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Hao J, Feng Y, Wang X, Yu Q, Zhang F, Yang G, Ren G, Han X, Wang X, Ren C. Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156621. [PMID: 35691356 DOI: 10.1016/j.scitotenv.2022.156621] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.
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Affiliation(s)
- Jiaqi Hao
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Yongzhong Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China.
| | - Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Qi Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Fu Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Gaihe Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Guangxin Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xinhui Han
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaojiao Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, China
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Yang S, Xiao J, Liang T, He W, Tan H. Response of soil biological properties and bacterial diversity to different levels of nitrogen application in sugarcane fields. AMB Express 2021; 11:172. [PMID: 34919198 PMCID: PMC8683519 DOI: 10.1186/s13568-021-01331-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/22/2022] Open
Abstract
To select an eco-friendly nitrogen (N) application level for sugarcane production, soil fertility and soil bacterial diversity under different nitrogen application levels were analyzed. Four levels of urea applications were high Nitrogen (H, 964 kg ha−1), medium Nitrogen (M, 482 kg ha−1), low Nitrogen (L, 96 kg ha−1) and no Nitrogen (CK, 0 kg ha−1) treatments, respectively. The results showed that the soil microbial biomass carbon and phosphorus were altered significantly by CK and L treatments. Moreover, the indexes of soil bacterial richness and diversity in the sugarcane field could be significantly improved by L. At the genus level, SC-I-84, Mycobacterium, Micropepsaceae, Saccharimonadales, Subgroup_2 and Acetobacteraceae were the unique dominant bacteria in the soil with the H treatment. JG30-KF-CM45 and Jatrophihabitans were the unique dominant genera in the M treatment. Subgroup_6, HSB_OF53-F07, Streptomyces, 67–14, SBR1031 and KD4-96 were the unique dominant genera in the L treatment. In contrast, FCPS473, Actinospica, 1921–2, Sinomonas, and Ktedonobacteraceae were the unique dominant genera in the CK treatment. The findings suggest that soil fertility all could be changed by different N application levels, but the most increasing integral effect only could be found in L. Moreover, even though soil bacterial richness could be significantly promoted by the M and H treatments, but soil bacterial diversity could not be significantly improved. On the contrary, soil bacterial diversity and richness all could be improved by L treatment. In addition, higher abundance of unique soil dominant bacteria could be only found in L treatment which compared to the CK, M and H treatments. These findings suggest that the rate of 96 kg ha−1 N application is ecofriendly for sugarcane production in Guangxi.
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Kim HS, Lee SH, Jo HY, Finneran KT, Kwon MJ. Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148944. [PMID: 34298360 DOI: 10.1016/j.scitotenv.2021.148944] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
The land-use change from natural to managed farmland ecosystems can undergo perturbations and significantly impact soil environment and communities. To understand how anthropogenic land-use alteration determines in-depth relationships among soil environmental factors and soil bacterial communities, high-resolution characterization was performed using soil samples (27 spots × 3 depths; top 10-20 cm, middle 90-100 cm, bottom 180-190 cm) from a natural forest and a 50 year-old farmland. The soil bacterial community abundance (number of OTU's per sample) and diversity (Faith's phylogenetic diversity) was significantly higher in the top layer of farmland soil than in forest soil. However, the differences in bacterial community abundance between farmland and forest decreased with depth, suggesting that the effect of fertilization was limited to top and middle layers. The phyla Acidobacteria and Proteobacteria were distributed distinctively during the land-use change. The subgroups Gp1-3 of Acidobacteria were more abundant in the forest samples (pH 3.5-5), while Gp4-7 and Gp10 were predominant in the farmland (pH 4.5-9.5). Members belonging to α-Proteobacteria and Xanthomonadales in γ-Proteobacteria were dominant in the forest, whereas β-, δ-, and γ-Proteobacteria were relatively abundant in the farmland. Both multivariate and correlation network analyses revealed that Acidobacteria and Proteobacteria communities were significantly affected by soil pH, as well as toxic metals from pesticides (Zn, Cr, Ni, Cu, Cd, As) and terminal electron acceptors (NO3, bioavailable Fe(III), SO4). In line with the long history of anthropogenic fertilization, the farmland site showed high abundance of membrane and ATP-binding cassette transporter genes, suggesting the key for uptake of nutrients and for protection against toxic metals and environmental stresses. This study provides new insights into the use of both Acidobacteria and Proteobacteria community structures as a bacterial indicator for land-use change.
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Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Sang-Hoon Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kevin T Finneran
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29643, USA
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China. World J Microbiol Biotechnol 2021; 37:126. [PMID: 34180026 DOI: 10.1007/s11274-021-03087-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO3-) was significantly higher in secondary broad-leaved forests, while ammonium (NH4+) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.
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McGee KM, Eaton WD, Shokralla S, Hajibabaei M. Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area. MICROBIAL ECOLOGY 2019; 77:148-167. [PMID: 29858646 DOI: 10.1007/s00248-018-1206-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3-; NH4+; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3-. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.
