1
|
Ye F, Wang Y, Duan L, Wu W, Huang Y, Wang J, Chen Y, Zhao Z. Nitrous oxide (N 2O) emissions at the air-water-sediment interfaces of cascade reservoirs in the Yunnan-Guizhou Plateau: Spatial patterns and environmental controls. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124436. [PMID: 38925220 DOI: 10.1016/j.envpol.2024.124436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
The construction of cascade reservoirs can interfere with the natural hydrologic cycles of basins, causing negative environmental effects such as altering the emission patterns of the Nitrous oxide (N2O), a potent greenhouse gas. To elucidate the impact of cascade reservoirs construction on river N2O emissions, we utilized the thin boundary model and the incubation experiments to estimate the N2O fluxes at the air-water interface and at the water-sediment interface of cascade reservoirs on the Yunnan-Guizhou Plateau, respectively. Additionally, we explored the influence of various factors, with particular emphasis on damming, on N2O emissions and production. Moreover, we identified the main pathways of N2O production and proposed management strategies to mitigate N2O emissions from cascade reservoirs. The findings revealed that N2O fluxes at the air-water interface and the water-sediment interface were 4.73 ± 1.32 μmol m-2 · d-1 and 15.56 ± 1.98 μmol m-2 · d-1, respectively. Influenced by temperature, dissolved oxygen (DO), resource substances (active nitrogen substrates and dissolved organic carbon (DOC)) and reservoir properties (scale, hydraulic retention time (HRT), reservoir age, etc.), the N2O concentration and flux exhibited notable spatial heterogeneity, gradually increasing downstream. Temperature has a significant direct impact on N2O flux, as well as indirect effects through DO and resource chemicals. Furthermore, the correlation between dissolved oxygen utilization rate (AOU) and net N2O flux (ΔN2O) indicated that N2O emissions at the water-air interface were primarily attributable to nitrification, whereas those at the water-sediment interface were predominantly driven by denitrification. These findings not only enhance our comprehension of N2O emissions at various interfaces of cascade reservoirs but also offer theoretical backing for the formulation of management strategies aimed at efficiently mitigating N2O emissions from continuously dammed rivers.
Collapse
Affiliation(s)
- Fei Ye
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, China
| | - Yi Wang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, China
| | - Lei Duan
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, China.
| | - Wei Wu
- Xi'an University of Technology, Xi'an, 710048, China
| | - Yaqi Huang
- Xi'an University of Technology, Xi'an, 710048, China
| | - Jiawei Wang
- Xi'an University of Technology, Xi'an, 710048, China
| | - Yue Chen
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, China
| | - Zhengzheng Zhao
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region, Ministry of Education, Chang'an University, China
| |
Collapse
|
2
|
Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
Collapse
Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| |
Collapse
|
3
|
Kaushal R, Hsueh YH, Chen CL, Lan YP, Wu PY, Chen YC, Liang MC. Isotopic assessment of soil N 2O emission from a sub-tropical agricultural soil under varying N-inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154311. [PMID: 35257756 DOI: 10.1016/j.scitotenv.2022.154311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen fertilizers result in high crop productivity but also enhance the emission of N2O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N2O and N2 via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N2O production. Here, we report the results of N2O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N2O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N2O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N2O during the entire course of the incubation experiments. Peak N2O emissions of 122 ± 98 μg N2O-N m-2 h-1, 338 ± 49 μg N2O-N m-2 h-1 and 739 ± 296 μg N2O-N m-2 h-1 were observed for urea application rate of 40, 80, and 120 μg N g-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ15N, δ18O, and 15N site preference, we inferred co-occurrence of several microbial N2O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N2O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N2O emission pulse in intermediate urea-N levels. Signature of N2O consumption by reduction could be traced during declining emissions in treatment with high urea level.
