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Aaronson JK, Kulmatiski A, Forero LE, Grenzer J, Norton JM. Are Plant-Soil Feedbacks Caused by Many Weak Microbial Interactions? BIOLOGY 2023; 12:1374. [PMID: 37997973 PMCID: PMC10669423 DOI: 10.3390/biology12111374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
We used high-throughput sequencing and multivariate analyses to describe soil microbial community composition in two four-year field plant-soil feedback (PSF) experiments in Minnesota, USA and Jena, Germany. In descending order of variation explained, microbial community composition differed between the two study sites, among years, between bulk and rhizosphere soils, and among rhizosphere soils cultivated by different plant species. To try to identify soil organisms or communities that may cause PSF, we correlated plant growth responses with the microbial community composition associated with different plants. We found that plant biomass was correlated with values on two multivariate axes. These multivariate axes weighted dozens of soil organisms, suggesting that PSF was not caused by individual pathogens or symbionts but instead was caused by 'many weak' plant-microbe interactions. Taken together, the results suggest that PSFs result from complex interactions that occur within the context of a much larger soil microbial community whose composition is determined by factors associated with 'site' or year, such as soil pH, soil type, and weather. The results suggest that PSFs may be highly variable and difficult to reproduce because they result from complex interactions that occur in the context of a larger soil microbial community.
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Affiliation(s)
- Julia K. Aaronson
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Andrew Kulmatiski
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Leslie E. Forero
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Josephine Grenzer
- Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322, USA; (J.K.A.); (L.E.F.); (J.G.)
| | - Jeanette M. Norton
- Plants, Soils and Climate Department and the Ecology Center, Utah State University, Logan, UT 84322, USA;
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Kong Y, Zhang H, Tian L, Yuan J, Chen Y, Li Y, Chen J, Chang SX, Fang Y, Tavakkoli E, Cai Y. Relationships between denitrification rates and functional gene abundance in a wetland: The roles of single- and multiple-species plant communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160913. [PMID: 36529393 DOI: 10.1016/j.scitotenv.2022.160913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Wetland soil denitrification removes excess inorganic nitrogen (N) and prevents eutrophication in aquatic ecosystems. Wetland plants have been considered the key factors determining the capacity of wetland soil denitrification to remove N pollutants in aquatic ecosystems. However, the influences of various plant communities on wetland soil denitrification remain unknown. In the present study, we measured variations in soil denitrification under different herbaceous plant communities including single Phragmites karka (PK), single Paspalum thunbergia (PT), single Zizania latifolia (ZL), a mixture of Paspalum thunbergia plus Phragmites karka (PTPK), a mixture of Paspalum thunbergia plus Zizania latifolia (PTZL), and bare soil (CK) in the Estuary of Nantiaoxi River, the largest tributary of Qingshan Lake in Hangzhou, China. The soil denitrification rate was significantly higher in the surface (0-10 cm) than the subsurface (10-20 cm) layer. Wetland plant growth increased the soil denitrification rate by significantly increasing the soil water content, nitrate concentration, and ln(nirS) + ln(nirK). A structural equation model (SEM) showed that wetland plants indirectly regulated soil denitrification by altering the aboveground and belowground plant biomass, nitrate concentration, abundances of denitrifying functional genes, and denitrification potential. There was no significant difference in soil denitrification rates among PT, PK and ZL. The soil denitrification rate was significantly lower in PTZL than PTPK. Two-plant communities did not necessarily enhance the denitrification rate compared to single planting, the former had a greater competitiveness on N uptake and consequently reduced the amount of nitrate available for denitrification. As PTPK had the highest denitrification rate, co-planting P. thunbergia and P. karka could effectively improve N removal efficiency and help mitigate eutrophication in adjacent aquatic ecosystems. The results of this investigation provide useful information guiding the selection of appropriate wetland herbaceous plant species for wetland construction and the removal of N pollutants in aquatic ecosystems.
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Affiliation(s)
- Yushuang Kong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Haikuo Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Linlin Tian
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China.
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Jian Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Scott X Chang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Department of Renewable Resources, University of Alberta, Edmonton T6G 2E3, Canada
| | - Yunying Fang
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle 2568, Australia
| | - Ehsan Tavakkoli
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga 2650, Australia
| | - Yanjiang Cai
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
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3
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Niu Y, Hu W, Zhou T, He B, Chen X, Li Y. Diversity of nirS and nirK denitrifying bacteria in rhizosphere and non-rhizosphere soils of halophytes in Ebinur Lake Wetland. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2070030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yanhui Niu
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Wenge Hu
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Tingting Zhou
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Bo He
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Xuemei Chen
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
| | - Yang Li
- Comprehensive Microbe Resources Lab, School of life Sciences, Shihezi University, Shihezi, P. R. China
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Yao L, Gong Y, Ye C, Shi W, Zhang K, Du M, Zhang Q. Soil denitrification rates are more sensitive to hydrological changes than restoration approaches in a unique riparian zone. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lu Yao
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
| | - Yu Gong
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
| | - Chen Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
| | - Wenjun Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
- The University of Chinese Academy of Sciences Beijing People's Republic of China
| | - Kerong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
| | - Ming Du
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden of the Chinese Academy of Sciences Wuhan People's Republic of China
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Zhang X, Wang H, Que Y, Yu D, Wang H. The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease. PeerJ 2022; 9:e12601. [PMID: 34993020 PMCID: PMC8675258 DOI: 10.7717/peerj.12601] [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: 08/17/2021] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Wheat root rot disease due to soil-borne fungal pathogens leads to tremendous yield losses worth billions of dollars worldwide every year. It is very important to study the relationship between rhizosphere soil fungal diversity and wheat roots to understand the occurrence and development of wheat root rot disease. A significant difference in fungal diversity was observed in the rhizosphere soil of healthy and diseased wheat roots in the heading stage, but the trend was the opposite in the filling stage. The abundance of most genera with high richness decreased significantly from the heading to the filling stage in the diseased groups; the richness of approximately one-third of all genera remained unchanged, and only a few low-richness genera, such as Fusarium and Ceratobasidium, had a very significant increase from the heading to the filling stage. In the healthy groups, the abundance of most genera increased significantly from the heading to filling stage; the abundance of some genera did not change markedly, or the abundance of very few genera increased significantly. Physical and chemical soil indicators showed that low soil pH and density, increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Our results revealed that in the early stages of disease, highly diverse rhizosphere soil fungi and a complex community structure can easily cause wheat root rot disease. The existence of pathogenic fungi is a necessary condition for wheat root rot disease, but the richness of pathogenic fungi is not necessarily important. The increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Low soil pH and soil density are beneficial to the occurrence of wheat root rot disease.
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Affiliation(s)
- Xuejiang Zhang
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Heyun Wang
- HuBei University of Technology, Wuhan, Hubei Province, China
| | - Yawei Que
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Dazhao Yu
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Hua Wang
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, Hubei Province, China.,Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan, Hubei Province, China.,Institute of Plant Protection and Soil & Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
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Chen X, Wei H, Zhang J. Nitrogen and Sulfur Additions Improved the Diversity of nirK- and nirS-Type Denitrifying Bacterial Communities of Farmland Soil. BIOLOGY 2021; 10:biology10111191. [PMID: 34827184 PMCID: PMC8615190 DOI: 10.3390/biology10111191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic nitrogen (N) and sulfur (S) deposition can change above- and belowground biodiversity, including soil microbial diversity. The diversity of denitrifying microorganisms is of great significance to the calculation of the global nitrogen cycle and nitrogen flux. For a long time, nirK and nirS have been used as the functional genes to study denitrifying microorganisms, and have gradually become molecular markers for studying the composition and diversity of denitrifying bacteria. Here, three-time exposures to N and S applications (7, 30, and 60 days), were independently established. Additionally, the abundance, diversity, and structure of nirK- and nirS-type denitrifying communities were examined by sequencing analyses in response to three treatments, namely, N and S (TN/S), sodium chloride (TNaCl) and deionized water (pH = 7.0) (CK). Our results suggest that TN/S led to higher electrical conductivity (EC), total nitrogen (TN), total organic carbon (TOC), nitrate nitrogen (NO3--N), ammonium nitrogen (NH4+-N), and lower pH compared with TNaCl and CK, which affected the diversity of nirK- and nirS-type denitrifying bacterial communities. We also observed that the nirK-type denitrifying community demonstrated a higher sensitivity to N and S additions. Overall, our results are important for the understanding of nitrogen in soil and N2O emissions.
