterial communities in the PCOS-treated sediments of Buksin Bay is important for marine ecological functioning, especially for pollutant transformation.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
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61
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Fisk LM, Barton L, Maccarone LD, Jenkins SN, Murphy DV. Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil. Sci Rep 2022; 12:7299. [PMID: 35508560 PMCID: PMC9068766 DOI: 10.1038/s41598-022-10711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
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Affiliation(s)
- L M Fisk
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - L Barton
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - L D Maccarone
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S N Jenkins
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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62
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Newton K, Gonzalez E, Pitre FE, Brereton NJB. Microbial community origin and fate through a rural wastewater treatment plant. Environ Microbiol 2022; 24:2516-2542. [PMID: 35466495 DOI: 10.1111/1462-2920.16025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kymberly Newton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Emmanuel Gonzalez
- Canadian Center for Computational Genomics, Department of Human Genetics, McGill University, Montréal, H3A 1A4, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
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63
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Vilardi KJ, Cotto I, Rivera MS, Dai Z, Anderson CL, Pinto A. Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability in biofiltration systems. FEMS Microbiol Ecol 2022; 98:6553816. [PMID: 35325104 DOI: 10.1093/femsec/fiac032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/20/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this is due to competitive or cooperative interactions, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifiers is critical to manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosm-based experiments were used to investigate the impact of nitrogen source and loading on the population dynamics of nitrifiers in drinking water biofilter media. Shotgun sequencing of DNA followed by co-assembly and reconstruction of metagenome assembled genomes revealed clade A2 comammox bacteria were likely the primary nitrifiers within microcosms and increased in abundance over Nitrsomonas-like ammonia and Nitrospira-like nitrite oxidizing bacteria irrespective of nitrogen source type or loading. Changes in comammox bacterial abundance did not correlate with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential for cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with nitrite oxidizers in ammonia amended systems. This suggests potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.
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Affiliation(s)
- Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, MA, MA, USA
| | - Irmarie Cotto
- Department of Civil and Environmental Engineering, Northeastern University, MA, MA, USA
| | | | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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64
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Frey B, Varliero G, Qi W, Stierli B, Walthert L, Brunner I. Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. Front Microbiol 2022; 13:828977. [PMID: 35300488 PMCID: PMC8921678 DOI: 10.3389/fmicb.2022.828977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Gilda Varliero
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Centre for Microbial Ecology and Genomics, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Weihong Qi
- Functional Genomics Center Zurich (FGCZ), ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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65
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Effects of aquatic nitrogen pollution on particle-attached ammonia-oxidizing bacteria in urban freshwater mesocosms. World J Microbiol Biotechnol 2022; 38:64. [DOI: 10.1007/s11274-022-03251-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
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66
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Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052732. [PMID: 35270425 PMCID: PMC8910298 DOI: 10.3390/ijerph19052732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022]
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha-1 yr-1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha-1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g-1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g-1 dry soil with the N105 treatment (105 kg N ha-1 yr-1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha-1 yr-1 was optimum for the AOB community and wheat yield in the semi-arid area.
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67
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Koike K, Smith GJ, Yamamoto-Ikemoto R, Lücker S, Matsuura N. Distinct comammox Nitrospira catalyze ammonia oxidation in a full-scale groundwater treatment bioreactor under copper limited conditions. WATER RESEARCH 2022; 210:117986. [PMID: 34974343 DOI: 10.1016/j.watres.2021.117986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Microbial ammonia oxidation is the initial nitrification step used in biological nitrogen-removal during water treatment processes, and the discovery of complete ammonia-oxidizing (comammox) bacteria added a novel member to this functional group. It is important to identify and understand the predominant microorganisms responsible for ammonium removal in biotechnological process design and optimization. In this study, we used a full-scale bioreactor to treat ammonium in groundwater (9.3 ± 0.5 mg NH4+-N/L) and investigated the key ammonia-oxidizing prokaryotes present. The groundwater ammonium was stably and efficiently oxidized throughout ∼700 days of bioreactor operation. 16S rRNA gene amplicon sequencing of the bioreactor community showed a high abundance of Nitrospira (12.5-45.9%), with the dominant sequence variant (3.5-37.8%) most closely related to Candidatus Nitrospira nitrosa. Furthermore, analyses of amoA, the marker gene for ammonia oxidation, indicated the presence of two distinct comammox Nitrospira populations, however, the relative abundance of only one of these populations was strongly correlated to ammonia oxidation rates and was robustly expressed. After 380 days of operation copper wires were immersed into the reactor at 0.04-0.06 m2/m3 tank, which caused a gradual abundance increase of one discrete comammox Nitrospira population. However, further increase of the copper dosing (0.08 m2/m3 tank) inverted the most abundant ammonia-oxidizing population to Nitrosomonas sp. These results indicate that comammox Nitrospira were capable of efficient ammonium removal in groundwater without exogenous nutrients, but copper addition can stimulate comammox Nitrospira or lead to dominance of Nitrosomonas depending on dosage.