Collapse
Affiliation(s)
- Ritika Kaushal
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsin Hsueh
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan; Taiwan International Graduate Program-Earth Systems Science, Academia Sinica, Taipei, Taiwan
| | - Chi-Ling Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Ping Lan
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Ping-Yu Wu
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Chun Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Mao-Chang Liang
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
4
|
Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [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: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
Collapse
Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| |
Collapse
|
5
|
Yavitt JB, Roco CA, Debenport SJ, Barnett SE, Shapleigh JP. Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils. MICROBIAL ECOLOGY 2021; 81:758-769. [PMID: 33001224 DOI: 10.1007/s00248-020-01613-7] [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: 05/18/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.
Collapse
Affiliation(s)
- Joseph B Yavitt
- Department of Natural Resources, Cornell University, 226 Mann Drive, Fernow Hall, Ithaca, NY, 14853, USA.
| | - C Armanda Roco
- Department of Microbiology, Cornell University, 123 Wing Drive, Wing Hall, Ithaca, NY, 14853, USA
| | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, 306 Tower Road, Bradfield Hall, Ithaca, NY, 14853, USA
| | - Samuel E Barnett
- School of Integrative Plant Science, Cornell University, 306 Tower Road, Bradfield Hall, Ithaca, NY, 14853, USA
| | - James P Shapleigh
- Department of Microbiology, Cornell University, 123 Wing Drive, Wing Hall, Ithaca, NY, 14853, USA
| |
Collapse
|
6
|
Li J, Hua ZS, Liu T, Wang C, Li J, Bai G, Lücker S, Jetten MSM, Zheng M, Guo J. Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor. ISME COMMUNICATIONS 2021; 1:7. [PMID: 37938245 PMCID: PMC9723585 DOI: 10.1038/s43705-021-00005-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.
Collapse
Affiliation(s)
- Jiyun Li
- School of Environment, Tsinghua University, Beijing, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People's Republic of China
| | - Tao Liu
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing, China.
| | - Jie Li
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia
| | - Ge Bai
- School of Environment, Tsinghua University, Beijing, China
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, AJ, The Netherlands
| | - Min Zheng
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| | - Jianhua Guo
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
7
|
Wang W, Han L, Zhang X, Wei K. Plastic film mulching affects N 2O emission and ammonia oxidizers in drip irrigated potato soil in northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142113. [PMID: 32920397 DOI: 10.1016/j.scitotenv.2020.142113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
In soil, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are regarded as key factors mediating nitrous oxide (N2O) production and emission. However, there are scarce reports about the effect of film mulching on ammonia oxidizers, and the biological nitrification process of N2O emission is unclear. This study was based on potato field experiments under different mulching films, including polyethylene mulching film (PM), transparent degradable mulching film (TDM), black degradable mulching film (BDM), and bare land (CK). AOB and AOA abundances were estimated using real-time PCR, and their diversity and community structure were measured using high-throughput sequencing. Result revealed that the total N2O emission from CK was 12.32%-41.03% higher than that from film mulching soil. Under film mulching, according to total N2O emission from soil and N2O concentration in soil treatments were ordered as PM > BDM > TDM, and N2O production was closely correlated with copy numbers of the amoA gene. BDM significantly increased the number of amoA-AOB gene copies (P < 0.01), and PM significantly increased the those of amoA-AOA (P < 0.01). BDM and TDM increased AOB operational taxonomic units (OTUs), Chao1, Simpson, and Shannon indices, while PM increased the AOA OTUs and Chao1 index. Variations in AOA abundance and diversity were closely related to soil mineral N and temperature changes induced by polyethylene film mulching (P < 0.05), whereas AOB showed no significant association with soil properties. Meanwhile, we did not find a distinct treatment effect on AOB community structure. Our findings indicate that (i) degradable film mulching increased AOB abundance and diversity and N2O concentration, but obviously reduced N2O emissions, and (ii) AOA were more sensitive than AOB to polyethylene mulching film.