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Affiliation(s)
- Xuan Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.C.); (H.W.)
| | - Hui Wei
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.C.); (H.W.)
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.C.); (H.W.)
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
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Total and denitrifying bacterial communities associated with the interception of nitrate leaching by carbon amendment in the subsoil. Appl Microbiol Biotechnol 2021; 105:2559-2572. [PMID: 33651129 DOI: 10.1007/s00253-021-11189-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/30/2021] [Accepted: 02/17/2021] [Indexed: 10/22/2022]
Abstract
Nitrate leaching is severe in greenhouse where excessive nitrogen is often applied to maintain high crop productivities. In this study, we investigated the effects of carbon amendment in the subsoil on nitrate leaching and the emission of greenhouse gases (CH4 and N2O) using a soil column experiment. Carbon amendment resulted in over 39% reduction in nitrate leaching and 25.3% to 60.6% increase of total N content in the subsoil zone as compared to non-amended control. Strikingly, the abundance of nirS, nosZ, and 16S rRNA were higher in the treatment than the corresponding controls while no significant effect was detected for nirK. Carbon amendment explained 14%, 10%, and 4% of the variation in the community of nosZ, nirS, and nirK, respectively. It also considerably (more than 7 times) enriched genera such as Anaerovorax, Pseudobacteroides, Magnetospirillum, Prolixibacter, Sporobacter, Ignavibacterium, Syntrophobacter, Oxobacter, Hydrogenispora, Desulfosporomusa, Mangrovibacterium, and Sporomusa, as revealed by the analysis of 16S rRNA amplicon. Network analysis further uncovered that carbon amendment enriched three microbial hubs which mainly consists of positively correlated nirS, nosZ, and anaerobic bacterial populations. In summary, carbon amendment in the subsoil mitigated nitrate leaching and increased the nitrogen pool by possible activation of denitrifying and anaerobic bacterial populations. KEY POINTS: • Carbon amendment in subsoil reduced NO3- leaching by over 39% under high N input. • Carbon amendment increased the total N in subsoil from 25.3% to 60.6%. • Carbon amendment enriched nirS- and nosZ-type denitrifying bacteria in subsoil.
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Grover M, Bodhankar S, Sharma A, Sharma P, Singh J, Nain L. PGPR Mediated Alterations in Root Traits: Way Toward Sustainable Crop Production. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.618230] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The above ground growth of the plant is highly dependent on the belowground root system. Rhizosphere is the zone of continuous interplay between plant roots and soil microbial communities. Plants, through root exudates, attract rhizosphere microorganisms to colonize the root surface and internal tissues. Many of these microorganisms known as plant growth promoting rhizobacteria (PGPR) improve plant growth through several direct and indirect mechanisms including biological nitrogen fixation, nutrient solubilization, and disease-control. Many PGPR, by producing phytohormones, volatile organic compounds, and secondary metabolites play important role in influencing the root architecture and growth, resulting in increased surface area for nutrient exchange and other rhizosphere effects. PGPR also improve resource use efficiency of the root system by improving the root system functioning at physiological levels. PGPR mediated root trait alterations can contribute to agroecosystem through improving crop stand, resource use efficiency, stress tolerance, soil structure etc. Thus, PGPR capable of modulating root traits can play important role in agricultural sustainability and root traits can be used as a primary criterion for the selection of potential PGPR strains. Available PGPR studies emphasize root morphological and physiological traits to assess the effect of PGPR. However, these traits can be influenced by various external factors and may give varying results. Therefore, it is important to understand the pathways and genes involved in plant root traits and the microbial signals/metabolites that can intercept and/or intersect these pathways for modulating root traits. The use of advanced tools and technologies can help to decipher the mechanisms involved in PGPR mediated determinants affecting the root traits. Further identification of PGPR based determinants/signaling molecules capable of regulating root trait genes and pathways can open up new avenues in PGPR research. The present review updates recent knowledge on the PGPR influence on root architecture and root functional traits and its benefits to the agro-ecosystem. Efforts have been made to understand the bacterial signals/determinants that can play regulatory role in the expression of root traits and their prospects in sustainable agriculture. The review will be helpful in providing future directions to the researchers working on PGPR and root system functioning.
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Shtangeeva I, Vīksna A, Bērtiņš M, Ryumin A, Grebnevs V. Variations in the concentrations of macro- and trace elements in two grasses and in the rhizosphere soil during a day. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114265. [PMID: 32142978 DOI: 10.1016/j.envpol.2020.114265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/01/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
The aim of the research was to study short-term variations in concentrations of 17 elements in two widely distributed natural plant species (couch grass and plantain) and in the rhizosphere soil of the plants. The plant and soil samples were collected in a field from a small site over a daytime. In the course of the day, the variations of the total amounts of C, N, and H in the rhizosphere soil were rather marked and different for the soils taken from roots of plantain and couch grass. The concentrations of some other elements in the rhizosphere soil of the plants varied in a similar way. The short-term variations of element concentrations in roots and leaves of the plants were also rather large. In many cases, a decrease of element concentration in roots correlated with an increase of its concentration in leaves. Although couch grass and plantain were collected simultaneously and from the same site, mean concentrations of many elements in the two plant species were statistically significantly different. This may be result of the fact that the plants belong to different clades. The differences between concentrations of most part of elements in roots and leaves of the plants were also statistically significant. The concentrations of many trace elements were higher in roots than in leaves, while the concentrations of essential plant nutrients were often higher in leaves compared to roots. The distribution of elements between different plant parts were not the same in couch grass and plantain.
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Affiliation(s)
- Irina Shtangeeva
- Institute of Earth Sciences, St. Petersburg University, Universitetskaya nab.,7/9, St. Petersburg, 199034, Russia.
| | - Arturs Vīksna
- Faculty of Chemistry, University of Latvia, Jelgavas street 1, LV-1004, Riga, Latvia
| | - Māris Bērtiņš
- Faculty of Chemistry, University of Latvia, Jelgavas street 1, LV-1004, Riga, Latvia
| | - Alexander Ryumin
- Institute of Earth Sciences, St. Petersburg University, Universitetskaya nab.,7/9, St. Petersburg, 199034, Russia
| | - Vladlens Grebnevs
- Faculty of Chemistry, University of Latvia, Jelgavas street 1, LV-1004, Riga, Latvia
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Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, the specific amplifications of six denitrification-associated genes using PCR(Polymerase Chain Reaction) primer sets were compared. Thereafter, the PCR primer sets that were determined to be suitable for each denitrification-associated gene were used to test samples from sixteen aqueous environments (three from groundwater, three from stream water, and ten from hyporheic zone water). The specific amplification was determined using PCR primer sets for denitrification-associated genes and nucleic acids from eleven types of strains. NosZ was the most frequently amplified gene from the nucleic acid of type, with a specific band seen in all eleven strains. The specific band amplification and PCR time of the strains were analyzed to select one PCR primer set for each gene. The selected PCR primer sets were used to analyze sixteen samples from the aqueous environments in which denitrifying microorganisms were expected to be present. Specific bands of narG, nirS, and nosZ were most frequently observed in the hyporheic water samples. The results showed that microorganisms containing nirG (involved in the reduction of nitrate to nitrite), nirS (involved in the reduction of nitrite to nitric oxide), and nosZ (involved in the reduction of nitrous oxide to nitrogen gas) were the most abundant in the hyporheic zone samples used in this study.