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Affiliation(s)
- Katie M McGee
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - William D Eaton
- Department of Biology, Pace University, 1 Pace Plaza, New York, NY, 10038, USA
| | - Shadi Shokralla
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics at Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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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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Griffin EA, Carson WP. Tree Endophytes: Cryptic Drivers of Tropical Forest Diversity. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Cao Q, Steinman AD, Su X, Xie L. Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:134-142. [PMID: 28797902 DOI: 10.1016/j.envpol.2017.08.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L-1) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L-1 in Soil A; 10, 100 1000 μg eq. MC-LR L-1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function.
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Affiliation(s)
- Qing Cao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alan D Steinman
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Xiaomei Su
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqiang Xie
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China.
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Buscardo E, Geml J, Schmidt SK, Silva ALC, Ramos RTJ, Barbosa SMR, Andrade SS, Dalla Costa R, Souza AP, Freitas H, Cunha HB, Nagy L. Of mammals and bacteria in a rainforest: Temporal dynamics of soil bacteria in response to simulated N pulse from mammalian urine. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erika Buscardo
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - József Geml
- Biodiversity Dynamics Research GroupNaturalis Biodiversity Center Leiden The Netherlands
- Faculty of SciencesLeiden University Leiden The Netherlands
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO USA
| | | | | | | | | | | | - Anete P. Souza
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
| | - Helena Freitas
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
| | - Hillândia B. Cunha
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - Laszlo Nagy
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
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Zhang X, Johnston ER, Barberán A, Ren Y, Lü X, Han X. Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity. GLOBAL CHANGE BIOLOGY 2017; 23:4318-4332. [PMID: 28585356 DOI: 10.1111/gcb.13783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.
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Affiliation(s)
- Ximei Zhang
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Yi Ren
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xiaotao Lü
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xingguo Han
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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12
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Pierre S, Hewson I, Sparks JP, Litton CM, Giardina C, Groffman PM, Fahey TJ. Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient. Ecology 2017; 98:1896-1907. [DOI: 10.1002/ecy.1863] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/06/2017] [Accepted: 03/27/2017] [Indexed: 11/07/2022]
Affiliation(s)
- S. Pierre
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - I. Hewson
- Department of Microbiology Cornell University Ithaca New York USA
| | - J. P. Sparks
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - C. M. Litton
- Department of Natural Resources and Environmental Management University of Hawaii at Manoa Honolulu Hawaii USA
| | - C. Giardina
- Institute of Pacific Islands Forestry Pacific Southwest Research Station US Forest Service Hilo Hawaii USA
| | - P. M. Groffman
- Cary Institute of Ecosystem Studies Millbrook New York USA
- CUNY Advanced Science Research Center New York New York USA
| | - T. J. Fahey
- Department of Natural Resources Cornell University Ithaca New York USA
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Araújo ASF, Lima LM, Santos VM, Schmidt R. Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19193-19200. [PMID: 27351878 DOI: 10.1007/s11356-016-7115-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.
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Affiliation(s)
| | - Luciano Moura Lima
- Soil Quality Laboratory Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Vilma Maria Santos
- Soil Quality Laboratory Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA
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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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Gerschlauer F, Dannenmann M, Kühnel A, Meier R, Kolar A, Butterbach-Bahl K, Kiese R. Gross Nitrogen Turnover of Natural and Managed Tropical Ecosystems at Mt. Kilimanjaro, Tanzania. Ecosystems 2016. [DOI: 10.1007/s10021-016-0001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Yang Z, Yang W, Li S, Hao J, Su Z, Sun M, Gao Z, Zhang C. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest. PLoS One 2016; 11:e0150618. [PMID: 26934044 PMCID: PMC4774956 DOI: 10.1371/journal.pone.0150618] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022] Open
Abstract
As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping crops with peanut; while hulled oat, mung bean or foxtail millet could be considered for sowing in wheat fields after harvest in North China.
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Affiliation(s)
- Zhenping Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, P. R. China
- * E-mail: (ZY); (SL)
| | - Wenping Yang
- College of Life Science, North China University of Science and Technology, Tangshan, P. R. China
| | - Shengcai Li
- College of Agriculture, Shanxi Agricultural University, Taigu, P. R. China
- * E-mail: (ZY); (SL)
| | - Jiaomin Hao
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, P. R. China
| | - Zhifeng Su
- College of Agriculture, Shanxi Agricultural University, Taigu, P. R. China
| | - Min Sun
- College of Agriculture, Shanxi Agricultural University, Taigu, P. R. China
| | - Zhiqiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu, P. R. China
| | - Chunlai Zhang
- Shanxi Academy of Agriculture Science Sorghum Research Institute, Jinzhong, P. R. China
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Schneider D, Engelhaupt M, Allen K, Kurniawan S, Krashevska V, Heinemann M, Nacke H, Wijayanti M, Meryandini A, Corre MD, Scheu S, Daniel R. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia). Front Microbiol 2015; 6:1339. [PMID: 26696965 PMCID: PMC4672069 DOI: 10.3389/fmicb.2015.01339] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/16/2015] [Indexed: 12/04/2022] Open
Abstract
Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.
