Progress 07/01/11 to 06/30/14
Outputs
Target Audience: Research results are being communicated at scientific and technical meetings and through peer-review publications. The improved understanding of microbial processes in nutrient cycling in forest soils are of interest to forest managers and ecologists, as well as US Forest Service. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? One undergraduate student has completed his senior honor's theses as part of this project. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals? We are continuing the taxonomic, genomic and physiological analyses of a suite ofAcidobacteria isolates. We are finlaizing our data analysis of the impact of prescribed burns on the bacterial community structure of NJ pinebarrens soils We have established stable isotope probing (SIP) experiments to identify the specific members of the microbial community active in C and N cycling that are still ongoing.
Impacts
What was accomplished under these goals?
The New Jersey Pine Barrens is a temperate forest composed of various species of conifers and broad-leaf trees dominated by pitch pines (Pinus rigidia), and a number of oaks (Quercus alba, Q. prinus, etc). The activities of the microbial community are a key factor in the carbon and nitrogen cycling in soil. In order to prevent wild fires, prescribed burn are often performed to reduce fuel loads of forest litter during the winter months. Burning forest litter deposits a limited amount of nitrogen and minerals into the soil, as well as cause changes in soil chemistry. This can have an impact on the availability of soil nutrients which may, in turn, affect soil microbial communities. It is not well understood which bacterial species respond to environmental change due to fire and whether the predictions at the organismal level may estimate ecosystem-scale respiration and nutrient turnover. Thus, the response of soil bacterial community to prescribed burn was studied at different soil depths and time durations after the burn and ash deposit. The aim of the experiment was to monitor the effects of prescribed fires on the overall bacterial community composition and their response after the burns. The burn site was treated in early March using standard prescribed burn procedures. Bacterial community profile was generated by terminal restriction fragment length polymorphism (TRFLP) analysis of the 16S rRNA genes indicated a complex heterogeneous bacterial community within the same sampling sites. Current data analysis suggest that the prescribed burns do not have a substantial effect on bacterial soil community, while soil depth and time duration after burn may explain much of the community composition differences.
Publications
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Progress 10/01/12 to 09/30/13
Outputs
Target Audience: Research results are being communicated at scientific and technical meetings and through peer-review publications. The improved understanding of microbial processes in nutrient cycling in forest soils are of interest to forest managers and ecologists, as well as US Forest Service. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two undergraduate students have completed their senior honor’s theses as part of this project. A 1-week short course on Environmental Microbiology was offered to graduate students at Universidad Nacional Santiago Antúnez De Mayolo, Huaraz, Peru in April 2013. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals? We are continuing the taxonomic, genomic and physiological analyses of a suite Acidobacteria isolates. We are analyzing the impact of prescribed burns on the bacterial community structure of NJ pinebarrens soils and have established stable isotope probing (SIP) experiments to identify the specific members of the microbial community active in C and N cycling.
Impacts
What was accomplished under these goals?