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11
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Szukics U, Grigulis K, Legay N, Kastl EM, Baxendale C, Bardgett RD, Clément JC, Lavorel S, Schloter M, Bahn M. Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:745-753. [PMID: 30134212 DOI: 10.1016/j.scitotenv.2018.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlated most strongly with N parameters, such as soil NO3--N, microbial N, leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers.
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Affiliation(s)
- Ute Szukics
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria
| | - Karl Grigulis
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Nicolas Legay
- École de la Nature et du Paysage, INSA Centre Val de Loire, 9 Rue Chocolaterie, 41000 Blois, France; CNRS, CITERES, UMR 7324, 37200 Tours, France
| | - Eva-Maria Kastl
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | | | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Sandra Lavorel
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | - Michael Bahn
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria.
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Saad RF, Kobaissi A, Echevarria G, Kidd P, Calusinska M, Goux X, Benizri E. Influence of new agromining cropping systems on soil bacterial diversity and the physico-chemical characteristics of an ultramafic soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:380-392. [PMID: 30029117 DOI: 10.1016/j.scitotenv.2018.07.106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Most of the research dedicated to agromining has focused on cultivating a single hyperaccumulator plant, although plant diversity has been shown to positively modify soil characteristics. Hence, we compared the effect of cropping a nickel-hyperaccumulator Alyssum murale with a legume (Vicia sativa) to A. murale's mono-culture, on the bacterial diversity and physico-chemical characteristics of an ultramafic soil. A pot experiment with 5 replicates was conducted in controlled conditions for 11 months. The treatments studied were: co-cropping and rotation vs. mineral fertilization controls and bare soil. The introduction of legumes induced a clearly positive effect on the soil's microbial biomass carbon and nitrogen. Arylsulfatase and urease activities tended to be enhanced in the co-cropping and rotation treatments and to be lessened in the mineral fertilization treatments. However, β-glucosidase and phosphatase activities were seen to decrease when legumes were used. Our results showed that the rotation treatment induced a higher organic matter content than the fertilized control did. Actinobacteria was the most-represented bacterial phyla and had lower relative abundance in treatments associating legumes. Conversely, the relative abundance of Acidobacteria and Gemmatimonadetes phyla increased but not significantly in treatments with legumes. The relative abundance of Chloroflexi phylum was shown to be significantly higher for the fertilized rotation control. The relative abundance of β-Proteobacteria subphylum increased but not significantly in treatments with legumes. NMDS analysis showed a clear separation between planted treatments and bare soil and between co-cropping and rotation and fertilized controls. Shannon index showed reduction in microbial diversity that was mainly due to chemical inputs in the soil. This study showed that these new cropping systems influenced both the bacterial diversity and the physico-chemical characteristics of an ultramafic soil. In addition, this study provides evidence that mineral fertilization can negatively impact bacterial communities and some of their functions linked to biogeochemical cycles.
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Affiliation(s)
- Ramez F Saad
- Université de Lorraine, INRA, Laboratoire Sols et Environnement, 54000 Nancy, France; Université Libanaise, Laboratoire «Applied Plant Biotechnology», Faculté des Sciences 1, Beyrouth, Lebanon
| | - Ahmad Kobaissi
- Université Libanaise, Laboratoire «Applied Plant Biotechnology», Faculté des Sciences 1, Beyrouth, Lebanon
| | - Guillaume Echevarria
- Université de Lorraine, INRA, Laboratoire Sols et Environnement, 54000 Nancy, France
| | - Petra Kidd
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Santiago de Compostela 15706, Spain
| | - Magdalena Calusinska
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg
| | - Xavier Goux
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg
| | - Emile Benizri
- Université de Lorraine, INRA, Laboratoire Sols et Environnement, 54000 Nancy, France.
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13
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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14
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Baker BH, Brooks JP, Deng DD, Smith RK, Kröger R, Prince Czarnecki JM. Effects of Low-Grade Weirs on Soil Microbial Communities in Agricultural Drainage Ditches. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1155-1162. [PMID: 30272767 DOI: 10.2134/jeq2017.12.0489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agricultural fertilizer application throughout the Mississippi River basin has been identified as a major source of N pollution to the Gulf of Mexico. Using best management practices, such as low-grade weirs, has been identified as a potential solution to mitigate nutrient loads in agricultural runoff. This study assessed impacts of weir implementation in four agricultural drainage ditches (three with weirs and one control site) in the Mississippi Delta. Soil samples collected from field locations in spring 2013 were analyzed for denitrifier abundance using genes (16s ribosomal RNA [rRNA] genes, , , and ) via quantitative polymerase chain reaction (qPCR), microbial community profiles via terminal-restriction fragment length polymorphism (T-RFLP) of 16s rRNA genes, soil parameters (C, N, and moisture), and vegetation presence at sample locations. Gene quantification was successful, except for , which was found below detection limits (5000 gene copies g soil). Distance from weirs was negatively correlated with 16S rRNA genes and soil moisture, and soil moisture was positively correlated with 16s rRNA and S gene abundance. Results of empirical Bayesian kriging did not exhibit obvious patterns of microbial diversity in relation to weir proximity. Preliminary assessment of seasonal trends showed genes 16s rRNA and , soil N, and mean T-RF values to be greater in fall than in spring. Results highlight that weirs had no direct impact on microbial diversity or denitrification functional gene abundance. Correlations between microbial measures and environmental parameters suggest that adequate management of N runoff from agricultural landscapes will require ecological engineering beyond weirs to optimize N mitigation.
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15
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Morse N, Payne E, Henry R, Hatt B, Chandrasena G, Shapleigh J, Cook P, Coutts S, Hathaway J, Walter MT, McCarthy D. Plant-Microbe Interactions Drive Denitrification Rates, Dissolved Nitrogen Removal, and the Abundance of Denitrification Genes in Stormwater Control Measures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9320-9329. [PMID: 30059225 DOI: 10.1021/acs.est.8b02133] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbial community and function along with nitrate/nitrite (NOx) removal rates, and nitrogen (N) partitioning into "uptake", "denitrification", and "remaining" via isotope tracers, were studied in soil bioretention mesocolumns (8 unique plant species). Total denitrification gene reads per million (rpm) were positively correlated with % denitrified ( r = 0.69) but negatively correlated with total NOx removal following simulated rain events ( r = -0.79). This is likely due to plant-microbe interactions. Plant species with greater root volume, plant and microbial assimilation %, and NOx removal % had lower denitrification genes and rates. This implies that although microorganisms have access to N, advantageous functions, like denitrification, may not increase. At the conclusion of the 1.5-year experiment, the microbial community was strongly influenced by plant species within the Top zone dominated by plant roots, and the presence or absence of a saturated zone influenced the microbial community within the Bottom zone. Leptospermum continentale was an outlier from the other plants and had much lower denitrification gene rpm (average 228) compared to the other species (range: 277 to 413). The antimicrobial properties and large root volume of Leptospermum continentale likely caused this denitrification gene depression.
