Soil microbial community function and diversity

Project (past)

Project dates01 Mar 2008 to end of 31 Mar 2012
Researchers
Principal InvestigatorPenny Hirsch
FunderBiotechnology and Biological Sciences Research Council
Project numberS4961
4961
DepartmentPlant Pathology and Microbiology (PPM)
Research fish codeBBS/E/C/00004961
Grant IDBBS/E/C/00004961

Outputs

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Culture-independent molecular approaches to microbial ecology in soil and rhizosphere

B - Book chapters etc edited externally
Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2013. Culture-independent molecular approaches to microbial ecology in soil and rhizosphere. in: Debruijn, F. J. (ed.) Molecular microbial ecology of the rhizosphere, Volume 1 John Wiley & Sons Hoboken, N.J.. pp. 45-55

Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits?

B - Book chapters etc edited externally
Hirsch, P. R., Miller, A. J. and Dennis, P. G. 2013. Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits? in: Debruijn, F. J. (ed.) Molecular microbial ecology of the rhizosphere, Volume 1 John Wiley & Sons Hoboken, N.J.. pp. 229-242

Mutualism: plant-microorganism interactions

B - Book chapters etc edited externally
Mauchline, T. H. 2012. Mutualism: plant-microorganism interactions. in: Hirsch, P. R. and Ogilvie, L. A. (ed.) Microbial ecology theory: current perspectives Caister Academic Press, Norwich, Norfolk. pp. 43-55

The Pochonia chlamydosporia serine protease gene vcp1 is subject to regulation by carbon, nitrogen and pH: implications for nematode biocontrol

A - Papers appearing in refereed journals
Ward, E., Kerry, B. R., Manzanilla-Lopez, R. H., Mutua, G., Devonshire, J., Kimenju, J. and Hirsch, P. R. 2012. The Pochonia chlamydosporia serine protease gene vcp1 is subject to regulation by carbon, nitrogen and pH: implications for nematode biocontrol. PLOS ONE. 7, p. e35657. https://doi.org/10.1371/journal.pone.0035657

Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment

A - Papers appearing in refereed journals
Clark, I. M., Buchkina, N., Jhurreea, D., Goulding, K. W. T. and Hirsch, P. R. 2012. Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment. Philosophical Transactions of the Royal Society B-Biological Sciences. 367, pp. 1235-1244. https://doi.org/10.1098/rstb.2011.0314

A genomic network to monitor Earth

G - Articles in popular magazines and other technical publications
Davies, N., Field, D. and Hirsch, P. R. 2012. A genomic network to monitor Earth. Nature. 481 (7380), p. 145. https://doi.org/10.1038/481145a

Enhancing survival attributes of entomopathogenic nematodes

C2 - Non-edited contributions to conferences
Perry, R. N. and Ehlers, R-U. 2011. Enhancing survival attributes of entomopathogenic nematodes.

Soil metagenomics reveals impacts of land management on microbial communities in long-term field experiments

C2 - Non-edited contributions to conferences
Hirsch, P. R. 2011. Soil metagenomics reveals impacts of land management on microbial communities in long-term field experiments. Abstracts 2011 International Conference on Soil Omics (ICSO), Nanjing, 19-24 November 2011 .

The role of soil bacteria in nitrogen cycling

C2 - Non-edited contributions to conferences
Hirsch, P. R. 2011. The role of soil bacteria in nitrogen cycling. Abstracts SEE11: Joint Meeting of the Royal Entomological Society of London and the Soil Ecology Society, Plymouth, 14-16 September 2011 .