Our studies focus on the recently discovered bacterial phylum, the Acidobacteria. Members of the Acidobacteria are ubiquitous and one of the most dominant bacteria in acidic soils throughout temperate, boreal and Arctic regions, as well as in areas such as the New Jersey pine barrens. The overall objective of the project is to elucidate the roles of Acidobacteria in carbon and nitrogen turnover in acidic forest soils and to assess the mechanisms promoting their activity and dominance in these environments. Acidobacteria communities appear to represent a key microbial guild that is central in carbon cycling in acidic soils systems. Our concerted efforts have led to the cultivation of several new slow-growing and fastidious Acidobacteria from acidic soils, including both NJ pine barrens and Arctic tundra heath environments. We are continuing the combined genomic and physiological analysis of these novel Acidobacteria strains to obtain an understanding of their regulatory and metabolic networks involved in biogeochemical carbon and nutrient cycling. We have reported on the genome analysis of three subdivision 1 Acidobacteria in a series of publications. The species are cold-adapted acidophiles and versatile heterotrophs that hydrolyze a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. We infer that gene content and biochemical mechanisms encoded in the Acidobacteria genomes strains is shaped to allow for breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides and resilience to fluctuating temperatures and nutrient-deficient conditions. Our study provides genomic insights into the ecology of these Acidobacteria communities in turnover of soil organic carbon in acidic soil environments. This genomic knowledge base forms the foundation for the integrated field studies to understand how shifts in environmental variables impact carbon cycling processes mediated by Acidobacteria.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Rawat SR, M�nnist� MK, Starovoytov V, Goodwin L, Nolan M, Hauser LJ, Land M, Davenport KW Woyke T, H�ggblom MM (2013) Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil. Standards in Genomic Sciences 9:71-82.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Rawat SR, M�nnist� MK, Starovoytov V, Goodwin L, Nolan M, Hauser LJ, Land M, Davenport KW Woyke T, H�ggblom MM (2013) Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil. Standards in Genomic Sciences. 9:449-461.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
H�ggblom MM, M�nnist� MK, Rawat SR, Tiirola M, Dunzik B-A, Ganzert L (2013) Acidobacteria Communities in Arctic Tundra Soils. Fifth International Conference on Polar & Alpine Microbiology, Big Sky, MO Sept. 8012, 2013.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Rawat SR, Welander PV, Summons RE, H�ggblom MM (2013) Biohopanoids in Acidobacteria from Arctic tundra soils: a role in tolerance to extreme conditions. Fifth International Conference on Polar & Alpine Microbiology, Big Sky, MO Sept. 8012, 2013.
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Progress 10/01/11 to 09/30/12
Outputs
OUTPUTS: The overall objective of this recently-initiated project is to elucidate the roles of Acidobacteria in carbon and nitrogen turnover in acidic forest soils, such as in the New Jersey Pinelands, and to assess the mechanisms promoting their activity and dominance in these environments. Acidobacteria communities appear to represent a key microbial guild that is central in carbon cycling in acidic soils systems. Our goal is a systems- and ecosystem-level understanding of the metabolic networks of Acidobacteria and other species consortia involved in biogeochemical cycling of carbon and nitrogen, in particular the biodegradation of plant polysaccharides, including starches, cellulose and hemicellulose, and their various oligomers. Our studies will address how and to what extent Acidobacteria respond to environmental change and whether the predictions on the organismal level of this key microbial guild in turn may estimate ecosystem-scale respiration and nutrient turnover. Our concerted efforts led to the cultivation of several new slow growing and fastidious Acidobacteria from acidic soils. We have completed the combined genomic and physiological analysis of novel Acidobacteria strains to obtain an understanding of their regulatory and metabolic networks involved in biogeochemical carbon and nutrient cycling. This genomic knowledge base will form the foundation for the integrated field studies to understand how shifts in environmental variables impact carbon cycling processes mediated by Acidobacteria. The Acidobacteria genomes showed an abundance of genes assigned to metabolism and transport of carbohydrates and contained an abundance of conserved genes/gene clusters encoding for modules of the carbohydrate-active enzyme (CAZyme) family. Furthermore, a large number of glycoside hydrolases and glycosyl transferases were prevalent. We infer that gene content and biochemical mechanisms encoded in the genomes of three Arctic tundra soil