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Affiliation(s)
- Kazuyoshi Koike
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Garrett J Smith
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, Nijmegen, AJ 6525, the Netherlands
| | - Ryoko Yamamoto-Ikemoto
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, Nijmegen, AJ 6525, the Netherlands
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.
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68
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Pan J, Liu Y, Yang Y, Cheng Z, Lan X, Hu W, Shi G, Zhang Q, Feng H. Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem. Environ Microbiol 2022; 24:3598-3611. [PMID: 35048487 DOI: 10.1111/1462-2920.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongjun Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, China
| | - Yue Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongxia Cheng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaomei Lan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weigang Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guoxi Shi
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
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69
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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: 15] [Impact Index Per Article: 7.5] [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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70
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Cao Y, Wang X, Zhang X, Misselbrook TH, Bai Z, Wang H, Ma L. The effects of electric field assisted composting on ammonia and nitrous oxide emissions varied with different electrolytes. BIORESOURCE TECHNOLOGY 2022; 344:126194. [PMID: 34710594 DOI: 10.1016/j.biortech.2021.126194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Enhancing electron transfer through directly elevating electric potential has been verified to reduce gaseous emissions from composting. Reducing electric resistance of composting biomass might be a choice to further strengthening electron transfer. Here, the effects of chemical electrolytes addition on gaseous Nitrogen emission in electric field assistant composting were investigated. Results suggest that adding acidic electrolyte (ferric chloride) significantly reduced ammonia (NH3) emission by 72.1% but increased nitrous oxide (N2O) emission (by 24-fold) (P < 0.05), because of a dual effect on nitrifier activity: i) an elevated abundance and proportion of ammonia oxidizing bacteria Nitrosomonadaceae, and ii) delayed growth of nitrite oxidizing bacteria. Neutral and alkaline electrolytes had no negative or positive effect on N2O or NH3 emission. Hence, there is a potential trade-off between NH3 and N2O mitigation if using ferric chloride as acidic electrolyte, and electrolyte addition should aim to enhance electron production promote N2O mitigation.
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Affiliation(s)
- Yubo Cao
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Xuan Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Xinyuan Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Tom H Misselbrook
- Sustainable Agricultural Sciences, Rothamsted Research, North Wyke, Okehampton EX20 2SB, UK
| | - Zhaohai Bai
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Hongge Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Lin Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China.
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71
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Lu S, Liu X, Liu C, Cheng G, Zhou R, Li Y. A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China. Front Microbiol 2021; 12:775794. [PMID: 34917055 PMCID: PMC8671037 DOI: 10.3389/fmicb.2021.775794] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chong Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Guofeng Cheng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Runfeng Zhou
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yayuan Li
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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72
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Fang J, Dong J, Li C, Chen H, Wang L, Lyu T, He H, Liu J. Response of microbial community composition and function to emergent plant rhizosphere of a constructed wetland in northern China. APPLIED SOIL ECOLOGY 2021; 168:104141. [DOI: 10.1016/j.apsoil.2021.104141] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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73
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Zhao B, Li X, Wang Y, Tan X, Qi W, Li H, Wei J, You Y, Shi W, Zhang Q. Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68155-68173. [PMID: 34264489 DOI: 10.1007/s11356-021-15197-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO3-, NH4+, DOC/NO3-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.
