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Zhou F, Cui J, Zhou J, Yang J, Li Y, Leng Q, Wang Y, He D, Song L, Gao M, Zeng J, Chan A. Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:776-784. [PMID: 29602116 DOI: 10.1016/j.scitotenv.2018.03.217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha-1 when its ratio of NH4+/NO3--N (RN) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha-1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and RN (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha-1) had similar reduced effects on microbial activity. Furthermore, both ADN flux and RN significantly reduced soil bacterial alpha diversity (p<0.05) and altered bacterial community structure (e.g., the relative abundances of genera Dyella and Rhodoblastus affiliated to Proteobacteria increased). Redundancy analysis demonstrated that ADN flux and RN were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil.
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Affiliation(s)
- Fengwu Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jian Cui
- Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Jing Zhou
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - John Yang
- Department of Agriculture and Environmental Science, Lincoln University of Missouri, Jefferson City, MO 65201, USA
| | - Yong Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Qiangmei Leng
- Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Yangqing Wang
- Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Dongyi He
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyan Song
- Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Min Gao
- Centre of Atmospheric Environment Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jun Zeng
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Andy Chan
- Division of Environment, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih 43500, Malaysia
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Eduok S, Ferguson R, Jefferson B, Villa R, Coulon F. Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:232-241. [PMID: 28746890 DOI: 10.1016/j.scitotenv.2017.07.178] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800mgkg-1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p=0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity.
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Affiliation(s)
- Samuel Eduok
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Robert Ferguson
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Bruce Jefferson
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Raffaella Villa
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - Frédéric Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK.
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Yu C, Hu X, Deng W, Li Y, Han G, Xiong C. Response of Bacteria Community to Long-Term Inorganic Nitrogen Application in Mulberry Field Soil. PLoS One 2016; 11:e0168152. [PMID: 27977728 PMCID: PMC5158035 DOI: 10.1371/journal.pone.0168152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/24/2016] [Indexed: 11/18/2022] Open
Abstract
The bacterial community and diversity in mulberry field soils with different application ages of inorganic nitrogen fertilizer (4Y, 4-year-old; 17Y, 17-year-old; 32Y, 32-year- old) were investigated using next-generation sequencing. The results demonstrated that the application ages of nitrogen fertilizer significantly altered soil bacterial community and diversity. Soil bacterial Shannon diversity index and Chao 1 index decreased with the consecutive application of nitrogen fertilizer, and the 4Y soil exhibited the highest bacterial relative abundance and diversity. Of 45 bacterial genera (relative abundance ratio of genera greater than 0.3%), 18 were significantly affected by the plant age, and seven belong to Acidobacteria. The relative abundances of Acidobacteria Gp 1, Gp4 and Gp6 in the 4Y soil were significantly lower than that of in the 17Y and 32Y soils. However, the relative abundance of Pseudononas sp. in the 4Y soil was significantly higher than that of in the 17Y and 32Y soils. Most microbial parameters were significantly affected by soil pH and organic matter content which were significantly changed by long-term application of inorganic nitrogen fertilizer.
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Affiliation(s)
- Cui Yu
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (CY); (XH)
| | - Xingming Hu
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (CY); (XH)
| | - Wen Deng
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yong Li
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guangming Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chao Xiong
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, China
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Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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Chroňáková A, Schloter-Hai B, Radl V, Endesfelder D, Quince C, Elhottová D, Šimek M, Schloter M. Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering. PLoS One 2015; 10:e0135627. [PMID: 26274496 PMCID: PMC4537298 DOI: 10.1371/journal.pone.0135627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/24/2015] [Indexed: 12/04/2022] Open
Abstract
Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.