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Affiliation(s)
- Natalie Morse
- Department of Biological and Environmental Engineering , Cornell University , 11 Wing Drive , Riley-Robb Hall B62, Ithaca , New York 14850 , United States
| | - Emily Payne
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering , Monash University , Clayton , Victoria 3800 , Australia
| | - Rebekah Henry
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering , Monash University , Clayton , Victoria 3800 , Australia
| | | | | | - James Shapleigh
- Department of Microbiology , Cornell University , Ithaca , New York 14850 , United States
| | - Perran Cook
- Water Studies Centre, School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | - Scott Coutts
- MICROMON , Monash University , Clayton , Victoria 3800 , Australia
| | - Jon Hathaway
- Department of Civil and Environmental Engineering , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering , Cornell University , 11 Wing Drive , Riley-Robb Hall B62, Ithaca , New York 14850 , United States
| | - David McCarthy
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering , Monash University , Clayton , Victoria 3800 , Australia
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16
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Webster AJ, Groffman PM, Cadenasso ML. Controls on denitrification potential in nitrate-rich waterways and riparian zones of an irrigated agricultural setting. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2018; 28:1055-1067. [PMID: 29465768 DOI: 10.1002/eap.1709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
Denitrification, the microbial conversion of NO3- to N gases, is an important process contributing to whether lotic and riparian ecosystems act as sinks for excess NO3- from agricultural activities. Though agricultural waterways and riparian zones have been a focus of denitrification research for decades, almost none of this research has occurred in the irrigated agricultural settings of arid and semiarid climates. In this study, we conducted a broad survey of denitrification potential in riparian soils and channel sediments from 79 waterway reaches in the irrigated agricultural landscape of California's Central Valley. With this approach, we sought to capture the wide range of variation that arose from diverse waterway management and fluctuating flow conditions, and use this variation to identify promising management interventions. We explored associations of denitrification potentials with surface water NO3- -N, organic matter, flow conditions, vegetation cover, near-channel riparian bank slope, and channel geomorphic features using generalized linear mixed models. We found strong associations of sediment denitrification potentials with reach flow conditions, which we hypothesize was the result of variation in microbial communities' tolerance to dry-wet cycles. Denitrification potentials in riparian soils, in contrast, did not appear affected by flow conditions, but instead were associated with organic matter, vegetation cover, and bank slope in the riparian zone. These results suggest a strong need for further work on how denitrification responds to varying flow conditions and dry-wet cycles in non-perennial lotic ecosystems. Our findings also demonstrate that denitrifier communities respond to key features of waterway management, which can therefore be leveraged to control denitrification through a variety of management actions.
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Affiliation(s)
- Alex J Webster
- Department of Plant Sciences, University of California Davis, Shields Avenue, Davis, California, 95616, USA
- Graduate Group in Ecology, University of California Davis, Shields Avenue, Davis, California, 95616, USA
| | - Peter M Groffman
- Cary Institute of Ecosystem Studies, Millbrook, New York, 12545, USA
- Advanced Research Center and Brooklyn College, City University of New York, New York, New York, 12210, USA
| | - Mary L Cadenasso
- Department of Plant Sciences, University of California Davis, Shields Avenue, Davis, California, 95616, USA
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17
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Holzem RM, Gardner CM, Stapleton HM, Gunsch CK. Using laboratory-generated biosolids to evaluate the microbial ecotoxicity of triclosan in a simulated land application scenario. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:11084-11099. [PMID: 29411281 DOI: 10.1007/s11356-017-1147-z] [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: 10/23/2017] [Accepted: 12/26/2017] [Indexed: 06/08/2023]
Abstract
Land application accounts for approximately 50% of wastewater solids disposal in the USA. Yet, little is known regarding the ecological impacts of many non-regulated chemicals found in biosolids. In most previous studies aimed at assessing ecological impacts, a model biosolid is generated by spiking high concentrations of the target chemical into a soil or biosolid. This approach does not account for the interaction of the chemical of interest with the solids throughout the biosolids production process (a.k.a., aging) which may impact the bioavailability and, thus, ultimate toxicity of the chemical. In the present study, using a lab-scale wastewater and digestion treatment system, we generated biosolids which contained aged triclosan and compared ecological impacts to that of spiked biosolids. Ecotoxicity was assessed based on functional and community structure changes to soil denitrifiers, microorganisms critical to nitrogen cycling. A decrease in denitrifier abundance and diversity was observed in the aged biosolids at concentrations of 17.9 ± 1.93 μg/kg while decreases in activity were observed at 26.9 ± 4.6 μg/kg. In the spiked biosolids treatment, lower denitrifier abundance, diversity, and activity were observed at triclosan (TCS) concentrations of 68.6 ± 26.9 μg/kg. This difference suggests a need to better understand TCS bioavailability dynamics.
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Affiliation(s)
- Ryan M Holzem
- Department of Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, WI, 54311, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Duke University, 121 Hudson Hall, Box 90287, Durham, NC, 27708-0287, USA
| | | | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, 121 Hudson Hall, Box 90287, Durham, NC, 27708-0287, USA.
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18
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Jiang X, Yao L, Guo L, Liu G, Liu W. Multi-scale factors affecting composition, diversity, and abundance of sediment denitrifying microorganisms in Yangtze lakes. Appl Microbiol Biotechnol 2017; 101:8015-8027. [PMID: 28956101 DOI: 10.1007/s00253-017-8537-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/11/2017] [Accepted: 09/17/2017] [Indexed: 11/25/2022]
Abstract
Sediment denitrification is the dominant nitrogen removal pathway in many aquatic habitats and can be regulated by local-, landscape-, and regional-scale factors. However, the mechanisms for how these multiple scale factors and their interactions affect the sediment denitrifying communities remain poorly understood. In this study, we investigated the community composition, diversity, and abundance of nitrite reductase genes (nirK and nirS)-encoding denitrifiers in 74 sediment samples from 22 Yangtze lakes using clone library and quantitative PCR techniques. Information of location, climate, catchment land use, water quality, sediment properties, and plant communities at each sampling site was analyzed to elucidate the effects of regional, landscape, and local factors on the characteristics of sediment denitrifying communities. Results of canonical correspondence analysis indicated that local factors were the key determinants of denitrifying community composition, accounting for over 20% of the total variation. Additionally, certain regional and landscape factors, including elevation and catchment built-up land, were also significantly related to the composition of denitrifying communities. Variance partitioning analyses revealed that diversity and abundance in the nirK denitrifier community were largely influenced by local factors, while those in the nirS community were controlled by both local and regional factors. Our findings highlight the importance of using different scale factors to explain adequately the composition and structure of denitrifying communities in aquatic environments.
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Affiliation(s)
- Xiaoliang Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Lumo Road No.1, Wuchang District, Wuhan, 430074, China
| | - Lu Yao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Lumo Road No.1, Wuchang District, Wuhan, 430074, China
| | - Laodong Guo
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, 53204, USA
| | - Guihua Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Lumo Road No.1, Wuchang District, Wuhan, 430074, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Lumo Road No.1, Wuchang District, Wuhan, 430074, China.
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, 53204, USA.
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19
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Chen R, Deng M, He X, Hou J. Enhancing Nitrate Removal from Freshwater Pond by Regulating Carbon/Nitrogen Ratio. Front Microbiol 2017; 8:1712. [PMID: 28943869 PMCID: PMC5596099 DOI: 10.3389/fmicb.2017.01712] [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: 04/13/2017] [Accepted: 08/24/2017] [Indexed: 11/13/2022] Open
Abstract
Nitrogen accumulation is a serious environmental problem in freshwater ponds, which can lead to massive death of fish and shrimps as well as the eutrophication. The removal of nitrate by regulating the carbon to nitrogen (C/N) ratio and the underlying mechanisms were investigated. The nitrate removal system comprised 530-mL medium containing 5 mg/L NO3−-N and 0–66.6 mg/L COD (i.e., C/N ratio of 0–13.3) and 20 g ponds sediments. When the C/N ratio was higher than 8, the nitrate removal efficiency nearly reached 100% during the incubation period and the accumulation of nitrite was negligible. When the C/N ratio was below 8, the nitrate removal efficiency was lower and significant nitrite accumulation occurred. The nitrate removal rate increased with the C/N ratio increased, which was ascribed to the increase in the absolute abundance of denitrifiers (nirS, nirK, and nosZ). Although both nirS-type and nirK-type denitrifiers were found in the sediments of freshwater pond, nirS-type denitrifiers were predominant. Dechloromonas was the major nirS-type denitrifier for nitrate removal in nirS-type with the C/N ratios above 5.33, while the majority of the nirK-type denitrifiers were unclassified. Thus, this study implied that the appropriate C/N ratio played an important role on the removal of excess nitrate from freshwater ponds.