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Affiliation(s)
- Binjie Zhao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinshuai Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenhua Qi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongran Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junwei Wei
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, China
- College of Science, Tibet University, Lhasa, 850000, China
| | - Yong You
- College of Land and Resources, China West Normal University, Nanchong, 637009, China
| | - Wenjun Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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74
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Zhang B, Zhou M, Zhu B, Xiao Q, Wang T, Tang J, Yao Z, Kiese R, Butterbach-Bahl K, Brüggemann N. Soil type affects not only magnitude but also thermal sensitivity of N 2O emissions in subtropical mountain area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149127. [PMID: 34311350 DOI: 10.1016/j.scitotenv.2021.149127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
It is a concern whether the effect of soil type on N2O emissions has to be considered for regional mitigation strategies and emission estimates in mountainous areas with inherent spatial heterogeneities of soil type. To date, there were few field experiments which investigated soil type effects on N2O emissions. Thus a 2-year field study was conducted to measure N2O emissions and soil environmental variables from three different soils that were formed from similar parental rock under the same climate. Seasonal N2O fluxes ranged from 0.18 to 0.40 kg N ha-1 for wheat seasons and 0.40 to 1.50 kg N ha-1 for maize seasons across different experimental soils. The intra- and inter-annual variations in N2O emissions were mainly triggered by temporal dynamics of soil temperature and moisture conditions. On average, seasonal N2O fluxes for acidic soils were significantly lower than for neutral and alkaline soils in cold-dry wheat seasons while significantly greater than for neutral and alkaline soils in warm-wet maize seasons. These determined differences of N2O emissions were mainly caused by differences of initial soil properties across different soils. Moreover, seasonal N2O fluxes were positively correlated with soil pH in wheat seasons, but negatively correlated in maize seasons. The temperature sensitivity coefficient (Q10) of soil N2O emissions for acidic soil (4.06) were significantly greater than those for neutral (1.82) and alkaline (1.15) soils. Overall, N2O emissions for acidic soils were not only higher than those for neutral and alkaline soils but also more sensitive to changing temperature. The present study highlights that soil type is needed to be carefully considered for regional estimate and proposing mitigation strategy of N2O emissions especially in subtropical mountain regions with inherent great heterogeneity of soil type.
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Affiliation(s)
- Bowen Zhang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China; University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Minghua Zhou
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China.
| | - Bo Zhu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China
| | - Qianying Xiao
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China; University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Tao Wang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China
| | - Jialiang Tang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, PR China
| | - Zhisheng Yao
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, 100029 Beijing, PR China
| | - Ralf Kiese
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Klaus Butterbach-Bahl
- Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences - Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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75
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Soil bacterial community as impacted by addition of rice straw and biochar. Sci Rep 2021; 11:22185. [PMID: 34773058 PMCID: PMC8589988 DOI: 10.1038/s41598-021-99001-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/09/2021] [Indexed: 01/19/2023] Open
Abstract
The application of straw and biochar can effectively improve soil quality, but whether such application impacts paddy soil bacterial community development remains to be clarified. Herein, the impacts of three different field amendment strategies were assessed including control (CK) treatment, rice straw (RS) application (9000 kg ha−1), and biochar (BC) application (3150 kg ha−1). Soil samples were collected at five different stages of rice growth, and the bacterial communities therein were characterized via high-throughput 16S rDNA sequencing. The results of these analyses revealed that soil bacterial communities were dominated by three microbial groups (Chloroflexi, Proteobacteria and Acidobacteria). Compared with the CK samples, Chloroflexi, Actinobacteria, Nitrospirae and Gemmatimonadetes levels were dominated phyla in the RS treatment, and Acidobacteria, Actinobacteria, Nitrospirae and Patescibacteria were dominated phyla in the BC treatment. Compared with the RS samples, Chloroflexi, Acidobacteria, Actinobacteria, and Verrucomicrobia levels were increased, however, Proteobacteria, Gemmatimonadetes, Nitrospirae, and Firmicute levels were decreased in the BC samples. Rhizosphere soil bacterial diversity rose significantly following RS and BC amendment, and principal component analyses confirmed that there were significant differences in soil bacterial community composition among treatment groups when comparing all stages of rice growth other than the ripening stage. Relative to the CK treatment, Gemmatimonadaceae, Sphingomonadaceae, Thiovulaceae, Burkholderiaceae, and Clostridiaceae-1 families were dominant following the RS application, while Thiovulaceae and uncultured-bacterium-o-C0119 were dominant following the BC application. These findings suggest that RS and BC application can improve microbial diversity and richness in paddy rice soil in Northeast China.
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76
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Hamiruddin NA, Awang NA, Mohd Shahpudin SN, Zaidi NS, Said MAM, Chaplot B, Azamathulla HM. Effects of wastewater type on stability and operating conditions control strategy in relation to the formation of aerobic granular sludge - a review. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:2113-2130. [PMID: 34810301 DOI: 10.2166/wst.2021.415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Currently, research trends on aerobic granular sludge (AGS) have integrated the operating conditions of extracellular polymeric substances (EPS) towards the stability of AGS systems in various types of wastewater with different physical and biochemical characteristics. More attention is given to the stability of the AGS system for real site applications. Although recent studies have reported comprehensively the mechanism of AGS formation and stability in relation to other intermolecular interactions such as microbial distribution, shock loading and toxicity, standard operating condition control strategies for different types of wastewater have not yet been discussed. Thus, the dimensional multi-layer structural model of AGS is discussed comprehensively in the first part of this review paper, focusing on diameter size, thickness variability of each layer and diffusion factor. This can assist in facilitating the interrelation between disposition and stability of AGS structure to correspond to the changes in wastewater types, which is the main objective and novelty of this review.