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Affiliation(s)
- Alica Chroňáková
- Biology Centre of the Czech Academy of Sciences, v. v. i.—Institute of Soil Biology, Na Sádkách 7, České Budějovice, Czech Republic
- * E-mail:
| | - Brigitte Schloter-Hai
- Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstraße 1, Neuherberg, Germany
| | - Viviane Radl
- Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstraße 1, Neuherberg, Germany
| | - David Endesfelder
- Helmholtz Zentrum München, Research Unit for Scientific Computing, Ingolstädter Landstraße 1, Neuherberg, Germany
| | - Christopher Quince
- University of Glasgow, Department of Civil Engineering, Glasgow, Lanark, United Kingdom
| | - Dana Elhottová
- Biology Centre of the Czech Academy of Sciences, v. v. i.—Institute of Soil Biology, Na Sádkách 7, České Budějovice, Czech Republic
| | - Miloslav Šimek
- Biology Centre of the Czech Academy of Sciences, v. v. i.—Institute of Soil Biology, Na Sádkách 7, České Budějovice, Czech Republic
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstraße 1, Neuherberg, Germany
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Ma B, Lyu XF, Zha T, Gong J, He Y, Xu JM. Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa
) rhizosphere gradient. J Appl Microbiol 2015; 118:890-900. [DOI: 10.1111/jam.12756] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 12/18/2014] [Accepted: 01/11/2015] [Indexed: 10/24/2022]
Affiliation(s)
- B. Ma
- Institute of Soil and Water Resources and Environmental Science; Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition; Zhejiang University; Hangzhou China
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
| | - X.-F. Lyu
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
| | - T. Zha
- Institute of Soil and Water Resources and Environmental Science; Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition; Zhejiang University; Hangzhou China
| | - J. Gong
- Laboratory of Microbial Ecology and Matter Cycles; Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
| | - Y. He
- Institute of Soil and Water Resources and Environmental Science; Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition; Zhejiang University; Hangzhou China
| | - J.-M. Xu
- Institute of Soil and Water Resources and Environmental Science; Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition; Zhejiang University; Hangzhou China
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Franke-Whittle IH, Walter A, Ebner C, Insam H. Investigation into the effect of high concentrations of volatile fatty acids in anaerobic digestion on methanogenic communities. WASTE MANAGEMENT (NEW YORK, N.Y.) 2014; 34:2080-9. [PMID: 25164858 PMCID: PMC4227971 DOI: 10.1016/j.wasman.2014.07.020] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/16/2014] [Accepted: 07/29/2014] [Indexed: 05/02/2023]
Abstract
A study was conducted to determine whether differences in the levels of volatile fatty acids (VFAs) in anaerobic digester plants could result in variations in the indigenous methanogenic communities. Two digesters (one operated under mesophilic conditions, the other under thermophilic conditions) were monitored, and sampled at points where VFA levels were high, as well as when VFA levels were low. Physical and chemical parameters were measured, and the methanogenic diversity was screened using the phylogenetic microarray ANAEROCHIP. In addition, real-time PCR was used to quantify the presence of the different methanogenic genera in the sludge samples. Array results indicated that the archaeal communities in the different reactors were stable, and that changes in the VFA levels of the anaerobic digesters did not greatly alter the dominating methanogenic organisms. In contrast, the two digesters were found to harbour different dominating methanogenic communities, which appeared to remain stable over time. Real-time PCR results were inline with those of microarray analysis indicating only minimal changes in methanogen numbers during periods of high VFAs, however, revealed a greater diversity in methanogens than found with the array.
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Affiliation(s)
- Ingrid H Franke-Whittle
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
| | - Andreas Walter
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Christian Ebner
- Abwasserverband Zirl und Umgebung, Meilbrunnen 5, 6170 Zirl, Austria
| | - Heribert Insam
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:289478. [PMID: 23533328 PMCID: PMC3603158 DOI: 10.1155/2013/289478] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/15/2013] [Indexed: 12/28/2022]
Abstract
Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.
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Pereira e Silva MC, Dias ACF, van Elsas JD, Salles JF. Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils. PLoS One 2012; 7:e51554. [PMID: 23284712 PMCID: PMC3527478 DOI: 10.1371/journal.pone.0051554] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/02/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. METHODOLOGY/PRINCIPAL FINDINGS In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. CONCLUSIONS Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.
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Affiliation(s)
- Michele C Pereira e Silva
- Department of Microbial Ecology, Centre for Life Sciences, University of Groningen, Groningen, The Netherlands.