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Affiliation(s)
- 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
| | - Kara Allen
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany
| | - Syahrul Kurniawan
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany ; Department of Soil Science, Faculty of Agriculture, University of Brawijaya Malang, Indonesia
| | - Valentyna Krashevska
- Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, 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
| | - Heiko Nacke
- 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
| | - Marife D Corre
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany
| | - Stefan Scheu
- Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
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Wang M, Wu C, Cheng Z, Meng H, Zhang M, Zhang H. Soil chemical property changes in eggplant/garlic relay intercropping systems under continuous cropping. PLoS One 2014; 9:e111040. [PMID: 25340875 PMCID: PMC4207794 DOI: 10.1371/journal.pone.0111040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 09/23/2014] [Indexed: 11/23/2022] Open
Abstract
Soil sickness is a critical problem for eggplant (Solanum melongena L.) under continuous cropping that affects sustainable eggplant production. Relay intercropping is a significant technique on promoting soil quality, improving eco-environment, and raising output. Field experiments were conducted from September 2010 to November 2012 in northwest China to determine the effects of relay intercropping eggplant with garlic (Allium sativum L.) on soil enzyme activities, available nutrient contents, and pH value under a plastic tunnel. Three treatments were in triplicate using randomized block design: eggplant monoculture (CK), eggplant relay intercropping with normal garlic (NG) and eggplant relay intercropping with green garlic (GG). The major results are as follows: (1) the activities of soil invertase, urease, and alkaline phosphatase were generally enhanced in NG and GG treatments; (2) relay intercropping significantly increased the soil available nutrient contents, and they were mostly higher in GG than NG. On April 11, 2011, the eggplant/garlic co-growth stage, the available nitrogen content in GG was 76.30 mg·kg−1, significantly higher than 61.95 mg·kg−1 in NG. For available potassium on April 17, 2012, they were 398.48 and 387.97 mg·kg−1 in NG and GG, both were significantly higher than 314.84 mg·kg−1 in CK; (3) the soil pH showed a significantly higher level in NG treatment, but lower in GG treatment compared with CK. For the last samples in 2012, soil pH in NG and GG were 7.70 and 7.46, the highest and lowest one among them; (4) the alkaline phosphatase activity and pH displayed a similar decreasing trend with continuous cropping. These findings indicate that relay intercropping eggplant with garlic could be an ideal farming system to effectively improve soil nutrient content, increase soil fertility, and alleviate soil sickness to some extent. These findings are important in helping to develop sustainable eggplant production.
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Affiliation(s)
- Mengyi Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Cuinan Wu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
| | - Huanwen Meng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengru Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongjing Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
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Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China. Appl Environ Microbiol 2014; 80:5593-602. [PMID: 25002421 DOI: 10.1128/aem.01617-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.
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Pires APF, Guariento RD, Laque T, Esteves FA, Farjalla VF. The negative effects of temperature increase on bacterial respiration are independent of changes in community composition. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:131-5. [PMID: 24596285 DOI: 10.1111/1758-2229.12143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/17/2013] [Indexed: 05/10/2023]
Abstract
Temporal changes in environmental conditions and in bacterial community composition (BCC) regulate bacterial processes and ecosystem services. An increase in temperature accelerates bacterial processes in polar or temperate regions, but this relationship has not been documented for the tropics. Here, we tested the interactive effects of changing the BCC and increasing the water temperature on tropical bacterial respiration (BR). The BCC was manipulated through successional changes of the bacterial community in a filtered water sample from a tropical coastal lagoon. Four succession incubation periods (120, 240, 288 and 336 h) and four different water temperatures (23, 28, 33 and 38(o)C) were tested in a full-factorial design microcosm experiment. Both the BCC and the temperature had significant individual, but not interactive, effects on BR. Temperature increasing consistently decreased BR, while there was no clear pattern of successional effects on BR observed. No BCC tested was able to diminish the negative effects of temperature increases on BR. Our results suggest that the effects of an increasing temperature can negatively affect BR, even in tropical ecosystems with different BCC.