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Affiliation(s)
- N A Hamiruddin
- School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang, Malaysia E-mail:
| | - N A Awang
- School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang, Malaysia E-mail:
| | - S N Mohd Shahpudin
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
| | - N S Zaidi
- School of Civil Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Malaysia
| | - M A M Said
- School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang, Malaysia E-mail:
| | - B Chaplot
- Department of Geography, M.J.K College, Bettiah, a constituent unit of B.R.A., Bihar University, Bettiah, Muzaffarpur, India
| | - H M Azamathulla
- Faculty of Engineering, The University of the West Indies, St. Augustine, Trinidad
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77
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Tatsumi C, Azuma WA, Ogawa Y, Komada N. Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest. MICROBIAL ECOLOGY 2021; 82:919-931. [PMID: 33606088 DOI: 10.1007/s00248-021-01707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.
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Affiliation(s)
- Chikae Tatsumi
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Wakana A Azuma
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, 657-8501, Japan.
| | - Yuya Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Natsuki Komada
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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78
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Finn DR, Lee S, Lanzén A, Bertrand M, Nicol GW, Hazard C. Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial. FEMS Microbiol Ecol 2021; 97:6374554. [PMID: 34555173 DOI: 10.1093/femsec/fiab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022] Open
Abstract
Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.
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Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, 38116 Braunschweig, Germany.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Sungeun Lee
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Anders Lanzén
- NEIKER, Basque Institute of Agricultural Research and Development, c/ Berreaga 1, 48160 Derio, Spain
| | - Michel Bertrand
- UMR Agronomie, INRAE AgroParisTech Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
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79
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Wang YF, Gu JD, Dick RP, Han W, Yang HX, Liao HQ, Zhou Y, Meng H. Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1769-1779. [PMID: 33432457 DOI: 10.1007/s10646-020-02327-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.
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Affiliation(s)
- Yong-Feng Wang
- Institute of Environment and Ecology, Institute of Environmental Health and Ecological Security, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, PR China.
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, PR China
| | - Richard P Dick
- School of Environment and Natural Resources, The Ohio State University, 2021 Coffey Road, Columbus, OH, 43210-1085, USA
| | - Wei Han
- Agro-Technical Station of Shandong Province, Jinan, PR China
| | - Hui-Xiao Yang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China
| | - Huan-Qin Liao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China
| | - Yi Zhou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China.
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
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80
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Marchal C, Germain J, Raveton M, Lyonnard B, Arnoldi C, Binet MN, Mouhamadou B. Molecular Characterization of Fungal Biodiversity in Long-Term Polychlorinated Biphenyl-Contaminated Soils. Microorganisms 2021; 9:microorganisms9102051. [PMID: 34683371 PMCID: PMC8541467 DOI: 10.3390/microorganisms9102051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/05/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) belong to the organic pollutants that are toxic to humans and harmful to environments. Numerous studies dealing with the impact of PCBs on soil microorganisms have focused on bacterial communities. The effects of PCBs on fungal communities in three different PCB-polluted soils from former industrial sites were investigated using high-throughput sequencing of the internal transcribed spacer 1 region. Significant differences in fungal alpha diversity were observed mainly due to soil physico-chemical properties. PCBs only influenced the richness of the fungal communities by increasing it. Fungal composition was rather strongly influenced by both PCBs and soil properties, resulting in different communities associated with each soil. Sixteen Ascomycota species were present in all three soils, including Stachybotrys chartarum, Fusarium oxysporum, Penicillium canescens, Penicillium chrysogenum,Penicillium citrosulfuratum and Penicillium brevicompactum, which are usually found in PCB-polluted soils, and Fusarium solani, Penicillium canescens, Penicillium citrosulfuratum and Penicillium chrysogenum, which are known PCB degraders. This study demonstrated that PCBs influence the richness and the composition of fungal communities. Their influence, associated with that of soil physico-chemical properties, led to distinct fungal communities, but with sixteen species common to the three soils which could be considered as ubiquitous species in PCB-polluted soils.