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Cao P, Zhang LM, Shen JP, Zheng YM, Di HJ, He JZ. Distribution and diversity of archaeal communities in selected Chinese soils. FEMS Microbiol Ecol 2012; 80:146-58. [DOI: 10.1111/j.1574-6941.2011.01280.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Yuan-Ming Zheng
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
| | - Hong J. Di
- Centre for Soil and Environmental Research; Lincoln University; Lincoln; Christchurch; New Zealand
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing; China
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Fortuna AM, Honeycutt CW, Vandemark G, Griffin TS, Larkin RP, He Z, Wienhold BJ, Sistani KR, Albrecht SL, Woodbury BL, Torbert HA, Powell JM, Hubbard RK, Eigenberg RA, Wright RJ, Alldredge JR, Harsh JB. Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry. JOURNAL OF ENVIRONMENTAL QUALITY 2012; 41:262-272. [PMID: 22218194 DOI: 10.2134/jeq2011.0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties.
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Affiliation(s)
- Ann-Marie Fortuna
- Dep. of Crop & Soil Sci., Washington State Univ., Pullman, WA 99164-6420, USA.
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Rajala T, Peltoniemi M, Hantula J, Mäkipää R, Pennanen T. RNA reveals a succession of active fungi during the decay of Norway spruce logs. FUNGAL ECOL 2011. [DOI: 10.1016/j.funeco.2011.05.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Caliz J, Vila X, Martí E, Sierra J, Nordgren J, Lindgren PE, Bañeras L, Montserrat G. The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation. CHEMOSPHERE 2011; 83:104-116. [PMID: 21295817 DOI: 10.1016/j.chemosphere.2011.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/21/2010] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg(-1). Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg(-1) MCP and TCP, and above 100 mg kg(-1) PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them. The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5d of incubation in laboratory assays (initial pollutant concentration of 50 mg L(-1)). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.
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Affiliation(s)
- Joan Caliz
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Avda Montilivi s/n, Girona, Spain
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14
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Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME JOURNAL 2010; 5:908-17. [PMID: 21085198 DOI: 10.1038/ismej.2010.171] [Citation(s) in RCA: 636] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea, primarily Crenarchaeota, are common in soil; however, the structure of soil archaeal communities and the factors regulating their diversity and abundance remain poorly understood. Here, we used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe. Relative archaeal abundance, the percentage of all 16S rRNA gene sequences recovered that were archaeal, averaged 2% across all soils and ranged from 0% to >10% in individual soils. Soil C:N ratio was the only factor consistently correlated with archaeal relative abundances, being higher in soils with lower C:N ratios. Soil archaea communities were dominated by just two phylotypes from a constrained clade within the Crenarchaeota, which together accounted for >70% of all archaeal sequences obtained in the survey. As one of these phylotypes was closely related to a previously identified putative ammonia oxidizer, we sampled from two long-term nitrogen (N) addition experiments to determine if this taxon responds to experimental manipulations of N availability. Contrary to expectations, the abundance of this dominant taxon, as well as archaea overall, tended to decline with increasing N. This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
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Affiliation(s)
- Scott T Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA.
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15
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Singh BK, Nunan N, Millard P. Response ofâ fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil. FEMS Microbiol Ecol 2009; 70:109-17. [DOI: 10.1111/j.1574-6941.2009.00731.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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16
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Lehtovirta LE, Prosser JI, Nicol GW. Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol Ecol 2009; 70:367-76. [PMID: 19732147 DOI: 10.1111/j.1574-6941.2009.00748.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Archaeal communities in many acidic forest soil systems are dominated by a distinct crenarchaeal lineage Group 1.1c. In addition, they are found consistently in other acidic soils including grassland pasture, moorland and alpine soils. To determine whether soil pH is a major factor in determining their presence and abundance, Group 1.1c community size and composition were investigated across a pH gradient from 4.5 to 7.5 that has been maintained for > 40 years. The abundances of Group 1.1c Crenarchaeota, total Crenarchaeota and total bacteria were assessed by quantitative PCR (qPCR) targeting 16S rRNA genes and the diversity of Group 1.1c crenarchaeal community was investigated by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. The abundance of Group 1.1c Crenarchaeota declined as the pH increased, whereas total Crenarchaeota and Bacteria showed no clear trend. Community diversity of Group 1.1c Crenarchaeota was also influenced with different DGGE bands dominating at different pH. Group 1.1c Crenarchaeota were also quantified in 13 other soils representing a range of habitats, soil types and pH. These results exhibited the same trend as that shown across the pH gradient with Group 1.1c Crenarchaeota representing a greater proportion of total Crenarchaeota in the most acidic soils.