Collapse
Affiliation(s)
- Wen Wang
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China.
| | - Lu Han
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
| | - Xiong Zhang
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
| | - Ku Wei
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
| |
Collapse
|
8
|
Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan. FORESTS 2020. [DOI: 10.3390/f12010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biogeographic separation has been an important cause of faunal and floral distribution; however, little is known about the differences in soil microbial communities across islands. In this study, we determined the structure of soil microbial communities by analyzing phospholipid fatty acid (PLFA) profiles and comparing enzymatic activities as well as soil physio-chemical properties across five subtropical granite-derived and two tropical volcanic (andesite-derived) islands in Taiwan. Among these islands, soil organic matter, pH, urease, and PLFA biomass were higher in the tropical andesite-derived than subtropical granite-derived islands. Principal component analysis of PLFAs separated these islands into three groups. The activities of soil enzymes such as phosphatase, β-glucosidase, and β-glucosaminidase were positively correlated with soil organic matter and total nitrogen. Redundancy analysis of microbial communities and environmental factors showed that soil parent materials and the climatic difference are critical factors affecting soil organic matter and pH, and consequently the microbial community structure.
Collapse
|
9
|
Zhou Y, Lambrides CJ, Li J, Xu Q, Toh R, Tian S, Yang P, Yang H, Ryder M, Denton MD. Nitrifying Microbes in the Rhizosphere of Perennial Grasses are Modified by Biological Nitrification Inhibition. Microorganisms 2020; 8:microorganisms8111687. [PMID: 33138329 PMCID: PMC7693952 DOI: 10.3390/microorganisms8111687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.
Collapse
Affiliation(s)
- Yi Zhou
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Christopher J. Lambrides
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Jishun Li
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
- Correspondence: ; Tel.: +86-531-8872-8276
| | - Qili Xu
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Ruey Toh
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Shenzhong Tian
- Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Jinan 250013, China;
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Hetong Yang
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Maarten Ryder
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Matthew D. Denton
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| |
Collapse
|
10
|
Takahashi Y, Fujitani H, Hirono Y, Tago K, Wang Y, Hayatsu M, Tsuneda S. Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils. Front Microbiol 2020; 11:1737. [PMID: 32849373 PMCID: PMC7396549 DOI: 10.3389/fmicb.2020.01737] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/02/2020] [Indexed: 12/02/2022] Open
Abstract
In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.
Collapse
Affiliation(s)
- Yu Takahashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| |
Collapse
|
11
|
Cassman NA, Soares JR, Pijl A, Lourenço KS, van Veen JA, Cantarella H, Kuramae EE. Nitrification inhibitors effectively target N 2 O-producing Nitrosospira spp. in tropical soil. Environ Microbiol 2019; 21:1241-1254. [PMID: 30735001 PMCID: PMC6850170 DOI: 10.1111/1462-2920.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.
Collapse
Affiliation(s)
- Noriko A. Cassman
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Johnny R. Soares
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Agata Pijl
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Késia S. Lourenço
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Johannes A. van Veen
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Heitor Cantarella
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Eiko E. Kuramae
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| |
Collapse
|
12
|
Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
Collapse
Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
| |
Collapse
|
13
|
Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol 2019; 103:177-189. [PMID: 30415428 PMCID: PMC6311188 DOI: 10.1007/s00253-018-9486-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 11/30/2022]
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.
Collapse
Affiliation(s)
- Hanna Koch
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Sebastian Lücker
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
14
|
Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization. Appl Environ Microbiol 2018; 84:AEM.01031-18. [PMID: 30006397 DOI: 10.1128/aem.01031-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/04/2018] [Indexed: 11/20/2022] Open
Abstract
Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.
Collapse
|
15
|
Lourenço KS, Cassman NA, Pijl AS, van Veen JA, Cantarella H, Kuramae EE. Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop. Front Microbiol 2018; 9:674. [PMID: 29692763 PMCID: PMC5902487 DOI: 10.3389/fmicb.2018.00674] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.