Acidobacteria strains is shaped to allow for breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides and resilience to fluctuating temperatures and nutrient-deficient conditions. Our genomic analysis of the three soils strains is supported by physiological characterization to assess the mechanisms promoting their activity, dominance and survival in their soil environments. We infer that gene content and biochemical mechanisms encoded in the Acidobacteria genomes strains is shaped to allow for breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides and resilience to fluctuating temperatures and nutrient-deficient conditions. Our study provides genomic insights into the ecology of these Acidobacteria communities in turnover of soil organic carbon in acidic soil environments. We conclude that Acidobacteria communities are central to carbon cycling in acidic forests and tundra soil systems and play a significant role in degradation of accumulated biomass. PARTICIPANTS: Max M Haggblom, Principal Investigator, Rutgers Dr. Lee Kerkhof, Co-PI, Rutgers Dr. John Dighton. Co-PI, Rutgers Collaborators: Dr. Suman Rawat, Laboratory Manager, Rutgers Other Collaborators Minna Mannisto, Finnish Forest Research Institute Partner Organizations and Project Funding: Academy of Finland TARGET AUDIENCES: The improved understanding of microbial processes in nutrient cycling in forest soils is of interest to forest managers and ecologists, as well as to the US Forest Service. Research results are being communicated at scientific and technical meetings and through peer-review publications. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Microbes are the key drivers of carbon and nitrogen cycling in terrestrial environments, however the factors controlling soil microbial community composition, dynamics and nutrient cycling are poorly understood. Our objective is to elucidate the role(s) of Acidobacteria in carbon and nitrogen turnover in acidic forest soils, such as in the New Jersey Pinelands, and to assess the mechanisms promoting their activity and dominance in these environments. Northern terrestrial environments are large stores of organic carbon accounting for one third of global soil C pool. Furthermore, increased annual temperature and changes in the amount and form (snow/water) of precipitation are predicted to have significant consequences for the decomposition of organic matter in these ecosystems. Hence, there is growing interest in understanding the controls on soil microbial communities and their functions in carbon and nitrogen cycling. Changing soil temperature and precipitation patterns are likely to impact soil microbial communities and alter carbon and nitrogen cycling rates which, in turn, affect other ecosystem processes. Predicting processes of the global carbon cycle will require a detailed understanding of the functional activities encoded in the genomes of microbes and how these impact the biogeochemical processes of their ecosystem. Our studies focus on the recently discovered bacterial phylum, the Acidobacteria. Members of the Acidobacteria are ubiquitous and one of the most dominant bacteria in acidic soils throughout temperate, boreal and Arctic regions, as well as in areas such as the New Jersey pine barrens. We seek to understand how and to what extent Acidobacteria respond to environmental change and whether the predictions on the organismal level of this key microbial guild in turn may estimate ecosystem-scale respiration and nutrient turnover. The information will allow for better predictions of microbial responses to a changing climate and environmental perturbations. The results from the work are expected to improve our understanding of microbial processes in nutrient cycling in forest soils, providing foundational research for sustaining healthy and productive forests. Our characterization of the forest soil Acidobacteria community will be integrated with several ongoing field studies in the New Jersey pine barrens. This will allow us to examine the microbial community structure and response to a number of different environmental variables and perturbations. These include 1) ground cover vegetation types; 2) forest manipulation; 3) altitudinal cline; and 4) prescribed burning. We are becoming more and more convinced that soil moisture appears to be a driving force for process in pine barrens soils with the microbial community responding to altering rainfall patterns. Multi-year field plots have been established, and additional sets are planned, to examine these effects and we will use these sites to elucidate their impact on the soil Acidobacteria community.
Publications
- Rawat S, Mannisto MK, Bromberg Y, Haggblom MM (2012) Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils. FEMS Microbiology Ecology 82:341-355.
- Rawat S, Mannisto MK, Starovoytov V, Goodwin L, Nolan M, Hauser L, Land M, Davenport KW, Woyke T, Haggblom MM (2012) Complete genome sequence of Terriglobus saanensis strain SP1PR4T, an Acidobacteria from tundra soil. Stand. Genomic Sciences 7:59-69.