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Affiliation(s)
- Laura E Lehtovirta
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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17
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Cresser MS, Aitkenhead MJ, Mian IA. A reappraisal of the terrestrial nitrogen cycle: what can we learn by extracting concepts from Gaia theory? THE SCIENCE OF THE TOTAL ENVIRONMENT 2008; 400:344-355. [PMID: 18678394 DOI: 10.1016/j.scitotenv.2008.06.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/25/2008] [Accepted: 06/25/2008] [Indexed: 05/26/2023]
Abstract
Although soil scientists and most environmental scientists are acutely aware of the interactions between the cycling of carbon and nitrogen, for conceptual convenience when portraying the nitrogen cycle in text books the N cycle tends to be considered in isolation from its interactions with the cycling of other elements and water, usually as a snap shot at the current time; the origins of dinitrogen are rarely considered, for example. The authors suggest that Lovelock's Gaia hypothesis provides a useful and stimulating framework for consideration of the terrestrial nitrogen cycle. If it is used, it suggests that urbanization and management of sewage, and intensive animal rearing are probably bigger global issues than nitrogen deposition from fossil fuel combustion, and that plant evolution may be driven by the requirement of locally sustainable and near optimal soil mineral N supply dynamics. This may, in turn, be partially regulating global carbon and oxygen cycles. It is suggested that pollutant N deposition may disrupt this essential natural plant and terrestrial ecosystem evolutionary process, causing biodiversity change. Interactions between the Earth and other bodies in the solar system, and possibly beyond, also need to be considered in the context of the global N cycle over geological time scales. This is because of direct potential impacts on the nitrogen content of the atmosphere, potential long-term impacts of past boloid collisions on plate tectonics and thus on global N cycling via subduction and volcanic emissions, and indirect effects upon C, O and water cycling that all may impact upon the N cycle in the long term.
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18
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Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl Environ Microbiol 2008; 74:6417-26. [PMID: 18676703 DOI: 10.1128/aem.00843-08] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86 degrees C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were transcribed in situ in one spring and the transcripts were closely related to the amoA genes amplified from the same spring. Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA.
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Abstract
Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology.
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Affiliation(s)
- Elena V Pikuta
- National Space Sciences and Technology Center, NASA, Astrobiology Laboratory, Huntsville, Alabama 35805, USA.
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20
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Poplawski AB, Mårtensson L, Wartiainen I, Rasmussen U. Archaeal diversity and community structure in a Swedish barley field: Specificity of the EK510R/(EURY498) 16S rDNA primer. J Microbiol Methods 2006; 69:161-73. [PMID: 17289189 DOI: 10.1016/j.mimet.2006.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 12/15/2006] [Accepted: 12/15/2006] [Indexed: 11/27/2022]
Abstract
The aim of this study was to analyze a total euryarchaeal community at DNA and RNA levels in a Swedish barley field with relation to soil depth (0-10 and 20-30 cm layers), soil fraction (bulk soil and rhizosphere) and time (August and November sample collection). Amplification of 16S rRNA gene using the archaeal universal A2F and Euryarchaea specific EK510R/(EURY498) primer pair, combined with denaturing gradient gel electrophoresis (DGGE), revealed distinct differences between rDNA and rRNA DGGE profiles. The soil depth, time, or rhizosphere effects did not significantly influence Archaeal community structure. Surprisingly, sequence analysis of DGGE-derived amplicons revealed the presence of Euryarchaea as well as uncultured soil Crenarchaea affiliated with group 1. In agreement, sequence comparison analyses showed that the majority of uncultured Crenarchaea group 1 had almost 100% sequence complementarity to the 3' end of the EK510R/(EURY498) primer. Therefore, we propose that EK510R/(EURY498R) is a universal archaeal primer rather than a Euryarchaea specific SSUrRNA primer. Hence, considerable care should be taken during application of this primer in studies of euryarchaeal biodiversity in soil environments.
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Mahmood S, Prosser JI. The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil. FEMS Microbiol Ecol 2006; 56:444-54. [PMID: 16689876 DOI: 10.1111/j.1574-6941.2006.00070.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. 'Total' and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation.