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81
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Haiming T, Chao L, Kaikai C, Lihong S, Li W, Weiyan L, Xiaoping X, Ke W. Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field. J Appl Microbiol 2021; 132:1307-1318. [PMID: 34487604 DOI: 10.1111/jam.15289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/27/2022]
Abstract
AIMS The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. METHODS AND RESULTS The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. CONCLUSIONS The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. SIGNIFICANCE AND IMPACT OF STUDY The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.
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Affiliation(s)
- Tang Haiming
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Chao
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Cheng Kaikai
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Shi Lihong
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Wen Li
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Li Weiyan
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Xiao Xiaoping
- Hunan Soil and Fertilizer Institute, Changsha, China
| | - Wang Ke
- Hunan Soil and Fertilizer Institute, Changsha, China
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82
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Wang X, Bai J, Xie T, Wang W, Zhang G, Yin S, Wang D. Effects of biological nitrification inhibitors on nitrogen use efficiency and greenhouse gas emissions in agricultural soils: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112338. [PMID: 34015632 DOI: 10.1016/j.ecoenv.2021.112338] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
To maintain and increase crop yields, large amounts of nitrogen fertilizers have been applied to farmland. However, the nitrogen use efficiency (NUE) of chemical fertilizer remains very low, which may lead to serious environmental problems, including nitrate pollution, air quality degradation and greenhouse gas (GHG) emissions. Nitrification inhibitors can alleviate nitrogen loss by inhibiting nitrification; thus, biological nitrification inhibition by plants has gradually attracted increasing attention due to its low cost and environmental friendliness. Research progress on BNI is reviewed in this article, including the source, mechanisms, influencing factors and application of BNIs. In addition, the impact of BNI on agriculture and GHG emissions is summarized from the perspective of agricultural production and environmental protection, and the key future research prospects of BNIs are also noted.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Tian Xie
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Shuo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dawei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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83
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Clark IM, Hughes DJ, Fu Q, Abadie M, Hirsch PR. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils. Sci Rep 2021; 11:15905. [PMID: 34354121 PMCID: PMC8342464 DOI: 10.1038/s41598-021-95100-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.
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Affiliation(s)
- Ian M Clark
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - David J Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Qingling Fu
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Maïder Abadie
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Penny R Hirsch
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK.
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84
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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85
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Nejidat A, Diaz-Reck D, Gelfand I, Zaady E. Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest. FEMS Microbiol Ecol 2021; 97:6323997. [PMID: 34279614 DOI: 10.1093/femsec/fiab106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/15/2021] [Indexed: 11/14/2022] Open
Abstract
At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1-10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23-26%) than in the other corrals and the control (33-38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1-10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.
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Affiliation(s)
- Ali Nejidat
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Damiana Diaz-Reck
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-G urion 84990, Israel
| | - Ilya Gelfand
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Eli Zaady
- Department of Natural Resources, Gilat Research Center, Agriculture Research Organization, Mobile, Post Negev 8531100, Israel
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86
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Lundsgaard NU, Cramp RL, Franklin CE, Kern PL. Effects on the embryonic and larval development of cane toads (
Rhinella marina
) reared in alkaline artesian spring water. AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niclas U. Lundsgaard
- School of Biological Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Rebecca L. Cramp
- School of Biological Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Craig E. Franklin
- School of Biological Sciences The University of Queensland Brisbane Queensland 4072 Australia
| | - Pippa L. Kern
- School of Biological Sciences The University of Queensland Brisbane Queensland 4072 Australia
- Bush Heritage Australia PO Box 329, Flinders Lane Melbourne Victoria 8009 Australia
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87
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Kitamura R, Kozaki T, Ishii K, Iigo M, Kurokura T, Yamane K, Maeda I, Iwabuchi K, Saito T. Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization. Microbes Environ 2021; 36. [PMID: 33907062 PMCID: PMC8209447 DOI: 10.1264/jsme2.me20148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.
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Affiliation(s)
- Rika Kitamura
- Center for Bioscience Research and Education, Utsunomiya University
| | - Toshinori Kozaki
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology
| | | | - Masayuki Iigo
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Takeshi Kurokura
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Kenji Yamane
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Isamu Maeda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Kazunori Iwabuchi
- Department of Bioresource and Environmental Engineering, Faculty of Agriculture, Hokkaido University
| | - Takahiro Saito
- Department of Environmental Engineering, Faculty of Agriculture, Utsunomiya University
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88
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Li Y, Liang Y, Zhang H, Liu Y, Zhu J, Xu J, Zhou Z, Ma J, Liu K, Yu F. Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 217:112274. [PMID: 33930771 DOI: 10.1016/j.ecoenv.2021.112274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 04/12/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China
| | - Ying Liang
- College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Haichun Zhang
- College of Life Science, Guangxi Normal University, 541004 Guilin, China
| | - Yuan Liu
- College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jing Zhu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jie Xu
- College of Life Science, Guangxi Normal University, 541004 Guilin, China
| | - Zhenming Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China.