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Affiliation(s)
- Rong Chen
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China.,School of Environmental Studies, China University of GeosciencesWuhan, China
| | - Min Deng
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China
| | - Xugang He
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China.,Hubei Provincial Engineering Laboratory for Pond AquacultureWuhan, China
| | - Jie Hou
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China
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20
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Meng H, Wu R, Wang YF, Gu JD. A comparison of denitrifying bacterial community structures and abundance in acidic soils between natural forest and re-vegetated forest of Nanling Nature Reserve in southern China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:41-49. [PMID: 28500915 DOI: 10.1016/j.jenvman.2017.04.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/02/2017] [Accepted: 04/22/2017] [Indexed: 06/07/2023]
Abstract
Denitrification plays a key role in converting reactive nitrogen species to dinitrogen gas back into the atmosphere to maintain the equilibrium of nitrogen cycling in ecosystems. In this study, functional genes of nirK and nosZ were used to detect the community structure and abundance of denitrifying microorganisms in acidic forest soils in southern China. Three sets of factors were considered for a comparison among 5 forests, including forest types (natural vs. re-vegetated), depths (surface layer vs. lower layer) and seasons (winter vs. summer). The community of nirK gene detected from these acidic forest soils was closely related to Proteobacteria especially α-Proteobacteria and uncultured soil sequences, while that of nosZ gene was affiliated with the α-, β- and γ-Proteobacteria. Higher diversity of denitrifiers was observed in re-vegetated forest soils than natural ones. Not only the community but also the abundance showed significant differences between forest types as well as depths. The abundance of denitrifiers ranged from 105 to 107 gene copies g-1 dry soil in this study. For nirK gene, the abundance was much higher in the lower layer than surface layer in both forest types, and the differences between winter and summer in natural forest soils were higher than those in re-vegetated forest soils. The abundance of nosZ and nirK genes showed a similar trend in natural forest, but the former was higher in matured forest than re-vegetated forest. This study provided a direct comparison on community composition and abundance of denitrifying bacteria in natural and re-vegetated acidic forest soils to allow further assessment of the nitrogen cycling.
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Affiliation(s)
- Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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21
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Harter J, El-Hadidi M, Huson DH, Kappler A, Behrens S. Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N 2O formation. Sci Rep 2017; 7:3338. [PMID: 28611409 PMCID: PMC5469825 DOI: 10.1038/s41598-017-03282-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/25/2017] [Indexed: 11/29/2022] Open
Abstract
Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (N2O). Soil biochar amendment has been shown to significantly decrease N2O emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and N2O-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct N2O reduction from the environment. Our results point towards a potential coupling of biochar-induced N2O emission reduction and an increase in microbial N2O reduction activity among specific groups of typical and atypical N2O reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.
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Affiliation(s)
- Johannes Harter
- Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, 72074, Tuebingen, Germany
| | - Mohamed El-Hadidi
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, 72074, Tuebingen, Germany.,Bioinformatics, Center for Informatics Science (CIS), Nile University, Giza, Egypt
| | - Daniel H Huson
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, 72074, Tuebingen, Germany
| | - Andreas Kappler
- Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, 72074, Tuebingen, Germany
| | - Sebastian Behrens
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, 55455, MN, USA. .,BioTechnology Institute, University of Minnesota, Minneapolis, 55455, MN, USA.
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22
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Remmas N, Melidis P, Paschos G, Statiris E, Ntougias S. Protozoan indicators and extracellular polymeric substances alterations in an intermittently aerated membrane bioreactor treating mature landfill leachate. ENVIRONMENTAL TECHNOLOGY 2017; 38:53-64. [PMID: 27194208 DOI: 10.1080/09593330.2016.1190792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/12/2016] [Indexed: 06/05/2023]
Abstract
A membrane bioreactor was operated under intermittent aeration and various organic loading rates (OLR: 0.070, 0.159 and 0.291 g COD L-1 d-1) to remove carbon and nitrogen from mature landfill leachate, where external carbon source (glycerol) addition resulted in effective nitrate removal. A relative increase in soluble microbial product (SMP) over extracellular polymeric substances (EPS) was observed at the highest OLR and glycerol addition, whereas no membrane biofouling occurred. SMP (proteins and carbohydrates) and carbohydrate EPS correlated positively and negatively, respectively, with suspended solids and transmembrane pressure (TMP). Moreover, proteinous SMP significantly correlated with carbon and nitrogen load. Principal component analysis also revealed the influence of leachate organic and nitrogen content on biomass production, TMP and sessile ciliate densities. Although filamentous index (FI) was sustained at high levels (3-4), with Haliscomenobacter hydrossis being the main filamentous bacterium identified, no bulking phenomena occurred. High glycerol addition resulted in a rapid increase in sessile ciliate population. Increased Epistylis and Vorticella microstoma population was detected by microscopic examination during high glycerol addition, while a remarkable Rhogostoma population (supergroup Rhizaria) was identified by molecular techniques. The contribution of Rhizaria in nitrogen processes may lead to the dominance of Rhogostoma during landfill leachate treatment.
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Affiliation(s)
- Nikolaos Remmas
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Paraschos Melidis
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Georgios Paschos
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Evangelos Statiris
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
| | - Spyridon Ntougias
- a Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering , Democritus University of Thrace , Xanthi , Greece
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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Fan Z, Han RM, Ma J, Wang GX. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14102-14114. [PMID: 27048324 DOI: 10.1007/s11356-016-6390-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.
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Affiliation(s)
- Zhou Fan
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Rui-Ming Han
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ma
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Guo-Xiang Wang
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China.
- Nanjing Normal University, School of Geography Science, Wenyuan Road 1, Nanjing, 210023, China.
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Palmer K, Köpp J, Gebauer G, Horn MA. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen. Front Microbiol 2016; 7:727. [PMID: 27313566 PMCID: PMC4887476 DOI: 10.3389/fmicb.2016.00727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen.
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Affiliation(s)
- Katharina Palmer
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany; Water Resources and Environmental Engineering Research Group, University of OuluOulu, Finland
| | - Julia Köpp
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Gerhard Gebauer
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods. PLoS One 2016; 11:e0154697. [PMID: 27140199 PMCID: PMC4854452 DOI: 10.1371/journal.pone.0154697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 04/18/2016] [Indexed: 11/22/2022] Open
Abstract
In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.
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Lammel DR, Feigl BJ, Cerri CC, Nüsslein K. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils. Front Microbiol 2015; 6:1057. [PMID: 26500618 PMCID: PMC4594008 DOI: 10.3389/fmicb.2015.01057] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 09/14/2015] [Indexed: 11/30/2022] Open
Abstract
Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.