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Progress 07/01/11 to 12/31/11
Outputs
OUTPUTS: The overall objective of the recently initiated project is to elucidate the roles of Acidobacteria in carbon and nitrogen turnover in acidic forest soils, such as in the New Jersey Pinelands, and to assess the mechanisms promoting their activity and dominance in these environments. This will be accomplished through an integrated genomic, physiological and ecological research approach. Specifically we will: 1) Elucidate the dynamics and diversity of the Acidobacteria communities in NJ pine barrens; 2) Measure the carbon utilization activity of Acidobacteria species in situ and reveal the metabolic networks of biomass degradation in Pinelands soils though stable isotope probing experiments in the laboratory and field; and 3) Elucidate changing patterns of carbon and nitrogen utilization in pine barrens soils as influenced by environmental fluctuations such as changing precipitation, increasing temperature and freeze-thaw cycles. Our goal is a systems- and ecosystem-level understanding of the metabolic networks of Acidobacteria and other species consortia involved in biogeochemical cycling of carbon and nitrogen, in particular the biodegradation of plant polysaccharides, including starches, cellulose and hemicellulose, and their various oligomers. Our overall hypothesis is that Acidobacteria communities represent a key microbial guild that is central in carbon cycling in acidic soils systems. Our studies will address how and to what extent Acidobacteria respond to environmental change and whether the predictions on the organismal level of this key microbial guild in turn may estimate ecosystem-scale respiration and nutrient turnover. This foundational research will allow for better predictions of microbial responses to a changing climate and greatly improve our understanding of microbial processes in nutrient cycling in forest soils. Our concerted efforts led to the cultivation of several new slow growing and fastidious Acidobacteria from acidic soils. We have completed the initial analysis of the genomes of three novel cold-adapted strains of subdivision 1 Acidobacteria, Granulicella mallensis, Granulicella tundricola and Terriglobus saanensis. Our genomic analysis of the three soils strains is supported by physiological characterization to assess the mechanisms promoting their activity, dominance and survival in their soil environments. We infer that gene content and biochemical mechanisms encoded in the Acidobacteria genomes strains is shaped to allow for breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides and resilience to fluctuating temperatures and nutrient-deficient conditions. Our study provides genomic insights into the ecology of these Acidobacteria communities in turnover of soil organic carbon in acidic soil environments. PARTICIPANTS: Max M Haggblom, Principal Investigator, Rutgers Dr. Lee Kerkhof, Co-PI, Rutgers Dr. John Dighton. Co-PI, Rutgers Collaborators: Dr. Suman Rawat, Laboratory Manager. Other Collaborators Minna Mannisto, Finnish Forest Research Institute Partner Organizations and Project Funding: Academy of Finland TARGET AUDIENCES: The improved understanding of microbial processes in nutrient cycling in forest soils is of interest to forest managers and ecologists, as well as US Forest Service. Research results are being communicated at scientific and technical meetings and through peer-review publications. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Microbes are the key drivers of carbon and nitrogen cycling in terrestrial environments. However the factors controlling soil microbial community composition, dynamics and nutrient cycling are poorly understood. Northern terrestrial environments are large stores of organic carbon, accounting for one third of global soil C pool. Furthermore, increased annual temperature and changes in the amount and form (snow/water) of precipitation are predicted to have significant consequences for the decomposition of organic matter in these ecosystems. Hence, there is growing interest in understanding the controls on soil microbial communities and their functions in carbon and nitrogen cycling. Changing soil temperature and precipitation patterns are likely to impact soil microbial communities and alter carbon and nitrogen cycling rate which, in turn, affect other ecosystem processes. Predicting processes of the global carbon cycle will require a detailed understanding of the functional activities encoded in the genomes of microbes and how these impact the biogeochemical processes of their ecosystem. However, very little is known about the composition of soil microbial communities, their activity, and community dynamics, despite their critical role in carbon and nutrient cycling. Our studies focus on the recently discovered bacterial phylum, the Acidobacteria. Members of the Acidobacteria are ubiquitous and one of the most dominant bacteria in acidic soils throughout temperate, boreal and Arctic regions, as well as in areas such as the New Jersey pine barrens. However, despite their dominant distribution, relatively little is known about the diversity, distribution and, most critically, the function of Acidobacteria. The phylogenetic diversity, ubiquity and abundance of this group suggest that they play an important ecological role in soils. We seek to understand how and to what extent Acidobacteria respond to environmental change and whether the predictions on the organismal level of this key microbial guild in turn may estimate ecosystem-scale respiration and nutrient turnover. The information will allow for better predictions of microbial responses to a changing climate and environmental perturbations. Results from this research are expected to improve our understanding of microbial processes in nutrient cycling in forest soils, providing foundational research for sustaining healthy and productive forests.
Publications
- Mannisto MK, Rawat S, Starovoytov V, Haggblom MM (2011) Terriglobus saanensis sp. nov., an aidobacterium isolated from tundra soil. Int. J. System. Evol. Microbiol. 61:1823-1828. (doi:10.1099/ijs.0.026005-0)
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