Collapse
Affiliation(s)
- Késia S Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Noriko A Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Agata S Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| |
Collapse
|
16
|
Jo JH, Kim W, Lim J. Ammonia-oxidizers' diversity in wastewater treatment processes. ENVIRONMENTAL TECHNOLOGY 2018; 39:887-894. [PMID: 28394197 DOI: 10.1080/09593330.2017.1316317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
The diversity of ammonia-oxidizing bacteria (AOB) within the beta-subclass of Proteobacteria was investigated by genus- and family-specific real-time quantitative PCR (qPCR) assays on samples drawn from wastewater treatment systems. The 16S rRNA gene copy numbers ranged from 7.0 × 103 to 6.8 × 106, 1.1 × 107 to 1.8 × 107, and 2.9 × 105 to 1.5 × 107 copies/mL, respectively. Volumetric ammonium load (VAL) in the wastewater treatment systems calculated using the AOB numbers was in the range of 2.1-12.6 mM/d. Distribution patterns of eutrophic (i.e. Nitrosomonas europaea and Nitrosomonas nitrosa clusters) and oligotrophic (i.e. Nitrosomonas cryotolerans cluster) AOB groups were correlated with the VAL values. A high possibility of potential false-positive detection by family-specific qPCR assays was established by evaluating theoretical specificity in in silico and experimental investigations. The specificities of genus-specific qPCR assays were confirmed by amoA PCR, followed by cloning and sequencing. VAL must be the factor influencing the inclusion of AOB species. However, there was no significant correlation between the volatile suspended solid concentration representing chemical oxygen demand and N. europaea's community population, indicating that the degree of ammonia oxidation influenced the community cluster of Nitrosomonas relatively more.
Collapse
Affiliation(s)
- Ji Hye Jo
- a Division of Resource Circulation , Korea Environment Institute , Sejong , Republic of Korea
| | - Woong Kim
- b Department of Environmental Engineering , Kyungpook National University , Daegu , Republic of Korea
- c Advanced Institute of Water Industry , Kyungpook National University , Daegu , Republic of Korea
| | - Juntaek Lim
- d Department of Chemical and Biomolecular Engineering , KAIST , Daejeon , Republic of Korea
| |
Collapse
|
17
|
Cardenas E, Orellana LH, Konstantinidis KT, Mohn WW. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. Sci Rep 2018; 8:3142. [PMID: 29453368 PMCID: PMC5816661 DOI: 10.1038/s41598-018-21197-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/31/2018] [Indexed: 01/23/2023] Open
Abstract
Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profile variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment effects on gene profiles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these effects varied among ecozones. Our results suggest that ecozone-specific nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.
Collapse
Affiliation(s)
- Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Luis H Orellana
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | | | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
18
|
Hydroxylamine released by nitrifying microorganisms is a precursor for HONO emission from drying soils. Sci Rep 2018; 8:1877. [PMID: 29382914 PMCID: PMC5790002 DOI: 10.1038/s41598-018-20170-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/15/2018] [Indexed: 11/22/2022] Open
Abstract
Nitrous acid (HONO) is an important precursor of the hydroxyl radical (OH), the atmosphere´s primary oxidant. An unknown strong daytime source of HONO is required to explain measurements in ambient air. Emissions from soils are one of the potential sources. Ammonia-oxidizing bacteria (AOB) have been identified as possible producers of these HONO soil emissions. However, the mechanisms for production and release of HONO in soils are not fully understood. In this study, we used a dynamic soil-chamber system to provide direct evidence that gaseous emissions from nitrifying pure cultures contain hydroxylamine (NH2OH), which is subsequently converted to HONO in a heterogeneous reaction with water vapor on glass bead surfaces. In addition to different AOB species, we found release of HONO also in ammonia-oxidizing archaea (AOA), suggesting that these globally abundant microbes may also contribute to the formation of atmospheric HONO and consequently OH. Since biogenic NH2OH is formed by diverse organisms, such as AOB, AOA, methane-oxidizing bacteria, heterotrophic nitrifiers, and fungi, we argue that HONO emission from soil is not restricted to the nitrifying bacteria, but is also promoted by nitrifying members of the domains Archaea and Eukarya.