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Affiliation(s)
- Daniel R Lammel
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil ; Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Brigitte J Feigl
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Carlos C Cerri
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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Guiz J, Hillebrand H, Borer ET, Abbas M, Ebeling A, Weigelt A, Oelmann Y, Fornara D, Wilcke W, Temperton VM, Weisser WW. Long-term effects of plant diversity and composition on plant stoichiometry. OIKOS 2015. [DOI: 10.1111/oik.02504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jordan Guiz
- Inst. for Chemistry and Biology of the Marine Environment (ICBM), Univ. Oldenburg; Schleusenstrasse 1 DE-26382 Wilhemshaven Germany
| | - Helmut Hillebrand
- Inst. for Chemistry and Biology of the Marine Environment (ICBM), Univ. Oldenburg; Schleusenstrasse 1 DE-26382 Wilhemshaven Germany
| | - Elizabeth T. Borer
- Dept of Ecology, Evolution and Behavior; Univ. of Minnesota; St. Paul MN USA
| | - Maike Abbas
- Inst. for Chemistry and Biology of the Marine Environment (ICBM), Univ. Oldenburg; Schleusenstrasse 1 DE-26382 Wilhemshaven Germany
| | - Anne Ebeling
- Inst. of Ecology, FSU Jena; Dornburger str. 159 DE-07743 Jena Germany
| | - Alexandra Weigelt
- Inst. of Biology I, Univ. of Leipzig; Johannisalle 21-23 DE-04103 Leipzig Germany
| | - Yvonne Oelmann
- Geoecology, Univ. of Tübingen; Rümelinstrasse 19-23 DE-72070 Tübingen Germany
| | - Dario Fornara
- Agri-Food and Biosciences Institute (AFBI); Newforge Lane, Belfast UK
| | - Wolfgang Wilcke
- Inst. of Geography and Geoecology, Karlsruhe Inst. of Technology (KIT); Reinhard-Baumeister-Platz 1 DE-76131 Karlsruhe Germany
| | - Vicky M. Temperton
- Inst. of Bio- and Geosciences (IBG-2 Plant Sciences); Jülich Forschungszentrum DE-52428 Jülich Germany
| | - Wolfgang W. Weisser
- Dept of Ecology and Ecosystem management; Technische Univ. München; Hans-Carl-von-Carlowitz-Platz 2 DE- 85350 Freising-Weihenstephan Germany
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Impacts of Long-Term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure. Appl Environ Microbiol 2015; 81:7143-58. [PMID: 26253672 DOI: 10.1128/aem.02188-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/23/2015] [Indexed: 01/06/2023] Open
Abstract
Freshwater scarcity and regulations on wastewater disposal have necessitated the reuse of treated wastewater (TWW) for soil irrigation, which has several environmental and economic benefits. However, TWW irrigation can cause nutrient loading to the receiving environments. We assessed bacterial community structure and associated biogeochemical changes in soil plots irrigated with nitrate-rich TWW (referred to as pivots) for periods ranging from 13 to 30 years. Soil cores (0 to 40 cm) were collected in summer and winter from five irrigated pivots and three adjacently located nonirrigated plots. Total bacterial and denitrifier gene abundances were estimated by quantitative PCR (qPCR), and community structure was assessed by 454 massively parallel tag sequencing (MPTS) of small-subunit (SSU) rRNA genes along with terminal restriction fragment length polymorphism (T-RFLP) analysis of nirK, nirS, and nosZ functional genes responsible for denitrification of the TWW-associated nitrate. Soil physicochemical analyses showed that, regardless of the seasons, pH and moisture contents (MC) were higher in the irrigated (IR) pivots than in the nonirrigated (NIR) plots; organic matter (OM) and microbial biomass carbon (MBC) were higher as a function of season but not of irrigation treatment. MPTS analysis showed that TWW loading resulted in the following: (i) an increase in the relative abundance of Proteobacteria, especially Betaproteobacteria and Gammaproteobacteria; (ii) a decrease in the relative abundance of Actinobacteria; (iii) shifts in the communities of acidobacterial groups, along with a shift in the nirK and nirS denitrifier guilds as shown by T-RFLP analysis. Additionally, bacterial biomass estimated by genus/group-specific real-time qPCR analyses revealed that higher numbers of total bacteria, Acidobacteria, Actinobacteria, Alphaproteobacteria, and the nirS denitrifier guilds were present in the IR pivots than in the NIR plots. Identification of the nirK-containing microbiota as a proxy for the denitrifier community indicated that bacteria belonged to alphaproteobacteria from the Rhizobiaceae family within the agroecosystem studied. Multivariate statistical analyses further confirmed some of the above soil physicochemical and bacterial community structure changes as a function of long-term TWW application within this agroecosystem.
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30
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Moreau D, Pivato B, Bru D, Busset H, Deau F, Faivre C, Matejicek A, Strbik F, Philippot L, Mougel C. Plant traits related to nitrogen uptake influence plant-microbe competition. Ecology 2015; 96:2300-10. [DOI: 10.1890/14-1761.1] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Yin C, Fan F, Song A, Cui P, Li T, Liang Y. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil. Appl Microbiol Biotechnol 2015; 99:5719-29. [DOI: 10.1007/s00253-015-6461-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
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Bardgett RD, Mommer L, De Vries FT. Going underground: root traits as drivers of ecosystem processes. Trends Ecol Evol 2014; 29:692-9. [PMID: 25459399 DOI: 10.1016/j.tree.2014.10.006] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 09/30/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
Abstract
Ecologists are increasingly adopting trait-based approaches to understand how community change influences ecosystem processes. However, most of this research has focussed on aboveground plant traits, whereas it is becoming clear that root traits are important drivers of many ecosystem processes, such as carbon (C) and nutrient cycling, and the formation and structural stability of soil. Here, we synthesise emerging evidence that illustrates how root traits impact ecosystem processes, and propose a pathway to unravel the complex roles of root traits in driving ecosystem processes and their response to global change. Finally, we identify research challenges and novel technologies to address them.
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Affiliation(s)
- Richard D Bardgett
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Liesje Mommer
- Nature Conservation and Plant Ecology Group, Wageningen University, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Franciska T De Vries
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Legay N, Baxendale C, Grigulis K, Krainer U, Kastl E, Schloter M, Bardgett RD, Arnoldi C, Bahn M, Dumont M, Poly F, Pommier T, Clément JC, Lavorel S. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities. ANNALS OF BOTANY 2014; 114:1011-21. [PMID: 25122656 PMCID: PMC4171078 DOI: 10.1093/aob/mcu169] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/03/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. METHODS In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. KEY RESULTS Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. CONCLUSIONS The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
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Affiliation(s)
- N Legay
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - C Baxendale
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - K Grigulis
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France Station Alpine Joseph Fourier, UMS 3370 CNRS - Université Joseph Fourier, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
| | - U Krainer
- Institute of Ecology, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - E Kastl
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - M Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - R D Bardgett
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK and
| | - C Arnoldi
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - M Bahn
- Institute of Ecology, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - M Dumont
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - F Poly
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - T Pommier
- Laboratoire d'Ecologie Microbienne, Université Lyon1, Université de Lyon, 15 USC INRA 1364, UMR CNRS 5557, Villeurbanne Cedex, France
| | - J C Clément
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
| | - S Lavorel
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France
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Liu L, Wang D, Deng H, Li Y, Chang S, Wu Z, Yu L, Hu Y, Yu Z, Chen Z. The capability of estuarine sediments to remove nitrogen: implications for drinking water resource in Yangtze Estuary. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:10890-10899. [PMID: 24770927 DOI: 10.1007/s11356-014-2914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/14/2014] [Indexed: 06/03/2023]
Abstract
Water in the Yangtze Estuary is fresh most of the year because of the large discharge of Yangtze River. The Qingcaosha Reservoir built on the Changxing Island in the Yangtze Estuary is an estuarine reservoir for drinking water. Denitrification rate in the top 10 cm sediment of the intertidal marshes and bare mudflat of Yangtze Estuarine islands was measured by the acetylene inhibition method. Annual denitrification rate in the top 10 cm of sediment was 23.1 μmol m(-2) h(-1) in marshes (ranged from 7.5 to 42.1 μmol m(-2) h(-1)) and 15.1 μmol m(-2) h(-1) at the mudflat (ranged from 6.6 to 26.5 μmol m(-2) h(-1)). Annual average denitrification rate is higher at mashes than at mudflat, but without a significant difference (p = 0.084, paired t test.). Taking into account the vegetation and water area of the reservoir, a total 1.42 × 10(8) g N could be converted into nitrogen gas (N2) annually by the sediment, which is 97.7 % of the dissolved inorganic nitrogen input through precipitation. Denitrification in reservoir sediment can control the bioavailable nitrogen level of the water body. At the Yangtze estuary, denitrification primarily took place in the top 4 cm of sediment, and there was no significant spatial or temporal variation of denitrification during the year at the marshes and mudflat, which led to no single factor determining the denitrification process but the combined effects of the environmental factors, hydrologic condition, and wetland vegetation.
