Progress 10/01/04 to 09/30/07
Outputs
The Planctomycetes are the only group of organisms to contain species known to carry out the anaerobic oxidation of ammonium. Planctomycetes have also recently been observed to be abundant in soils raising the interesting possibility that these organisms may account for a previously undetected component of the soil nitrogen cycle. To characterize the Planctomycete community in soils a specific PCR primer pair was designed to target Planctomycete 16S rRNA genes. Once validated this primer pair was used to conduct a survey of Planctomycete 16S rRNA genes in experimental agricultural plots. Soil samples were collected with respect to plant row effects (within and between planting rows) and presence or absence of organic matter. Planctomycete 16S rRNA genes were amplified, cloned, and sequenced to characterize the richness and community structure within the treatments at the site. In addition, with the help of collaborators, Planctomycete 16S rRNA gene specific primers were
used to perform denaturing gradient gel electrophoresis to examine the relationship variation in the Planctomycetes community as a function of variation in soil parameters across the experiment site. Following identification in soil of a unique group of Planctomycetes that are closely related to those known to carry out anammox a new set of PCR primers were developed that encompass these specific groups. These primers were validated and used to detect anammox-like organisms in a range of both aerobic and anaerobic soils representing a range of organic matter contents.
Impacts
This project has revealed the extent of phylogenetic diversity of Planctomycetes within soil. Over 300 different taxa were detected within a single agricultural field. Remarkably, the majority of these sequences were less than 80 percent similar to any previously identified sequences present in public sequence databases suggesting that the diversity of this group remains vastly under sampled with respect to other microbial groups in the soil. This research also revealed the presence of a group of Planctomycetes in soil that are closely related to the anammox Planctomycetes. Both maximum likelihood and parsimony analyses with different sets of full length 16S rRNA sequences support that these soil sequences form a monophyletic group with the anammox bacteria to the exclusion of other non-cultivated sequence clusters within the Planctomycete line of descent. Local variations in soil characteristics associated with agricultural management were observed to alter the
composition of Planctomycete communities which suggest that selective pressures acting at small scales may act on these communities and that the total diversity of these organisms across terrestrial ecosystems may be extraordinarily high. These results suggest that local conditions within a contiguous landscape can select for locally adapted strains within particular bacterial groups in soil. Treatment effects at the site had significant impacts on both richness and community structure of Planctomycetes as samples taken from tree rows were significantly more diverse than those from grass lanes and organic matter addition had significant impacts on the phylogenetic composition of the community. Variation in community composition was significantly correlated with variation in soil nitrate content suggesting a possible interaction with the soil nitrogen cycle that as yet remains. Following discovery of novel soil Plantomycetes associated with the anammox group a specific primer set was
designed to encompass both sets of organisms. The primer set was validated and used to assess the distribution of these organisms in a range of soil types. Findings suggest that this group is common in anaerobic soil samples. However, analyses of various samples failed to detect conclusive evidence of Planctomycetes which are known to carry our anammox. Many lineages were detected that are deeply divergent within the Planctomycetes group and which are closely related to but separate from the known anammox bacteria. These results demonstrate that if soil Planctomycetes are able to carry out anaerobic ammonium oxidation these organisms are likely to be distinct from those that have been previously observed in wastewater and sediment systems. This research promises to greatly expand our understanding of the functional significance of non-cultivated microorganisms in soil, and to reveal ecological and evolutionary insights on soil microbial communities.
Publications
- Buckley, D. H., V. Huangyutitham, T. A. Nelson, A. Rumberger and J. E. Thies. 2006. Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Applied and Environmental Microbiology. 72:4522-4531.