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Affiliation(s)
- Aliny P F Pires
- Instituto de Biologia, Departamento de Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo. Appl Environ Microbiol 2013; 79:7290-7. [PMID: 24056463 DOI: 10.1128/aem.02541-13] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
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22
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Litter quality versus soil microbial community controls over decomposition: a quantitative analysis. Oecologia 2013; 174:283-94. [DOI: 10.1007/s00442-013-2758-9] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
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Shen JP, Cao P, Hu HW, He JZ. Differential response of archaeal groups to land use change in an acidic red soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 461-462:742-749. [PMID: 23774250 DOI: 10.1016/j.scitotenv.2013.05.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/21/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Land use management, one of the most important aspects of anthropogenic disturbance to terrestrial ecosystems, has exerted overriding impacts on soil biogeochemical cycling and inhabitant microorganisms. However, the knowledge concerning response of different archaeal groups to long-term land use changes is still limited in terrestrial environments. Here we used quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE) approaches to investigate the response of archaeal communities to four different land use practices, i.e. cropland, pine forest, restoration land and degradation land. qPCR analyses showed that expression of the archaeal amoA gene responds more sensitively to changes of land use. In particular, we observed, occurring at significantly lower numbers of archaeal amoA genes in degradation land samples, while the abundance of total archaea and Group 1.1c based on 16S rRNA gene copy numbers remained constant among the different treatments examined. Soil nitrate content is significantly correlated with archaeal amoA gene abundance, but not their bacterial counterparts. The percentage of archaea among total prokaryote communities increases with increasing depth, but has no significant relationship with total carbon, total nitrogen or pH. Soil pH was significantly correlated with total bacterial abundance. Based on results from PCR-DGGE, three land use practices (i.e. cropland, pine forest, restoration land) showed distinct dominant bands, which were mostly affiliated with Group 1.1a. Degradation land, however, was dominated by sequences belonging to Group 1.1c. Results from this study suggest that community structure of ammonia oxidizing archaea were significantly impacted by land use practices.
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Affiliation(s)
- Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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24
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Wigley BJ, Coetsee C, Hartshorn AS, Bond WJ. What do ecologists miss by not digging deep enough? Insights and methodological guidelines for assessing soil fertility status in ecological studies. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2013. [DOI: 10.1016/j.actao.2013.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Ormeño-Orrillo E, Rogel-Hernández MA, Lloret L, López-López A, Martínez J, Barois I, Martínez-Romero E. Change in land use alters the diversity and composition of Bradyrhizobium communities and led to the introduction of Rhizobium etli into the tropical rain forest of Los Tuxtlas (Mexico). MICROBIAL ECOLOGY 2012; 63:822-834. [PMID: 22109095 DOI: 10.1007/s00248-011-9974-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/24/2011] [Indexed: 05/31/2023]
Abstract
Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or where secondary forests were established. Rhizobia were also trapped by using bean plants. Bradyrhizobium strains were classified into genospecies by dnaK sequence analysis supported by recA, glnII and 16S-23S rDNA IGS loci analyses. A total of 29 genospecies were identified, 24 of which did not correspond to any described taxa. A reduction in Bradyrhizobium diversity was observed when forest was turned to crop fields or pastures. Diversity seemed to recover to primary forest levels in secondary forests that derived from abandoned crop fields or pastures. The shifts in diversity were not related to soil characteristics but seemingly to the density of nodulating legumes present at each land use system (LUS). Bradyrhizobium community composition in soils was dependent on land use; however, similarities were observed between crop fields and pastures but not among forest and secondary forest. Most Bradyrhizobium genospecies present in forest were not recovered or become rare in the other LUS. Rhizobium etli was found as the dominant bean-nodulating rhizobia present in crop fields and pastures, and evidence was found that this species was introduced in Los Tuxtlas forest.
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Petersen DG, Blazewicz SJ, Firestone M, Herman DJ, Turetsky M, Waldrop M. Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska. Environ Microbiol 2012; 14:993-1008. [PMID: 22225623 DOI: 10.1111/j.1462-2920.2011.02679.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrification and denitrification processes are crucial to plant nutrient availability, eutrophication and greenhouse gas production both locally and globally. Unravelling the major environmental predictors for nitrification and denitrification is thus pivotal in order to understand and model environmental nitrogen (N) cycling. Here, we sampled five plant community types characteristic of interior Alaska, including black spruce, bog birch, tussock grass and two fens. We assessed abundance of functional genes affiliated with nitrification (bacterial and archaeal amoA) and denitrification (nirK/S and nosZ) using qPCR, soil characteristics, potential nitrification and denitrification rates (PNR and PDR) and gross mineralization rates. The main chemical and biological predictors for PNR and PDR were assigned through path analysis. The potential N cycling rates varied dramatically between sites, from some of the highest (in fens) to some of the lowest (in black spruce) measured globally. Based on path analysis, functional gene abundances were the most important variables to predict potential rates. PNR was best explained by bacterial amoA gene abundance followed by ammonium content, whereas PDR was best explained directly by nosZ gene abundance and indirectly by nirK/S gene abundance and nitrate. Hence, functional gene abundance is a valuable index that integrates recent environmental history and recent process activity, and therefore is a good predictor of potential rates. The results of this study contribute to our understanding of the relative importance of different biological and chemical factors in driving the potential for nitrification and denitrification across terrestrial ecosystems.