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China.
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89
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Jia X, Gao Y, Li X, Zhao Y, Wang L, Zhang C. Effects of cadmium on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings under elevated atmospheric CO 2 scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145023. [PMID: 33581544 DOI: 10.1016/j.scitotenv.2021.145023] [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: 09/08/2020] [Revised: 01/02/2021] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
The individual impacts of elevated CO2 and heavy metals on soil nitrification have been widely reported. However, studies on the combined effects of elevated CO2 and heavy metals on soil nitrification are still limited. Here, a 135-day growth chamber experiment was conducted to investigate the impacts of elevated CO2 and cadmium (Cd) levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. Elevated CO2 combined with Cd pollution generally stimulated ammonia monooxygenase (AMO), hydroxylamine oxidase (HAO), and nitrite oxidoreductase (NXR) activities. Compared to the control, the abundance of ammonia-oxidizing bacteria (AOB) at day 135 and ammonia-oxidizing archaea (AOA) increased significantly (p < 0.05) and the abundance of AOB at days 45 and 90 and that of the nitrite-oxidizing bacteria (NOB) decreased under elevated CO2 + Cd. Elevated CO2 mostly led to a significant (p < 0.05) decrease in soil nitrification intensity in the rhizosphere of R. pseudoacacia exposed to Cd. The effects of Cd, CO2, and their interaction on HAO and NXR activities were significant (p < 0.01). Soil pH, the C/N ratio, water-soluble organic carbon, water-soluble organic nitrogen (WSON), and total carbon were the dominant factors (p < 0.05) affecting nitrifying enzyme activities and nitrification intensity in rhizosphere soils. Elevated CO2 clearly affected AOA, AOB, and NOB community structures and dominant genera by shaping C/N ratio, pH, and Cd and WSON contents in rhizosphere soils under Cd exposure. Overall, the responses of pH, C/N ratio, WSON, and Cd to elevated CO2 led to changes in rhizosphere soil nitrification under the combination of elevated CO2 and Cd pollution.
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Affiliation(s)
- Xia Jia
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China.
| | - Yunfeng Gao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Xiaodi Li
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Yonghua Zhao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Lu Wang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Chunyan Zhang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
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90
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Yue P, Zuo X, Li K, Cui X, Wang S, Misselbrook T, Liu X. The driving effect of nitrogen-related functional microorganisms under water and nitrogen addition on N 2O emission in a temperate desert. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145470. [PMID: 33581515 DOI: 10.1016/j.scitotenv.2021.145470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/19/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas and a precursor of ozone depletion in the upper atmosphere, thus contributing to climate change and biological safety. The mechanisms and response characteristics of N2O emission in desert soils to precipitation and nitrogen (N) deposition are still unclear. To further elucidate this, an in-situ experiment was conducted in the Gurbantunggut Desert, a temperate desert in China, between June and September 2015 and 2016. The response in N2O flux to water addition (equivalent to 5 mm precipitation) was very transient in summer, only lasting one to two days. This was attributed to the rapid decrease in soil moisture following the water addition, due to the high temperature and drought conditions, and there was no significant change in N2O emission or in the abundance of N-related key functional genes. In contrast, N2O emissions increased significantly in response to N addition. This was associated with an increase in functional gene abundances of amoA (ammonia oxidizing bacteria (AOB)) and ammonia-oxidizing archaea (AOA), which responded positively to increasing soil NH4+-N content, but were inhibited by increasing soil NO3--N content. The abundance of the nirS (nitrate reductase) gene was significantly increased by increasing soil NO3--N content. Interestingly, the indirect effect of increased soil moisture in enhancing N2O emission by increasing the abundance of AOA was offset by a direct effect of soil moisture in inhibiting soil N2O emission. Overall, N2O emissions were mainly controlled by AOA rather than AOB in summer, and were more sensitive to soil available N than to soil moisture in this temperate desert.