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Affiliation(s)
- Lin Liu
- School of Resources and Environmental Science, East China Normal University, Shanghai, 200241, China
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35
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Wang HT, Su JQ, Zheng TL, Yang XR. Impacts of vegetation, tidal process, and depth on the activities, abundances, and community compositions of denitrifiers in mangrove sediment. Appl Microbiol Biotechnol 2014; 98:9375-87. [DOI: 10.1007/s00253-014-6017-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 07/30/2014] [Accepted: 08/05/2014] [Indexed: 12/18/2022]
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Abstract
Under different soil salinity levels, diversity of soil microbial communities from Hetao irrigated land of Inner Mongolia was studied by phospholipid fatty acid (PLFA) analysis. The study found that PLFAs biomass in saline soil was significantly lower than those of strongly salinized soil and slight salinized soil. Microbes was bacteria-based from these soil. The bacterial PLFA loading in saline soil is significantly less than those of strongly salinized soil and slight salinized soil . Cluster analysis showed that changes had obviously taken place on soil microbial composition and quantity under different soil salinity levels.About 76.89% of variation in PLFA patterns explained by PC1(the first principal components),and 17:1, 16:0, 18:1w9c, 18:1w9t, 18:2, 18:3w3c, 12:0 were strongly negatively correlated with PC1.However,soil salinity and pH were positively correlated with PC1.We conclude that soil salinity has a profound affect on the microbial community structure.
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Zhang Q, Peng J, Chen Q, Yang X, Hong Y, Su J. Abundance and composition of denitrifiers in response to Spartina alterniflora invasion in estuarine sediment. Can J Microbiol 2014; 59:825-36. [PMID: 24313455 DOI: 10.1139/cjm-2013-0516] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitrite reduction is regulated by nitrite reductase encoded by nirK and nirS genes. This study aimed to investigate the abundance and composition of nirK- and nirS-containing denitrifiers in response to Spartina alterniflora invasion at the Jiulong River estuary, China. The sediment samples (depth: 0-5.0 and 5.1-20 cm) were collected from 3 vegetation zones, 1 dominated by the exotic plant S. alterniflora, 1 dominated by the native plant Kandelia candel, and 1 dominated by the native plant Cyperus malaccensis, and from an unvegetated flat zone. nirK- and nirS-containing denitrifier population sizes were lower in the invaded and nonvegetated zones than in those dominated by native K. candel and C. malaccensis, which were impacted by depth - vegetation species interaction. The ratios of nirS to nirK abundance ranged from 42.10 to 677.27, with the lowest ratio found for the upper layer in the invaded zone. The nirK-containing denitrifier compositions showed a 35% similarity between invaded zone and others. Most of the sequences of nirK genes recovered from the S. alterniflora zone were specific and distinct from those of nirK genes recovered from other vegetation types; nirS genes in the invaded zone were highly divergent. These results reveal that S. alterniflora invasion has a significant effect on the abundance and composition of both nirK- and nirS-containing denitrifiers, and nirS-containing denitrifiers were less responsive to invasion than nirK-containing denitrifiers.
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Affiliation(s)
- Qiufang Zhang
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
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38
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Ammonia-oxidation as an engine to generate nitrous oxide in an intensively managed calcareous fluvo-aquic soil. Sci Rep 2014; 4:3950. [PMID: 24492201 PMCID: PMC3912618 DOI: 10.1038/srep03950] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/16/2014] [Indexed: 11/13/2022] Open
Abstract
We combine field observations, microcosm, stoichiometry, and molecular and stable isotope techniques to quantify N2O generation processes in an intensively managed low carbon calcareous fluvo-aquic soil. All the evidence points to ammonia oxidation and linked nitrifier denitrification (ND) being the major processes generating N2O. When NH4+-based fertilizers are applied the soil will produce high N2O peaks which are inhibited almost completely by adding nitrification inhibitors. During ammonia oxidation with high NH4+ concentrations (>80 mg N kg−1) the soil matrix will actively consume oxygen and accumulate high concentrations of NO2−, leading to suboxic conditions inducing ND. Calculated N2O isotopomer data show that nitrification and ND accounted for 35–53% and 44–58% of total N2O emissions, respectively. We propose that slowing down nitrification and avoiding high ammonium concentrations in the soil matrix are important measures to reduce N2O emissions per unit of NH4+-based N input from this type of intensively managed soil globally.
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39
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Nitrite reductase genes as functional markers to investigate diversity of denitrifying bacteria during agricultural waste composting. Appl Microbiol Biotechnol 2014; 98:4233-43. [PMID: 24442505 DOI: 10.1007/s00253-014-5514-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 12/26/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
Abstract
The purpose of this study was to investigate the diversity of denitrifier community during agricultural waste composting. The diversity and dynamics of the denitrifying genes (nirK and nirS) were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Relationships between physico-chemical parameters and denitrifying genes structures were simultaneously evaluated by redundancy analysis (RDA). Phylogenetic analysis indicated that nirK clones grouped into six clusters and nirS clones into two major clusters, respectively. The results showed a very high diversity of nir gene sequences within composting samples. RDA showed that the nirK and nirS gene structures were significantly related to pH and pile temperature (P < 0.05). Significant amounts of the variation (49.2 and 38.3 % for nirK and nirS genes, respectively) were explained by pH and pile temperature, suggesting that those two parameters were the most likely ones to influence, or be influenced by the denitrifiers harboring nirK and nirS genes.
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40
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Saggar S, Jha N, Deslippe J, Bolan NS, Luo J, Giltrap DL, Kim DG, Zaman M, Tillman RW. Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 465:173-95. [PMID: 23260378 DOI: 10.1016/j.scitotenv.2012.11.050] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/11/2012] [Accepted: 11/12/2012] [Indexed: 05/02/2023]
Abstract
In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.
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Affiliation(s)
- Surinder Saggar
- Ecosystems & Global Change Team, Landcare Research, Private Bag 11052, Palmerston North 4442, New Zealand.
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41
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Meyer A, Focks A, Radl V, Keil D, Welzl G, Schöning I, Boch S, Marhan S, Kandeler E, Schloter M. Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil. PLoS One 2013; 8:e73536. [PMID: 24039974 PMCID: PMC3765351 DOI: 10.1371/journal.pone.0073536] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022] Open
Abstract
Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.