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Affiliation(s)
- Dorthe Groth Petersen
- The Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
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27
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Falconer R, Bown J, White N, Crawford J. Linking individual behaviour to community scale patterns in fungi. FUNGAL ECOL 2011. [DOI: 10.1016/j.funeco.2010.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME JOURNAL 2010; 5:532-42. [PMID: 20703315 DOI: 10.1038/ismej.2010.130] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.
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Töwe S, Kleineidam K, Schloter M. Differences in amplification efficiency of standard curves in quantitative real-time PCR assays and consequences for gene quantification in environmental samples. J Microbiol Methods 2010; 82:338-41. [PMID: 20621132 DOI: 10.1016/j.mimet.2010.07.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/04/2010] [Accepted: 07/04/2010] [Indexed: 10/19/2022]
Abstract
High and comparable efficiency values are the key for reliable quantification of target genes from environmental samples using real-time PCR. Therefore it was the aim of this study to investigate if PCR amplification efficiencies of plasmid DNA used for the calculation of standard curves (i) remain constant along a logarithmic scale of dilutions and (ii) if these values are comparable to those of DNA extracted from environmental samples. It could be shown that comparable efficiency values within the standards cannot be achieved using log scale serial dilutions and a comparison of gene copy numbers from DNA extracted from environmental samples and standard DNA extracted from plasmids is only possible in a very small interval.
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Affiliation(s)
- Stefanie Töwe
- Technische Universität München, Chair of Soil Ecology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
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Reed SC, Townsend AR, Cleveland CC, Nemergut DR. Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia 2010; 164:521-31. [PMID: 20454976 DOI: 10.1007/s00442-010-1649-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 04/19/2010] [Indexed: 10/19/2022]
Abstract
The role of biodiversity in ecosystem function receives substantial attention, yet despite the diversity and functional relevance of microorganisms, relationships between microbial community structure and ecosystem processes remain largely unknown. We used tropical rain forest fertilization plots to directly compare the relative abundance, composition and diversity of free-living nitrogen (N)-fixer communities to in situ leaf litter N fixation rates. N fixation rates varied greatly within the landscape, and 'hotspots' of high N fixation activity were observed in both control and phosphorus (P)-fertilized plots. Compared with zones of average activity, the N fixation 'hotspots' in unfertilized plots were characterized by marked differences in N-fixer community composition and had substantially higher overall diversity. P additions increased the efficiency of N-fixer communities, resulting in elevated rates of fixation per nifH gene. Furthermore, P fertilization increased N fixation rates and N-fixer abundance, eliminated a highly novel group of N-fixers, and increased N-fixer diversity. Yet the relationships between diversity and function were not simple, and coupling rate measurements to indicators of community structure revealed a biological dynamism not apparent from process measurements alone. Taken together, these data suggest that the rain forest litter layer maintains high N fixation rates and unique N-fixing organisms and that, as observed in plant community ecology, structural shifts in N-fixing communities may partially explain significant differences in system-scale N fixation rates.
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Affiliation(s)
- Sasha C Reed
- US Geological Survey, Southwest Biological Science Center, Moab, UT 84532, USA.
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Ying JY, Zhang LM, He JZ. Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:304-312. [PMID: 23766082 DOI: 10.1111/j.1758-2229.2009.00130.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ammonia-oxidizers play a key role in nitrification, which is important for nitrogen cycling and soil function. However, little is known about how vegetation successions and agricultural practices caused by human activities impact the ammonia-oxidizers and nitrification process. Putative ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities under different land utilization patterns of restoration (forest), degradation (pasture), cropland and pine plantation were analysed in an acidic red soil based on bacterial and archaeal amoA genes together with archaeal 16S rRNA gene. Real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries were conducted to study their abundance and community structure. Land utilization pattern showed significant effects on the copy numbers of all these genes, but only the bacterial amoA gene correlated significantly with potential nitrification rates (PNR). The cropland plot possessed the highest bacterial amoA gene copies and PNR, while the degradation plot was opposite to that. There were no significant variations in the bacterial amoA gene structure, which was dominated by Clusters 10 and 11 in Nitrosospira. However, archaeal amoA gene structure varied among different land utilization patterns especially for the cropland. The degradation plot was dominated by Crenarchaea 1.1c-related groups from which the amoA gene could not been amplified in this study, while other plots were dominated by Crenarchaea 1.1a/b group based on archaeal 16S rRNA gene analysis. These results indicated significant effects of land utilization patterns on putative ammonia oxidizers, which were especially obvious in the degradation and cropland plots where frequent human disturbance occurred.