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Affiliation(s)
- Ping Yue
- Urat Desert-Grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoan Zuo
- Urat Desert-Grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000, China
| | - Kaihui Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xiaoqing Cui
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Shaokun Wang
- Urat Desert-Grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, 730000, China
| | - Tom Misselbrook
- Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK
| | - Xuejun Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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91
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Liang F, Wen Y, Dong X, Wang Y, Pan G, Jiang F, Luo H, Jin W, Wang J, Song H. Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29332-29343. [PMID: 33559074 DOI: 10.1007/s11356-020-12038-7] [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: 09/20/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.
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Affiliation(s)
- Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei, 230036, China
| | - Yiyao Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Guangyuan Pan
- Anhui General Station for Agricultural Technology Extension, Hefei, 230001, China
| | - Fangying Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huaying Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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92
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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93
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Yang L, Zhu G, Ju X, Liu R. How nitrification-related N 2O is associated with soil ammonia oxidizers in two contrasting soils in China? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:143212. [PMID: 33257072 DOI: 10.1016/j.scitotenv.2020.143212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 06/12/2023]
Abstract
As a key process contributing to N2O emissions, nitrification is regulated by soil microbes and mainly affected by soil pH, NH3 availability, temperature and O2 availability. Current knowledge gaps include how nitrification-related N2O is associated with soil microbes in different pH soils. In the current study, a microcosm incubation experiment was conducted with two contrasting soils of different pH (5.08, 8.30) under controlled conditions. The soils were amended with ammonium sulphate ((NH4)2SO4, 50 mg N kg-1) combined with or without nitrification inhibitors and incubated under 20 °C, 65% water hold capacity (WHC) for three weeks. N2O fluxes, mineral nitrogen (N) concentrations and ammonia oxidizers populations were measured during the incubation to investigate the correlations of nitrification-related N2O with ammonia oxidizers. The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) was used to inhibit nitrification albeit to various inhibition effects with different soils. Acetylene (0.1% v/v C2H2), an inhibitor of AOA and AOB ammonia monooxygenase (AMO), was used to distinguish N2O emissions by nitrifiers and denitrifiers. 1-octyne (5 μM aqueous), a selective specific AOB inhibitor, was used to assess the relative contributions of AOA and AOB to N2O emissions. The results showed that N2O yield for AOA and AOB varied with soil pH. AOB was the key microbial player in alkaline soil, contributing about 85% of nitrification-related N2O. Conversely, about 78% of nitrification-related N2O was contributed by AOA in acidic soil. Furthermore, there was a significant and positive relationship between mineral N (NO2-, NO3-), AOA and AOB populations and nitrification-related N2O in alkaline soil. However, in acidic soil, NO3- concentration and AOA had significantly positive relationships with nitrification-related N2O. To conclude, soil pH was a key factor affecting the contribution of ammonia oxidizers to nitrification-related N2O emissions. AOA-related N2O production dominated at low pH (5.08), while AOB-related N2O was favored in alkaline soil (pH 8.3).
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Affiliation(s)
- Liuqing Yang
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Gaodi Zhu
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaotang Ju
- College of Tropical Crops, Hainan University, Haikou 570228, China; Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Rui Liu
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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94
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Li D, Fang F, Liu G. Efficient Nitrification and Low-Level N 2O Emission in a Weakly Acidic Bioreactor at Low Dissolved-Oxygen Levels Are Due to Comammox. Appl Environ Microbiol 2021; 87:e00154-21. [PMID: 33975896 PMCID: PMC8208134 DOI: 10.1128/aem.00154-21r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/13/2021] [Indexed: 01/31/2023] Open
Abstract
Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous oxide (N2O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N2O emissions were tested in two weakly acidic (pH 6.3 to 6.8) reactors: one with dissolved oxygen (DO) at over 2.0 mg/liter and the other with DO at approximately 0.5 mg/liter. Efficient nitrification was achieved in both reactors. Compared to that in the high-DO reactor, N2O emission in the low-DO reactor decreased slightly, by 20%, and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N2O might not be produced mainly via nitrifier denitrification. Based on quantitative PCR (qPCR), quantitative fluorescent in situ hybridization (qFISH), and functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizers (comammox), i.e., Nitrospira organisms, significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low-DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N2O emission under long-term low DO in the weakly acidic reactor. This study demonstrated that the comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N2O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.IMPORTANCE Nitrification in wastewater treatment is an important process for eutrophication control and an emission source for the greenhouse gas N2O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/liter) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals, especially for wastewater without sufficient alkalinity. This paper demonstrates that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N2O emission. These findings indicate that comammox organisms are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N2O production as well as low energy and chemical consumption simultaneously.