Ecology of Pochonia chlamydosporia in the rhizosphere at the population, whole organism and molecular scales

B - Book chapters etc edited externally
Kerry, B. R. and Hirsch, P. R. 2011. Ecology of Pochonia chlamydosporia in the rhizosphere at the population, whole organism and molecular scales. in: Davies, K. G. and Spiegel, Y. (ed.) Biological control of plant-parasitic nematodes: building coherence between microbial ecology and molecular mechanisms Springer, Dordrecht. pp. 171-182

Metagenomic comparison of direct and indirect soil DNA extraction approaches

A - Papers appearing in refereed journals
Delmont, T. O., Robe, P., Clark, I. M., Simonet, P. and Vogel, T. M. 2011. Metagenomic comparison of direct and indirect soil DNA extraction approaches. Journal of Microbiological Methods. 86 (3), pp. 397-400. https://doi.org/10.1016/j.mimet.2011.06.013

Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia

A - Papers appearing in refereed journals
Rosso, L. C., Finetti-Sialer, M. M., Hirsch, P. R., Ciancio, A., Kerry, B. R. and Clark, I. M. 2011. Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia. Applied Microbiology and Biotechnology. 90, pp. 1981-1994. https://doi.org/10.1007/s00253-011-3282-7

Impacts of land use change on denitrifying bacteria and nitrous oxide emissions

C2 - Non-edited contributions to conferences
Hirsch, P. R., Jhurreea, D., Scott, T., Misselbrook, T. H., Goulding, K. W. T. and Clark, I. M. 2011. Impacts of land use change on denitrifying bacteria and nitrous oxide emissions. Abstracts Theo Murphy Scientific Meeting: Nitrous Oxide, the Forgotten Greenhouse Gas, Chicheley, 23-24 May 2011 .

Accessing the soil metagenome for studies of microbial diversity

A - Papers appearing in refereed journals
Delmont, T. O., Robe, P., Cecillon, S., Clark, I. M., Constancias, F., Simonet, P., Hirsch, P. R. and Vogel, T. M. 2011. Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology. 77 (4), pp. 1315-1324. https://doi.org/10.1128/AEM.01526-10

Exploring microbial diversity - methods and meaning

B - Book chapters etc edited externally
Ogilvie, L. A. and Hirsch, P. R. 2010. Exploring microbial diversity - methods and meaning. in: Tepper, G. H. (ed.) Species diversity and extinction Nova Science Publishers, Hauppauge. pp. 24pp

Arsenic speciation in phloem and xylem exudates of castor bean

A - Papers appearing in refereed journals
Ye, W-L., Wood, B. A., Stroud, J. L., Andralojc, P. J., Raab, A., McGrath, S. P., Feldmann, J. and Zhao, F-J. 2010. Arsenic speciation in phloem and xylem exudates of castor bean. Plant Physiology. 154, pp. 1505-1513. https://doi.org/10.1104/pp.110.163261

Effects of long-term fertilization and liming on microbial functions and diversity in the grassland site at Rothamsted Research, UK

C2 - Non-edited contributions to conferences
Wu, Liyou, Liang, Y., Clark, I. M., Wue, K., Deng, Y., He, Z., Van Nostrand, J., Macdonald, C., Hirsch, P. R., McGrath, S. P. and Zhou, J. 2010. Effects of long-term fertilization and liming on microbial functions and diversity in the grassland site at Rothamsted Research, UK. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .

Targeting the active bacterial communities in soil pores

C2 - Non-edited contributions to conferences
Mccabe, D., Clark, I. M., Sohi, S., Shaw, E. and Hirsch, P. R. 2010. Targeting the active bacterial communities in soil pores. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .

Effects of long-term fertilization on spatial distribution patterns of microbial functional genes from the Rothamsted Experimental site

C2 - Non-edited contributions to conferences
Liang, Y., Wu, Liyou, Clark, I. M., Xue, K., Deng, Y., He, Z., Hirsch, P. R., McGrath, S. P. and Zhou, J. 2010. Effects of long-term fertilization on spatial distribution patterns of microbial functional genes from the Rothamsted Experimental site. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .

Long-term agricultural experiments reveal N influence on ammonia oxidizers and the predominance of CA. nitrososphaera

C2 - Non-edited contributions to conferences
Giongo, A., Gano,K., Roesch, L., Casella, G., Daroub, S., Ramiez, K., Sayavedra-Soto, L., Arp, D., Clark, I. M., Hirsch, P. R., McGrath, S. P. and Triplett, E. 2010. Long-term agricultural experiments reveal N influence on ammonia oxidizers and the predominance of CA. nitrososphaera. Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .