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Affiliation(s)
- Jiao-Yan Ying
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Vance-Chalcraft HD, Willig MR, Cox SB, Lugo AE, Scatena FN. Relationship Between Aboveground Biomass and Multiple Measures of Biodiversity in Subtropical Forest of Puerto Rico. Biotropica 2009. [DOI: 10.1111/j.1744-7429.2009.00600.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bremer C, Braker G, Matthies D, Beierkuhnlein C, Conrad R. Plant presence and species combination, but not diversity, influence denitrifier activity and the composition ofnirK-type denitrifier communities in grassland soil. FEMS Microbiol Ecol 2009; 70:377-87. [DOI: 10.1111/j.1574-6941.2009.00732.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Fierer N, Carney KM, Horner-Devine MC, Megonigal JP. The biogeography of ammonia-oxidizing bacterial communities in soil. MICROBIAL ECOLOGY 2009; 58:435-45. [PMID: 19352770 DOI: 10.1007/s00248-009-9517-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 03/21/2009] [Indexed: 05/10/2023]
Abstract
Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.
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Affiliation(s)
- Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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Microbial activity in contrasting conditions of soil C and N availability in a tropical dry forest. JOURNAL OF TROPICAL ECOLOGY 2009. [DOI: 10.1017/s0266467409006166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:We studied the relationships between soil nutrient availability and microbial biomass and activity of two contrasting soil conditions in a tropical deciduous forest in western Mexico. Hilltops have higher pH, water, dissolved organic C, and ammonium concentrations than hillslopes. Our main hypothesis was that soil microbial biomass, microbial activity and bacterium species richness would be higher in soils with high availability of nutrients. Fifteen soil cores, 0–5 cm depth, were taken in the dry, early rainy and rainy season, from each of the ten replicate plots in hilltop and hillslope positions located on three contiguous small watersheds. We measured moisture, C, N and P availability, potential C mineralization, net nitrification, microbial biomass and culturable heterotrophic and nitrifying bacteria in composite samples from each plot. Microbial biomass, species richness of culturable heterotrophic bacteria and C mineralization were significantly higher on hilltops than on hillslopes. Net nitrification was, in contrast, significantly higher on hillslopes than on hilltops and counts of culturable nitrifying bacteria were also significantly higher in the rainy-season samples. Hilltops and hillslopes had low similarity in composition of culturable heterotrophic bacterial species, particularly during the rainy season. The results suggested that C and N availability and seasonal changes in soil moisture are important controlling factors for some soil culturable-bacterial species, which may affect both C mineralization and nitrification in these tropical deciduous forest soils.
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Diversity and distribution of anaeromyxobacter strains in a uranium-contaminated subsurface environment with a nonuniform groundwater flow. Appl Environ Microbiol 2009; 75:3679-87. [PMID: 19346346 DOI: 10.1128/aem.02473-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Versaphilic Anaeromyxobacter dehalogenans strains implicated in hexavalent uranium reduction and immobilization are present in the fractured saprolite subsurface environment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge (IFC) site near Oak Ridge, TN. To provide insight into the in situ distribution of Anaeromyxobacter strains in this system with a nonuniform groundwater flow, 16S rRNA gene-targeted primers and linear hybridization (TaqMan) probes were designed for Oak Ridge IFC Anaeromyxobacter isolates FRC-D1 and FRC-W, along with an Anaeromyxobacter genus-targeted probe and primer set. Multiplex quantitative real-time PCR (mqPCR) was applied to samples collected from Oak Ridge IFC site areas 1 and 3, which are not connected by the primary groundwater flow paths; however, transport between them through cross-plane fractures is hypothesized. Strain FRC-W accounted for more than 10% of the total quantifiable Anaeromyxobacter community in area 1 soils, while strain FRC-D1 was not detected. In FeOOH-amended enrichment cultures derived from area 1 site materials, strain FRC-D1 accounted for 30 to 90% of the total Anaeromyxobacter community, demonstrating that this strain was present in situ in area 1. The area 3 total Anaeromyxobacter abundance exceeded that of area 1 by 3 to 5 orders of magnitude, but neither strain FRC-W- nor FRC-D1-like sequences were quantifiable in any of the 33 area 3 groundwater or sediment samples tested. The Anaeromyxobacter community in area 3 increased from <10(5) cells/g sediment outside the ethanol biostimulation treatment zone to 10(8) cells/g sediment near the injection well, and 16S rRNA gene clone library analysis revealed that representatives of a novel phylogenetic cluster dominated the area 3 Anaeromyxobacter community inside the treatment loop. The combined applications of genus- and strain-level mqPCR approaches along with clone libraries provided novel information on patterns of microbial variability within a bacterial group relevant to uranium bioremediation.
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Characterization of fungal soil communities by F-RISA and arbuscular mycorrhizal fungi fromAraucaria angustifolia forest soils after replanting and wildfire disturbances. Symbiosis 2009. [DOI: 10.1007/bf03179995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Evidence for the functional significance of diazotroph community structure in soil. ISME JOURNAL 2008; 3:124-36. [PMID: 18769458 DOI: 10.1038/ismej.2008.82] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.