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Affiliation(s)
- Shahid Mahmood
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
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22
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Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y. Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl Environ Microbiol 2006; 72:1623-30. [PMID: 16461718 PMCID: PMC1392901 DOI: 10.1128/aem.72.2.1623-1630.2006] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the microbial community succession in a thermophilic methanogenic bioreactor under deteriorative and stable conditions that were induced by acidification and neutralization, respectively, was investigated using PCR-mediated single-strand conformation polymorphism (SSCP) based on the 16S rRNA gene, quantitative PCR, and fluorescence in situ hybridization (FISH). The SSCP analysis indicated that the archaeal community structure was closely correlated with the volatile fatty acid (VFA) concentration, while the bacterial population was impacted by pH. The archaeal community consisted mainly of two species of hydrogenotrophic methanogen (i.e., a Methanoculleus sp. and a Methanothermobacter sp.) and one species of aceticlastic methanogen (i.e., a Methanosarcina sp.). The quantitative PCR of the 16S rRNA gene from each methanogen revealed that the Methanoculleus sp. predominated among the methanogens during operation under stable conditions in the absence of VFAs. Accumulation of VFAs induced a dynamic transition of hydrogenotrophic methanogens, and in particular, a drastic change (i.e., an approximately 10,000-fold increase) in the amount of the 16S rRNA gene from the Methanothermobacter sp. The predominance of the one species of hydrogenotrophic methanogen was replaced by that of the other in response to the VFA concentration, suggesting that the dissolved hydrogen concentration played a decisive role in the predominance. The hydrogenotrophic methanogens existed close to bacteria in aggregates, and a transition of the associated bacteria was also observed by FISH analyses. The degradation of acetate accumulated during operation under deteriorative conditions was concomitant with the selective proliferation of the Methanosarcina sp., indicating effective acetate degradation by the aceticlastic methanogen. The simple methanogenic population in the thermophilic anaerobic digester significantly responded to the environmental conditions, especially to the concentration of VFAs.
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MESH Headings
- Anaerobiosis
- Base Sequence
- Bioreactors/microbiology
- DNA, Archaeal/genetics
- DNA, Bacterial/genetics
- Fatty Acids/metabolism
- Genes, Archaeal
- In Situ Hybridization, Fluorescence
- Methane/biosynthesis
- Methanobacteriaceae/genetics
- Methanobacteriaceae/metabolism
- Methanomicrobiaceae/genetics
- Methanomicrobiaceae/metabolism
- Methanosarcina/genetics
- Methanosarcina/metabolism
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Single-Stranded Conformational
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Waste Disposal, Fluid
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Affiliation(s)
- Tomoyuki Hori
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper C. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 2005; 7:1985-95. [PMID: 16309395 DOI: 10.1111/j.1462-2920.2005.00906.x] [Citation(s) in RCA: 461] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mesophilic crenarchaeota are frequently found in terrestrial and marine habitats worldwide, but despite their considerable abundance the physiology of these as yet uncultivated archaea has remained unknown. From a 1.2 Gb large-insert environmental fosmid library of a calcareous grassland soil, a 43 kb genomic fragment was isolated with a ribosomal RNA that shows its affiliation to group 1.1b of crenarchaeota repeatedly found in soils. The insert encoded a homologue of a copper-containing nitrite reductase with an unusual C-terminus that encoded a potential amicyanin-like electron transfer domain as well as two proteins related to subunits of ammonia monooxygenases or particulate methane monooxygenases (AmoAB/PmoAB) respectively. Expression of nirK and the amoA-like gene was shown by reverse transcription polymerase chain reaction (PCR) analyses in soil samples, the latter being found at higher levels when the soil was incubated with ammonia (measured by quantitative PCR). Further variants of both genes were amplified from soil samples and were found in the environmental database from the Sargasso Sea plankton. Taken together, our findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions.