Soil metagenomics: can we access the diversity?

C2 - Non-edited contributions to conferences
Delmont, T., Cecillon, S., Clark, I. M., Simonet, P., Hirsch, P. R. and Vogel, T. 2010. Soil metagenomics: can we access the diversity? Abstracts 13th International Symposium on Microbial Ecology, Seattle, 22-27 August 2010 .

Culture-independent molecular techniques for soil microbial ecology

A - Papers appearing in refereed journals
Hirsch, P. R., Mauchline, T. H. and Clark, I. M. 2010. Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry. 42 (6), pp. 878-887. https://doi.org/10.1016/j.soilbio.2010.02.019

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

A - Papers appearing in refereed journals
Dennis, P. G., Miller, A. J. and Hirsch, P. R. 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiology Ecology. 72 (3), pp. 313-327. https://doi.org/10.1111/j.1574-6941.2010.00860.x

Phytoextraction and management options to reduce cadmium and arsenic in food crops

C2 - Non-edited contributions to conferences
Zhao, F-J. and McGrath, S. P. 2009. Phytoextraction and management options to reduce cadmium and arsenic in food crops. Abstracts MARCO Symposium 2009: Challenges for Agro-Environmental Research in Monsoon Asia, Tsukuba, Japan, 5-7 October 2009 .

Are long-term changes in soil organic matter reflected in the soil communities?

C2 - Non-edited contributions to conferences
Murray, P. J., Hirsch, P. R., Gilliam, L. M., Sohi, S. P., Williams, J. K., Clark, I. M. and Brookes, P. C. 2009. Are long-term changes in soil organic matter reflected in the soil communities? Abstracts Forming Bridges in a Changing World: Society of Nematologists and Soil Ecology Society Conference, Burlington, 12-15 July 2009 .

Through the keyhole: a key to open the bacterial lock; aka using BrdU to target pore space diversity

C2 - Non-edited contributions to conferences
Mccabe, D., Clark, I. M., Sohi, S. P., Shaw, L. and Hirsch, P. R. 2009. Through the keyhole: a key to open the bacterial lock; aka using BrdU to target pore space diversity. Abstracts Micro Soil: Integrating Biological, Physical and Chemical Techniques for the Study of Soil Micro-Habitats, Dundee, 16-17 September 2009 . pp. 24-25

Microhabitat scale methods in microbial ecology

C2 - Non-edited contributions to conferences
Dennis, P., Miller, A. J., Kilburn, M., Taylor, R., Valsami-Jones, E., Grovenor, C. and Hirsch, P. R. 2009. Microhabitat scale methods in microbial ecology. Abstracts Micro Soil: Integrating Biological, Physical and Chemical Techniques for the Study of Soil Micro-Habitats, Dundee, 16-17 September 2009 . pp. 19

Microbial diversity maintained in soils starved of plant inputs for 50 years

C2 - Non-edited contributions to conferences
Clark, I. M., Gilliam, L. M., Sohi, S. P., Williams, J., Murray, P. J. and Hirsch, P. R. 2009. Microbial diversity maintained in soils starved of plant inputs for 50 years. Abstracts BAGECO 10: Bacterial Genetics and Ecology - Coexisting on a Changing Planet, Uppsala, 15-19 June 2009 . pp. 119

What can we learn from the Rothamsted Classical Experiments using molecular techniques

C2 - Non-edited contributions to conferences
Hirsch, P. R. 2009. What can we learn from the Rothamsted Classical Experiments using molecular techniques. Abstracts UK-Brazil Workshop on Soil Quality and Soil Processes, Rio de Janeiro, 20-27 March 2009 . pp. 13