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Wardle DA, Wiser SK, Allen RB, Doherty JE, Bonner KI, Williamson WM. Aboveground and belowground effects of single-tree removals in New Zealand rain forest. Ecology 2008; 89:1232-45. [PMID: 18543618 DOI: 10.1890/07-1543.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There has been considerable recent interest in how human-induced species loss affects community and ecosystem properties. These effects are particularly apparent when a commercially valuable species is harvested from an ecosystem, such as occurs through single-tree harvesting or selective logging of desired timber species in natural forests. In New Zealand mixed-species rain forests, single-tree harvesting of the emergent gymnosperm Dacrydium cupressinum, or rimu, has been widespread. This harvesting has been contentious in part because of possible ecological impacts of Dacrydium removal on the remainder of the forest, but many of these effects remain unexplored. We identified an area where an unintended 40-year "removal experiment" had been set up that involved selective extraction of individual Dacrydium trees. We measured aboveground and belowground variables at set distances from both individual live trees and stumps of trees harvested 40 years ago. Live trees had effects both above and below ground by affecting diversity and cover of several components of the vegetation (usually negatively), promoting soil C sequestration, enhancing ratios of soil C:P and N:P, and affecting community structure of soil microflora. These effects extended to 8 m from the tree base and were likely caused by poor-quality litter and humus produced by the trees. Measurements for the stumps revealed strong legacy effects of prior presence of trees on some properties (e.g., cover by understory herbs and ferns, soil C sequestration, soil C:P and N:P ratios), but not others (e.g., soil fungal biomass, soil N concentration). These results suggest that the legacy of prior presence of Dacrydium may remain for several decades or centuries, and certainly well over 40 years. They also demonstrate that, while large Dacrydium individuals (and their removal) may have important effects in their immediate proximity, within a forest, these effects should only be important in localized patches containing high densities of large trees. Finally, this study emphasizes that deliberate extraction of a particular tree species from a forest can exert influences both above and below ground if the removed species has a different functional role than that of the other plant species present.
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Affiliation(s)
- David A Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE901 83 Umeå, Sweden.
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40
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Dell EA, Bowman D, Rufty T, Shi W. Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems. MICROBIAL ECOLOGY 2008; 56:178-190. [PMID: 18040734 DOI: 10.1007/s00248-007-9335-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 10/14/2007] [Indexed: 05/25/2023]
Abstract
Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.
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Affiliation(s)
- Emily A Dell
- Department of Soil Science, North Carolina State University, Campus Box 7619, Raleigh, NC 27695, USA
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41
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Affiliation(s)
- M Claire Horner-Devine
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
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42
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Variation in prokaryotic community composition as a function of resource availability in tidal creek sediments. Appl Environ Microbiol 2008; 74:1836-44. [PMID: 18192417 DOI: 10.1128/aem.00854-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In anaerobic coastal sediments, hydrolytic and/or fermentative bacteria degrade polymeric material and produce labile intermediates, which are used by terminal metabolizers to complete the conversion of organic material to CO(2). We used molecular approaches to evaluate the response of two bacterial terminal metabolizer groups from a coastal tidal creek sediments, sulfate reducers and methanogens, to controlled changes in carbon resource supply. Tidal creek sediment bioreactors were established in April and August 2004. For each date, intact sediment sections were continuously supplied with flowthrough seawater that was either unamended or amended with the high-molecular-weight polysaccharide dextran. Biogeochemical data indicate that the activity of fermenting bacteria and the terminal metabolizers was limited by organic carbon supply during both experiments, with a significant increase in net volatile fatty acid (VFA) production and rates of sulfate reduction and methanogenesis following dextran addition. Community composition (measured by using terminal restriction fragment length polymorphism analysis, and functional gene [dsrA, mcrA] clone libraries) changed from April to August. However, community composition was not different between amended and unamended cores within each month, despite the change in resource level. Moreover, there was no relationship between community richness and evenness with resource level. This lack of variation in community composition with C addition could be attributed to the dynamic environment these sediment communities experience in situ. Fluctuations in VFA concentrations are most likely very high, so that the dominant bacterial species must be able to outcompete other species at both high and low resource levels.
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43
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Reed HE, Martiny JBH. Testing the functional significance of microbial composition in natural communities. FEMS Microbiol Ecol 2008; 62:161-70. [PMID: 17937673 DOI: 10.1111/j.1574-6941.2007.00386.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.