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Affiliation(s)
| | - Andreas Focks
- Department for Aquatic Ecology and Water Quality Management, Wageningen, The Netherlands
| | - Viviane Radl
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Environmental Genomics, Neuherberg, Germany
| | - Daniel Keil
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Soil Biology Section, Stuttgart, Germany
| | - Gerhard Welzl
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Environmental Genomics, Neuherberg, Germany
| | - Ingo Schöning
- University of Jena, Institute of Ecology, Jena, Germany
| | - Steffen Boch
- University of Bern, Institute of Plant Sciences, Bern, Switzerland
| | - Sven Marhan
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Soil Biology Section, Stuttgart, Germany
| | - Ellen Kandeler
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Soil Biology Section, Stuttgart, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Environmental Genomics, Neuherberg, Germany
- * E-mail:
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42
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Boz B, Mizanur Rahman M, Bottegal M, Basaglia M, Squartini A, Gumiero B, Casella S. Vegetation, soil and hydrology management influence denitrification activity and the composition of nirK-type denitrifier communities in a newly afforested riparian buffer. N Biotechnol 2013; 30:675-84. [DOI: 10.1016/j.nbt.2013.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 11/15/2022]
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43
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Guo GX, Deng H, Qiao M, Yao HY, Zhu YG. Effect of long-term wastewater irrigation on potential denitrification and denitrifying communities in soils at the watershed scale. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:3105-3113. [PMID: 23445539 DOI: 10.1021/es304714a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Wastewater irrigation mitigates the problem of water shortage but leads to the potential accumulation of pollutants and causes corresponding changes in denitrifying communities and denitrification, hence the potential ecological risk of long-term wastewater irrigation should not be overlooked. We investigated the relative contributions of different environmental factors to the abundance and diversity of denitrifying communities harboring nirK, nirS, and nosZ genes and the relative importance of these biotic and abiotic variables in potential denitrification activity (PDA) in soils with wastewater irrigation for around 25 years at a large watershed scale. Results showed that soil physicochemical properties, pollutants, including heavy metals and PAHs, and vegetation are the major factor groups influencing the abundance and structure of the three denitrifying communities and PDA. NirK-, nirS-, or nosZ-harboring denitrifiers responded in different manners to environmental changes, and were mainly influenced by substrate concentration, carbon source, or pollutants, respectively. The structure of the three denitrifying communities was more relevant to the environmental changes than their abundance. Conversely, the abundance, rather than diversity, was correlated with PDA. Pollutants and vegetation could affect PDA by both direct and indirect paths through soil physicochemical properties including pH, carbon and nitrogen sources, or through the abundance of denitrifying functional genes. The abundance of denitrifying functional genes is a valuable index that integrates potential activity and various environmental factors, and is therefore a good predictor of denitrification in the presence of environmental changes.
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Affiliation(s)
- Guang-Xia Guo
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Peking 100085, China
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44
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Yoshida M, Ishii S, Fujii D, Otsuka S, Senoo K. Identification of active denitrifiers in rice paddy soil by DNA- and RNA-based analyses. Microbes Environ 2012; 27:456-61. [PMID: 22972387 PMCID: PMC4103554 DOI: 10.1264/jsme2.me12076] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Denitrification occurs markedly in rice paddy fields; however, few microbes that are actively involved in denitrification in these environments have been identified. In this study, we used a laboratory soil microcosm system in which denitrification activity was enhanced. DNA and RNA were extracted from soil at six time points after enhancing denitrification activity, and quantitative PCR and clone library analyses were performed targeting the 16S rRNA gene and denitrification functional genes (nirS, nirK and nosZ) to clarify which microbes are actively involved in denitrification in rice paddy soil. Based on the quantitative PCR results, transcription levels of the functional genes agreed with the denitrification activity, although gene abundance did not change at the DNA level. Diverse denitrifiers were detected in clone library analysis, but comparative analysis suggested that only some of the putative denitrifiers, especially those belonging to the orders Neisseriales, Rhodocyclales and Burkholderiales, were actively involved in denitrification in rice paddy soil.
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Affiliation(s)
- Megumi Yoshida
- Department of Applied Biological Chemistry, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan.
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45
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Yuan Q, Liu P, Lu Y. Differential responses of nirK- and nirS-carrying bacteria to denitrifying conditions in the anoxic rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:113-122. [PMID: 23757237 DOI: 10.1111/j.1758-2229.2011.00311.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Denitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK-type denitrifiers did not change; but their abundance as determined by quantitative (real-time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK-type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T-RFLP) analysis of nirS genes revealed that the 100 bp T-RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T-RF had similarity of up to 90% with Herbaspirillum sp. T-RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK-type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.
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Affiliation(s)
- Quan Yuan
- College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
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46
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Chen Z, Liu J, Wu M, Xie X, Wu J, Wei W. Differentiated response of denitrifying communities to fertilization regime in paddy soil. MICROBIAL ECOLOGY 2012; 63:446-459. [PMID: 21811796 DOI: 10.1007/s00248-011-9909-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
The impact of fertilization regimes on sequential denitrifying communities was investigated in a rice paddy field with 17 years continuous fertilization, located in Taoyuan Agro-ecosystem Research Station (110°72″ E, 28°52″ N), China. The diversity, community composition, and size of denitrifying genes of narG, qnorB, and nosZ were determined using molecular tools including terminal restriction fragment length polymorphism, quantitative polymerase chain reaction (qPCR), cloning, and sequencing analysis. Soil samples were collected from the plots with no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). UR and BM caused marked increase in the community size of the denitrifying genes; however, BMR resulted in the highest abundance. The community size of narG was the most affected by the fertilization regimes, while qnorB was the least. Fertilization also induced some shifts in the composition of denitrifying genes, but the responses of different genes varied. However, fertilization regimes caused no significant changes to the diversity of the denitrifying genes. Potential denitrification activity (PDA) was significantly correlated with the abundance of narG and nosZ rather than qnorB, but there were no such correlations between PDA and the composition and diversity of denitrifying communities. Conclusively, long-term fertilization significantly affected denitrifying community size and composition, but not diversity. Among the sequential denitrifying genes, narG was the most, while qnorB was the least sensitive communities to fertilization regimes.
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Affiliation(s)
- Zhe Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
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47
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Braker G, Dörsch P, Bakken LR. Genetic characterization of denitrifier communities with contrasting intrinsic functional traits. FEMS Microbiol Ecol 2011; 79:542-54. [PMID: 22092293 DOI: 10.1111/j.1574-6941.2011.01237.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 10/04/2011] [Accepted: 10/24/2011] [Indexed: 11/28/2022] Open
Abstract
Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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48
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Yoshida M, Ishii S, Otsuka S, Senoo K. nirK-harboring denitrifiers are more responsive to denitrification- inducing conditions in rice paddy soil than nirS-harboring bacteria. Microbes Environ 2011; 25:45-8. [PMID: 21576852 DOI: 10.1264/jsme2.me09160] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed the quantity and diversity of nitrite reductase genes (nirS and nirK) in rice paddy soil before and after inducing denitrification. A quantitative PCR analysis showed that the copy number of nirK, but not nirS, increased significantly in response to the denitrification-inducing conditions. Diverse nirS and nirK clones were identified by clone library analyses. Clones related to the NirS of Burkholderiales and Rhodocyclales, and NirK distantly related to known denitrifiers increased their proportion in response to the denitrification-inducing conditions, and therefore, might be involved in denitrification in rice paddy soil.
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Affiliation(s)
- Megumi Yoshida
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo, Japan.
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49
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Guo GX, Deng H, Qiao M, Mu YJ, Zhu YG. Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:1886-1895. [PMID: 21497968 DOI: 10.1016/j.envpol.2011.03.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 03/18/2011] [Accepted: 03/19/2011] [Indexed: 05/30/2023]
Abstract
Toxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0-500 mg kg(-1)) followed by dose-response and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC(50) values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC(50) concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.
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Affiliation(s)
- Guang-Xia Guo
- State Key Lab of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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50
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Keil D, Meyer A, Berner D, Poll C, Schützenmeister A, Piepho HP, Vlasenko A, Philippot L, Schloter M, Kandeler E, Marhan S. Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils. FEMS Microbiol Ecol 2011; 77:95-106. [PMID: 21410493 DOI: 10.1111/j.1574-6941.2011.01091.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil.
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Affiliation(s)
- Daniel Keil
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany
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