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Affiliation(s)
- Deyong Li
- School of the Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Jinan University, Guangzhou, China
- School of the Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
| | - Fang Fang
- College of the Environment and Ecology, Chongqing University, Chongqing, China
| | - Guoqiang Liu
- School of the Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Jinan University, Guangzhou, China
- School of the Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
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95
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Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX. Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144993. [PMID: 33736320 DOI: 10.1016/j.scitotenv.2021.144993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.
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Affiliation(s)
- Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chen-Hao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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96
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Xenophontos C, Taubert M, Harpole WS, Küsel K. Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities. FEMS Microbiol Ecol 2021; 97:6136281. [PMID: 33587113 DOI: 10.1093/femsec/fiab017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.
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Affiliation(s)
- Constantinos Xenophontos
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Martin Taubert
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany
| | - W Stanley Harpole
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany.,Department of Physiological Diversity, Helmholtz-Center for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biology, Martin Luther University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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97
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Efficient nitrification and low N 2O emission in a weakly acidic bioreactor at low dissolved oxygen levels are due to comammox. Appl Environ Microbiol 2021; 87:AEM.00154-21. [PMID: 33741624 DOI: 10.1128/aem.00154-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous-oxide (N2O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N2O emissions were tested in two weakly acidic (pH = 6.3-6.8) reactors: one with dissolved oxygen (DO) over 2.0 mg/L and the other with DO approximately 0.5 mg/L. Efficient nitrification was achieved in both reactors. Compared to the high-DO reactor, N2O emission in the low-DO reactor decreased slightly by 20% and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N2O might not be mainly produced via nitrifier denitrification. Based on qPCR, qFISH, functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizer (comammox) Nitrospira significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N2O emission under long-term low DO in weakly acidic reactor. This study demonstrated that comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N2O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.ImportanceNitrification in wastewater treatment is an important process for eutrophication control and an emission source for greenhouse gas of N2O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/L) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals especially for wastewater without sufficient alkalinity. This manuscript demonstrated that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N2O emission. These findings indicate that comammox are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N2O production as well as low energy and chemical consumption simultaneously.
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98
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Font Nájera A, Serwecińska L, Mankiewicz-Boczek J. Culturable nitrogen-transforming bacteria from sequential sedimentation biofiltration systems and their potential for nutrient removal in urban polluted rivers. Sci Rep 2021; 11:7448. [PMID: 33811217 PMCID: PMC8018948 DOI: 10.1038/s41598-021-86212-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 11/09/2022] Open
Abstract
Novel heterotrophic bacterial strains—Bzr02 and Str21, effective in nitrogen transformation, were isolated from sequential sedimentation-biofiltration systems (SSBSs). Bzr02, identified as Citrobacter freundii, removed up to 99.0% of N–NH4 and 70.2% of N–NO3, while Str21, identified as Pseudomonas mandelii, removed up to 98.9% of N–NH4 and 87.7% of N–NO3. The key functional genes napA/narG and hao were detected for Bzr02, confirming its ability to reduce nitrate to nitrite and remove hydroxylamine. Str21 was detected with the genes narG, nirS, norB and nosZ, confirming its potential for complete denitrification process. Nitrogen total balance experiments determined that Bzr02 and Str21 incorporated nitrogen into cell biomass (up to 94.7% and 74.7%, respectively), suggesting that nitrogen assimilation was also an important process occurring simultaneously with denitrification. Based on these results, both strains are suitable candidates for improving nutrient removal efficiencies in nature-based solutions such as SSBSs.
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Affiliation(s)
- Arnoldo Font Nájera
- UNESCO Chair On Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland.,European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - Liliana Serwecińska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland.
| | - Joanna Mankiewicz-Boczek
- UNESCO Chair On Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland.,European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
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99
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Zheng M, He S, Feng Y, Wang M, Liu YX, Dang C, Wang J. Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems. J Environ Sci (China) 2021; 102:273-282. [PMID: 33637253 DOI: 10.1016/j.jes.2020.09.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 05/04/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g-1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g-1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.
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Affiliation(s)
- Maosheng Zheng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Shishi He
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yueqi Feng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Mingyuan Wang
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yong-Xin Liu
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyuan Dang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jiawen Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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100
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Li S, Gang D, Zhao S, Qi W, Liu H. Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment. CHEMOSPHERE 2021; 269:128702. [PMID: 33162161 DOI: 10.1016/j.chemosphere.2020.128702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.
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Affiliation(s)
- Siling Li
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Diga Gang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuangju Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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