Collapse
|
19
|
Isolation and characterization of urease-producing bacteria from tropical peat. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2017.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
20
|
Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
Collapse
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
| |
Collapse
|
21
|
Tolar BB, Wallsgrove NJ, Popp BN, Hollibaugh JT. Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities. Environ Microbiol 2016; 19:4838-4850. [PMID: 27422798 DOI: 10.1111/1462-2920.13457] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Urea nitrogen has been proposed to contribute significantly to nitrification by marine thaumarchaeotes. These inferences are based on distributions of thaumarchaeote urease genes rather than activity measurements. We found that ammonia oxidation rates were always higher than oxidation rates of urea-derived N in samples from coastal Georgia, USA (means ± SEM: 382 ± 35 versus 73 ± 24 nmol L-1 d-1 , Mann-Whitney U-test p < 0.0001), and the South Atlantic Bight (20 ± 8.8 versus 2.2 ± 1.7 nmol L-1 d-1 , p = 0.026) but not the Gulf of Alaska (8.8 ± 4.0 versus 1.5 ± 0.6, p > 0.05). Urea-derived N was relatively more important in samples from Antarctic continental shelf waters, though the difference was not statistically significant (19.4 ± 4.8 versus 12.0 ± 2.7 nmol L-1 d-1 , p > 0.05). We found only weak correlations between oxidation rates of urea-derived N and the abundance or transcription of putative Thaumarchaeota ureC genes. Dependence on urea-derived N does not appear to be directly related to pH or ammonium concentrations. Competition experiments and release of 15 NH3 suggest that urea is hydrolyzed to ammonia intracellularly, then a portion is lost to the dissolved pool. The contribution of urea-derived N to nitrification appears to be minor in temperate coastal waters, but may represent a significant portion of the nitrification flux in Antarctic coastal waters.
Collapse
Affiliation(s)
- Bradley B Tolar
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Natalie J Wallsgrove
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Brian N Popp
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| |
Collapse
|
22
|
Jenkins SN, Murphy DV, Waite IS, Rushton SP, O'Donnell AG. Ancient landscapes and the relationship with microbial nitrification. Sci Rep 2016; 6:30733. [PMID: 27480661 PMCID: PMC4969748 DOI: 10.1038/srep30733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/06/2016] [Indexed: 11/09/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.
Collapse
Affiliation(s)
- Sasha N Jenkins
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Daniel V Murphy
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Ian S Waite
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Steven P Rushton
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK
| | - Anthony G O'Donnell
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| |
Collapse
|
23
|
Briskey D, Tucker PS, Johnson DW, Coombes JS. Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD. Nitric Oxide 2016; 57:64-70. [DOI: 10.1016/j.niox.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/11/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
|
24
|
Daims H, Lücker S, Wagner M. A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria. Trends Microbiol 2016; 24:699-712. [PMID: 27283264 DOI: 10.1016/j.tim.2016.05.004] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.
Collapse
Affiliation(s)
- Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| |
Collapse
|
25
|
Gat D, Ronen Z, Tsesarsky M. Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:616-624. [PMID: 26689904 DOI: 10.1021/acs.est.5b04033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention.
Collapse
Affiliation(s)
- Daniella Gat
- The Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
| | - Zeev Ronen
- The Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev , Sede-Boqer Campus 8499000, Israel
| | - Michael Tsesarsky
- The Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
- The Department of Structural Engineering, Ben-Gurion University of the Negev , Beer-Sheva 8410501, Israel
| |
Collapse
|
26
|
Norman JS, Lin L, Barrett JE. Paired carbon and nitrogen metabolism by ammonia-oxidizing bacteria and archaea in temperate forest soils. Ecosphere 2015. [DOI: 10.1890/es14-00299.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
27
|
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci U S A 2015; 112:11371-6. [PMID: 26305944 DOI: 10.1073/pnas.1506533112] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.