Sampling bacteria at the microhabitat scale

C2 - Non-edited contributions to conferences
Hirsch, P. R., Dennis, P. G. and Miller, A. J. 2009. Sampling bacteria at the microhabitat scale. Abstracts Micro Soil: Integrating Biological, Physical and Chemical Techniques for the Study of Soil Micro-Habitats, Dundee, 16-17 September 2009 . pp. 9

What plants do for soil and what happens after they've gone

C2 - Non-edited contributions to conferences
Hirsch, P. R. and Clark, I. M. 2009. What plants do for soil and what happens after they've gone. Abstracts Plant Soil Interactions: Joint Meeting of the Scottish Root Group and the Scottish Discussion Group of the British Society of Soil Science, Aberdeen, 3 November 2009 .

Sequencing the microbial metagenome of an iconic grassland soil, the Rothamsted Park Grass Experiment

C2 - Non-edited contributions to conferences
Hirsch, P. R. and Clark, I. M. 2009. Sequencing the microbial metagenome of an iconic grassland soil, the Rothamsted Park Grass Experiment. Abstracts BAGECO 10: Bacterial Genetics and Ecology - Coexisting on a Changing Planet, Uppsala, 15-19 June 2009 . pp. 73

Advantages of the metagenomic approach for soil exploration: reply from Vogel et al

A - Papers appearing in refereed journals
Vogel, T. M., Hirsch, P. R., Simonet, P., Jansson, J. K., Tiedje, J. M., Van Elsas, J. D., Nalin, R., Philippot, L. and Bailey, M. J. 2009. Advantages of the metagenomic approach for soil exploration: reply from Vogel et al. Nature Reviews Microbiology. 7, pp. 756-757. https://doi.org/10.1038/nrmicro2119-c3

Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities

A - Papers appearing in refereed journals
Hirsch, P. R., Gilliam, L. M., Sohi, S. P., Williams, J. K., Clark, I. M. and Murray, P. J. 2009. Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities. Soil Biology and Biochemistry. 41 (9), pp. 2021-2024. https://doi.org/10.1016/j.soilbio.2009.07.011

The rice aquaporin Lsi1 mediates uptake of methylated arsenic species

A - Papers appearing in refereed journals
Li, R-Y., Ago, Y., Liu, W-J., Mitani, N., Feldmann, J., McGrath, S. P., Ma, J. F. and Zhao, F-J. 2009. The rice aquaporin Lsi1 mediates uptake of methylated arsenic species. Plant Physiology. 150, pp. 2071-2080. https://doi.org/10.1104/pp.109.140350

TerraGenome: a consortium for the sequencing of a soil metagenome

A - Papers appearing in refereed journals
Vogel, T. M., Simonet, P., Jansson, J. K., Hirsch, P. R., Tiedje, J. M., Van Elsas, J. D., Bailey, M. J., Nalin, R. and Philippot, L. 2009. TerraGenome: a consortium for the sequencing of a soil metagenome. Nature Reviews Microbiology. 7, p. 252. https://doi.org/10.1038/nrmicro2119

Linking rhizoplane pH and bacterial density at the microhabitat scale

A - Papers appearing in refereed journals
Dennis, P. G., Hirsch, P. R., Smith, S. J., Taylor, R. G., Valsami-Jones, E. and Miller, A. J. 2009. Linking rhizoplane pH and bacterial density at the microhabitat scale. Journal of Microbiological Methods. 76, pp. 101-104. https://doi.org/10.1016/j.mimet.2008.09.013

New approaches to an old problem: linking soil quality and microbial communities

C2 - Non-edited contributions to conferences
Hirsch, P. R. 2008. New approaches to an old problem: linking soil quality and microbial communities. Abstracts BSSS Autumn Meeting on Something Old, Something New: Integrating Molecular Biology with Other Techniques in Soil Science, Harpenden, 17 September 2008 .

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

C2 - Non-edited contributions to conferences
Clark, I. M. 2008. Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment. Abstracts BSSS Autumn Meeting on Something Old, Something New: Integrating Molecular Biology with Other Techniques in Soil Science, Harpenden, 17 September 2008 .