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Progress 01/01/06 to 12/31/06
Outputs
Planctomycetes are the only known group of organisms known to carry out the anaerobic oxidation of ammonium. Planctomycetes have also recently been observed to be abundant in soils raising the interesting possibility that these organisms may account for a previously undetected component of the soil nitrogen cycle. As an initial step to characterize the Planctomycete community in soils a survey of Planctomycete 16S rRNA genes was conducted in experimental agricultural plots. Soil samples were collected with respect to plant row effects (within row and between row) and presence or absence of compost. Planctomycete communities were characterized within a replicated field experiment in an agricultural field with respect to compost amendment and position (row effects). Planctomycete 16S rRNA genes were amplified, cloned, and sequenced to characterize the richness and community structure within the treatments at the site. The diversity of Planctomycetes within the site was
surprisingly high with the Chao1 estimator indicating 312 plus or minus 35 (mean plus or minus 95 percent c.i.) different operational taxonomic units (OTUs) at a sequence similarity cutoff of 99 percent. Remarkably, the majority of these sequences were less than 80 percent similar to any previously identified sequences present in public sequence databases suggesting that the diversity of this group remains vastly under sampled with respect to other microbial groups in the soil. Treatment effects at the site had significant impacts on both richness and community structure as samples taken from tree rows were significantly more diverse than those from grass lanes (255 plus or minus 43 verses 131 plus or minus 18 respectively (mean plus or minus 95 percent c.i.)) and LIBSHUFF analysis revealed that both compost treatment and row effects altered the phylogenetic composition of communities. These results suggest that local conditions within a contiguous landscape can select for locally
adapted strains within particular bacterial groups in soil. This research also revealed the presence of a group of Planctomycetes in soil that are closely related to the anammox Planctomycetes. Both maximum likelihood and parsimony analyses with different sets of full length 16S rRNA sequences support that these soil sequences form a monophyletic group with the anammox bacteria to the exclusion of other non-cultivated sequence clusters within the Planctomycete line of descent. PCR primers have been developed that target this anammox-like group of Planctomycetes as well as conventional anammox bacteria. These primers have been used to detect anammox-like organisms in soils and freshwater sediments. Efforts are currently underway to characterize the Planctomycetes that have been detected and to use 15N-labeled compounds to evaluate whether anammox occurs in these systems.
Impacts
This project has revealed the extent of phylogenetic diversity of Planctomycetes within soil. Over 300 different taxa were detected within a single agricultural field and local variations in soil characteristics within that field were observed to alter the composition of Planctomycete communities hinting that selective pressures acting at small scales may act on these communities and hinting that the total diversity of these organisms across terrestrial ecosystems may be extraordinarily high. This research promises to greatly expand our understanding of the functional significance of non-cultivated microorganisms in soil, and to reveal ecological and evolutionary insights on soil microbial communities.
Publications
- No publications reported this period
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Progress 01/01/05 to 12/31/05
Outputs
As an initial step to characterize the non-cultivated Planctomycete community in soils a survey of Planctomycete 16S rRNA genes was conducted in experimental agricultural plots. Soil samples were collected with respect to plant row effects (within row and between row) and presence or absence of compost. Planctomycete communities were characterized within a replicated field experiment in an agricultural field with respect to compost amendment and position (row effects). Planctomycete 16S rRNA genes were amplified, cloned, and sequenced to characterize the richness and community structure within the treatments at the site. The diversity of Planctomycetes within the site was surprisingly high with the Chao1 estimator indicating 312 plus or minus 35 (mean plus or minus 95 percent c.i.) different operational taxonomic units (OTUs) at a sequence similarity cutoff of 99 percent. Remarkably, the majority of these sequences were less than 80 percent similar to any previously
identified sequences present in public sequence databases suggesting that the diversity of this group remains vastly under sampled with respect to other microbial groups in the soil. Treatment effects at the site had significant impacts on both richness and community structure as samples taken from tree rows were significantly more diverse than those from grass lanes (255 plus or minus 43 verses 131 plus or minus 18 respectively (mean plus or minus 95 percent c.i.)) and LIBSHUFF analysis revealed that both compost treatment and row effects altered the phylogenetic composition of communities. These results suggest that local conditions within a contiguous landscape can select for locally adapted strains within particular bacterial groups in soil. This research also revealed the presence of a group of Planctomycetes in soil that are closely related to the anammox Planctomycetes. Both maximum likelihood and parsimony analyses with different sets of full length 16S rRNA sequences support
that these soil sequences form a monophyletic group with the anammox bacteria to the exclusion of other non-cultivated sequence clusters within the Planctomycete line of descent. PCR primers have been developed that target this anammox-like group of Planctomycetes as well as conventional anammox bacteria and these primers are currently being used to assess the distribution of these anammox-like bacteria in agricultural soils. These results are currently being prepared for publication and further tests are underway to look for anammox in soils.
Impacts
This project has revealed the extent of phylogenetic diversity of Planctomycetes within soil. Over 300 different taxa were detected within a single agricultural field and local variations in soil characteristics within that field were observed to alter the composition of Planctomycete communities hinting that selective pressures acting at small scales may act on these communities and hinting that the total diversity of these organisms across terrestrial ecosystems may be extraordinarily high. This research promises to greatly expand our understanding of the functional significance of non-cultivated microorganisms in soil, and to reveal ecological and evolutionary insights on soil microbial communities.
Publications
- No publications reported this period
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