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Affiliation(s)
- Alexander H Treusch
- University of Bergen, Department of Biology, Jahnebakken 5, N-5020 Bergen, Norway
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Mahmood S, Paton GI, Prosser JI. Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 2005; 7:1349-60. [PMID: 16104858 DOI: 10.1111/j.1462-2920.2005.00822.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The central aim of this study was to determine which components of an indigenous bacterial community in pristine grassland soil were capable of degrading pentachlorophenol (PCP) using two cultivation-independent, in situ, molecular techniques. The first involved polymerase chain reaction (PCR) and reverse transcription polymerase chain reaction (RT-PCR) amplification of 16S rRNA genes from DNA and RNA, respectively, extracted from PCP-amended soil. The second involved stable isotope probing (SIP), with incubation of soil with 13C-PCP and molecular analysis of 13C-labelled RNA, derived from cells incorporating PCP or its breakdown products, after separation from 12C-RNA by ultracentrifugation. Bacterial communities were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of amplification products. PCP was degraded at an approximate rate of 1.18+/-0.25 (SEM) mg kg-1 day-1 and 39% of the measurable PCP fraction was degraded after incubation for 63 days. PCP degradation was associated with significant changes in bacterial community structure, leading to the appearance of seven bands in both DNA- and RNA-based DGGE profiles, the latter providing clearer evidence of qualitative shifts in community structure. The majority of novel bands increased in relative intensity during the first 35 days and subsequently decreased in relative intensity as incubation continued. Sequence and phylogenetic analysis of six of these bands indicated most to have closest database relatives that were uncultured bacteria with sequence homologies to reported hydrocarbon degraders. No band could be detected in RNA-SIP-DGGE profiles derived from 13C-RNA fractions at day 0 but several faint bands appeared in these fractions after incubation of soil for 4 days, indicating assimilation of PCP or its degradation products. These bands increased in intensity during subsequent incubation for 21 days and decreased with further incubation. With one exception, RNA-SIP-DGGE and RNA-DGGE profiles were similar, indicating that RNA-targeted DGGE, in this case, provided a good indication of the metabolically active microbial community.
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Affiliation(s)
- Shahid Mahmood
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
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25
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Abstract
Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. However, many novel archaeal lineages that have been detected by molecular phylogenetic approaches have remained elusive because no laboratory-cultivated strains are available. Environmental genomic analyses have recently provided clues about the potential metabolic strategies of several of the uncultivated and abundant archaeal species, including non-thermophilic terrestrial and marine crenarchaeota and methanotrophic euryarchaeota. These initial studies of natural archaeal populations also revealed an unexpected degree of genomic variation that indicates considerable heterogeneity among archaeal strains. Here, we review genomic studies of uncultivated archaea within a framework of the phylogenetic diversity and ecological distribution of this domain.
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Affiliation(s)
- Christa Schleper
- Department of Biology, University of Bergen, Jahnebakken 5, N-5020 Bergen, Norway.
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26
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Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg A, Prosser JI. Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environ Microbiol 2005; 7:828-38. [PMID: 15892702 DOI: 10.1111/j.1462-2920.2005.00756.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a 13CO2 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of 13C-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded 13C compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from 12C and 13C RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.
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Affiliation(s)
- J Ignacio Rangel-Castro
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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27
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Nicol GW, Tscherko D, Embley TM, Prosser JI. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ Microbiol 2005; 7:337-47. [PMID: 15683394 DOI: 10.1111/j.1462-2920.2005.00698.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of soil archaeal community structures in relation to primary succession in bulk and rhizosphere soil was examined across the forefield of the receding Rotmoosferner glacier in Austria. Using cloning and denaturing gradient gel electrophoresis (DGGE) analysis of reverse transcription polymerase chain reaction (RT-PCR) products of extracted 16S rRNA, archaeal community structure was compared over a chronosequence representing approximately 150 years of soil development and to reference sites outside the glacier forefield, representing soil exposed for approximately 9500 years. Archaeal community composition was found to be dominated by members of the non-thermophilic or Group 1 Crenarchaeota, where a dramatic yet highly structured successional sequence was observed. Succession over the 150 years sequence could be identified as occurring in three stages, each of which had a phylogenetically distinct 1.1b crenarchaea community with those organisms present in pioneering and intermediate stages belonging to a lineage distinct from those in developed soils. Climax communities also contained organisms belonging to three other major non-thermophilic crenarchaeal lineages. Comparison of archaeal communities in the rhizosphere indicated that plant species composition was not the major driver of specific crenarchaeal populations. These results indicate the potential role of soil crenarchaea in the development of soil substrates, as well as ecological diversity within and between major Group 1 lineages.
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Affiliation(s)
- Graeme W Nicol
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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