Collapse
|
28
|
Wang YF, Gu JD. Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms. Appl Microbiol Biotechnol 2013; 98:3257-74. [DOI: 10.1007/s00253-013-5399-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/02/2013] [Accepted: 11/09/2013] [Indexed: 10/26/2022]
|
29
|
Herrmann M, Hädrich A, Küsel K. Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen. Environ Microbiol 2012; 14:3013-25. [PMID: 23016896 DOI: 10.1111/j.1462-2920.2012.02882.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 08/23/2012] [Indexed: 11/27/2022]
Abstract
We investigated the abundance, community composition and transcriptional activity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the acidic fen Schlöppnerbrunnen (Germany) that was subjected to water table manipulations. Quantitative PCR targeting amoA gene copies and transcripts showed that AOA dominated the ammonia-oxidizing community in the upper 20 cm of the peat soil. Numbers of archaeal amoA gene copies and transcripts as well as the relative fraction of AOA of the total archaea decreased with depth. AOA-AmoA sequences were 96.2-98.9% identical to that of Candidatus Nitrosotalea devanaterra while bacterial AmoA sequences affiliated with Nitrosospira clusters 2 and 4. Archaeal but not bacterial amoA transcripts were detected in short-term laboratory incubations of peat that showed nitrifying activity. Nitrate accumulated in the peat pore water after 6 weeks of induced drought during a field experiment. Subsequent rewetting resulted in a significant decrease of AOA transcriptional activity, indicating that AOA responded to water table fluctuations on the transcriptional level. Our results suggest that nitrification in this fen is primarily linked to archaeal ammonia oxidation. pH and anoxia appear to be key factors regulating AOA community composition, vertical distribution and activity in acidic fens.
Collapse
Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany.
| | | | | |
Collapse
|
30
|
Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 2012; 78:7501-10. [PMID: 22923400 DOI: 10.1128/aem.01960-12] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.
Collapse
|
31
|
Bouskill NJ, Eveillard D, O'Mullan G, Jackson GA, Ward BB. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure. Environ Microbiol 2010; 13:872-86. [PMID: 21054735 DOI: 10.1111/j.1462-2920.2010.02362.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.
Collapse
Affiliation(s)
- Nicholas J Bouskill
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA.
| | | | | | | | | |
Collapse
|
32
|
An YJ, Kim M. Effect of antimony on the microbial growth and the activities of soil enzymes. CHEMOSPHERE 2009; 74:654-659. [PMID: 19036401 DOI: 10.1016/j.chemosphere.2008.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 09/17/2008] [Accepted: 10/17/2008] [Indexed: 05/27/2023]
Abstract
The effects of antimony (Sb) on microbial growth inhibition and activities of soil enzymes were investigated in the present study. Test bacterial species were Escherichia coli, Bacillus subtilis and Streptococcus aureus. Among the microorganisms tested, S. aureus was the most sensitive. The 50% effects on the inhibition of specific growth rate of E. coli, B. subtilis, and, S. aureus were 555, 18.4, and 15.8 mg Sb L(-1), respectively. A silt loam soil was amended with antimony and incubated in a controlled condition. Microbial activities of dehydrogenase, acid phosphatase (P cycle), arylsulfatase (S cycle), beta-glucosidase (C cycle), urease (N cycle), and fluorescein diacetate hydrolase in soil were measured. Activities of urease and dehydrogenase were related with antimony and can be an early indication of antimony contamination. The maximum increase in soil urease activity by antimony was up to 168% after 3d compared with the control. The activities of other four enzymes (acid phosphatase, fluorescein diacetate hydrolase, arylsulfatase and ss-glucosidase) were less affected by antimony. This study suggested that antimony affects nitrogen cycle in soil by changing urease activity under the neutral pH, however, soil enzyme activities may not be a good protocol due to their complex response patterns to antimony pollution.
Collapse
Affiliation(s)
- Youn-Joo An
- Department of Environmental Science, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
| | | |
Collapse
|
33
|
Nicol GW, Leininger S, Schleper C, Prosser JI. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 2008; 10:2966-78. [PMID: 18707610 DOI: 10.1111/j.1462-2920.2008.01701.x] [Citation(s) in RCA: 535] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.