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Affiliation(s)
- Heather E Reed
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
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44
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Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa. ISME JOURNAL 2007; 1:763-5. [DOI: 10.1038/ismej.2007.81] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Firn J, Erskine PD, Lamb D. Woody species diversity influences productivity and soil nutrient availability in tropical plantations. Oecologia 2007; 154:521-33. [PMID: 17899202 DOI: 10.1007/s00442-007-0850-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 08/16/2007] [Indexed: 10/22/2022]
Abstract
We investigated the relationship between plant diversity and ecological function (production and nutrient cycling) in tropical tree plantations. Old plantations (65-72 years) of four different species, namely Araucaria cunninghamii, Agathis robusta, Toona ciliata and Flindersia brayleyana, as well as natural secondary forest were examined at Wongabel State Forest, in the wet tropics region of Queensland, Australia. Two young plantations (23 years) of Araucaria cunninghamii and Pinus caribaea were also examined. The close proximity of the older plantations and natural forests meant they had similar edaphic and climatic conditions. All plantations had been established as monocultures, but had been colonised by a range of native woody plants from the nearby rainforest. The extent to which this had occurred varied with the identity of the plantation species (from 2 to 17 species in 0.1 ha blocks). In many cases these additional species had grown up and joined the forest canopy. This study is one of the few to find a negative relationship between overstorey plant diversity and productivity. The conversion of natural forest with highly productive, low-diversity gymnosperm-dominated plantations (young and old Araucaria cunninghamii and Pinus caribaea) was found to be associated with lower soil nutrient availability (approximately five times less phosphorus and 2.5 times less nitrogen) and lower soil pH (mean=6.28) compared to the other, less productive plantations. The dominant effects of two species, Araucaria cunninghamii and Hodgkinsonia frutescens, indicate that ecosystem functions such as production and nutrient availability are not determined solely by the number of species, but are more likely to be determined by the characteristics of the species present. This suggests that monoculture plantations can be used to successfully restore some functions (e.g. nutrient cycling and production), but that the level to which such functions can be restored will depend upon the species chosen and site conditions.
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Affiliation(s)
- Jennifer Firn
- School of Integrative Biology, The University of Queensland, Brisbane, QLD 4072, Australia.
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46
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Chu H, Fujii T, Morimoto S, Lin X, Yagi K, Hu J, Zhang J. Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil. Appl Environ Microbiol 2006; 73:485-91. [PMID: 17098920 PMCID: PMC1796994 DOI: 10.1128/aem.01536-06] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of mineral fertilizer (NPK) and organic manure on the community structure of soil ammonia-oxidizing bacteria (AOB) was investigated in a long-term (16-year) fertilizer experiment. The experiment included seven treatments: organic manure, half organic manure N plus half fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). N fertilization greatly increased soil nitrification potential, and mineral N fertilizer had a greater impact than organic manure, while N deficiency treatment (PK) had no significant effect. AOB community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the amoA gene, which encodes the alpha subunit of ammonia monooxygenase. DGGE profiles showed that the AOB community was more diverse in N-fertilized treatments than in the PK-fertilized treatment or the control, while one dominant band observed in the control could not be detected in any of the fertilized treatments. Phylogenetic analysis showed that the DGGE bands derived from N-fertilized treatments belonged to Nitrosospira cluster 3, indicating that N fertilization resulted in the dominance of Nitrosospira cluster 3 in soil. These results demonstrate that long-term application of N fertilizers could result in increased soil nitrification potential and the AOB community shifts in soil. Our results also showed the different effects of mineral fertilizer N versus organic manure N; the effects of P and K on the soil AOB community; and the importance of balanced fertilization with N, P, and K in promoting nitrification functions in arable soils.
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Affiliation(s)
- Haiyan Chu
- National Institute for Agro-Environmental Sciences, Kannondai 3-1-3, Tsukuba 305-8604, Japan
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47
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Waldrop MP, Zak DR, Blackwood CB, Curtis CD, Tilman D. Resource availability controls fungal diversity across a plant diversity gradient. Ecol Lett 2006; 9:1127-35. [PMID: 16972876 DOI: 10.1111/j.1461-0248.2006.00965.x] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.
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Affiliation(s)
- Mark P Waldrop
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109-1115, USA.
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48
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Abstract
Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.
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Affiliation(s)
- M Claire Horner-Devine
- School of Aquatic and Fishery Science, University of Washington, Seattle, Washington 98195, USA.
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49
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Findlay S, Sinsabaugh RL. Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity. MICROBIAL ECOLOGY 2006; 52:491-500. [PMID: 16909347 DOI: 10.1007/s00248-006-9095-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 04/23/2006] [Indexed: 05/11/2023]
Abstract
We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.
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Affiliation(s)
- S Findlay
- Institute of Ecosystem Studies, Millbrook, NY 12545, USA.
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Carney KM, Matson PA. The influence of tropical plant diversity and composition on soil microbial communities. MICROBIAL ECOLOGY 2006; 52:226-38. [PMID: 16897297 DOI: 10.1007/s00248-006-9115-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 10/25/2004] [Indexed: 05/06/2023]
Abstract
There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.
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Affiliation(s)
- Karen M Carney
- Smithsonian Environmental Research Center, PO Box 28, Edgewater, MD 21037, USA.
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