Collapse
Affiliation(s)
- Graeme W Nicol
- Institute of Biological and Environmental Science, University of Aberdeen, Cruickshank Building, Aberdeen, UK
| | | | | | | |
Collapse
|
34
|
Dytczak MA, Londry KL, Oleszkiewicz JA. Nitrifying genera in activated sludge may influence nitrification rates. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2008; 80:388-396. [PMID: 18605378 DOI: 10.2175/106143007x221373] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sequencing batch reactors were acclimated under aerobic and alternating anoxic/aerobic conditions. Greater nitrification rates in the alternating reactor were investigated by comparing environmental conditions. In the alternating reactor, pH, alkalinity, oxygen, and nitrite were higher at the onset of aerobic nitrification. Kinetic studies and batch tests, with biomass developed under aerobic and alternating conditions, revealed that these factors were insufficient to explain the divergent nitrification rates. Nitrifying genera vary in nitrification kinetics and sensitivity to environmental conditions. Nitrosospira and Nitrospira spp. could dominate in aerobic reactors, as they are adapted to low nitrite and oxygen conditions. Nitrosomonas and Nitrobacter spp. are better competitors with abundant substrates and have higher nitrite tolerance, so they could excel under alternating conditions. This theoretical explanation is consistent with the kinetics and environmental conditions in these reactors and argues for using alternating treatment, because the harsh conditions select for populations with inherently faster nitrification rates.
Collapse
Affiliation(s)
- M A Dytczak
- Environmental Engineering, Department of Civil Engineering, University of Manitoba, Winnipeg, Canada
| | | | | |
Collapse
|
35
|
Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol 2008; 74:3559-72. [PMID: 18390676 DOI: 10.1128/aem.02722-07] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.
Collapse
|
36
|
. TH, . RK, . MT, . TN. Molecular Diversity of the Genes Encoding Ammonia Monooxygenase and Particulate Methane Monooxygenase from Deep-sea Sediments. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/jm.2007.530.537] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
37
|
Gieseke A, Tarre S, Green M, de Beer D. Nitrification in a biofilm at low pH values: role of in situ microenvironments and acid tolerance. Appl Environ Microbiol 2006; 72:4283-92. [PMID: 16751543 PMCID: PMC1489657 DOI: 10.1128/aem.00241-06] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sensitivity of nitrifying bacteria to acidic conditions is a well-known phenomenon and generally attributed to the lack and/or toxicity of substrates (NH3 and HNO2) with decreasing pHs. In contrast, we observed strong nitrification at a pH around 4 in biofilms grown on chalk particles and investigated the following hypotheses: the presence of less acidic microenvironments and/or the existence of acid-tolerant nitrifiers. Microelectrode measurements (in situ and under various experimental conditions) showed no evidence of a neutral microenvironment, either within the highly active biofilm colonizing the chalk surface or within a control biofilm grown on a nonbuffering (i.e., sintered glass) surface under acidic pH. A 16S rRNA approach (clone libraries and fluorescence in situ hybridizations) did not reveal uncommon nitrifying (potentially acid-tolerant) strains. Instead, we found a strongly acidic microenvironment, evidence for a clear adaptation to the low pH in situ, and the presence of nitrifying populations related to subgroups with low Km s for ammonia (Nitrosopira spp., Nitrosomonas oligotropha, and Nitrospira spp.). Acid-consuming (chalk dissolution) and acid-producing (ammonia oxidation) processes are equilibrated on a low-pH steady state that is controlled by mass transfer limitation through the biofilm. Strong affinity to ammonia and possibly the expression of additional functions, e.g., ammonium transporters, are adaptations that allow nitrifiers to cope with acidic conditions in biofilms and other habitats.
Collapse
Affiliation(s)
- Armin Gieseke
- Microsensor Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
| | | | | | | |
Collapse
|