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Phylogenetically distinct phylotypes modulate nitrification in a paddy soil.

Jun Zhao1, Baozhan Wang2, Zhongjun Jia3

  • 1State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, People's Republic of China University of Chinese Academy of Sciences, Beijing, People's Republic of China.

Applied and Environmental Microbiology
|March 1, 2015
PubMed
Summary
This summary is machine-generated.

Nitrifying microbial communities in paddy soils are diverse, with various ammonia-oxidizing bacteria and archaea driving nitrogen cycling. This study reveals distinct phylotypes involved in soil nitrification, highlighting functional diversification in these unique agricultural ecosystems.

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Area of Science:

  • Microbiology
  • Environmental Science
  • Soil Science

Background:

  • Paddy fields are unique, regularly flooded ecosystems crucial for rice cultivation.
  • The specific microbial groups responsible for soil nitrification in these environments are not well understood.
  • Nitrification is a key process in soil nitrogen cycling, influencing nutrient availability.

Purpose of the Study:

  • To identify the taxonomic composition of nitrifying microbial communities in neutral paddy soil.
  • To investigate the functional roles of different bacteria and archaea in soil nitrification using molecular techniques.
  • To understand the diversity and phylogenetic affiliations of active nitrifying microorganisms.

Main Methods:

  • Utilized high-throughput pyrosequencing and DNA-based stable isotope probing (SIP) for microbial community analysis.
  • Incubated soil microcosms with urea and 13C-labeled compounds to track active nitrifiers.
  • Analyzed 16S rRNA and amoA genes to identify ammonia-oxidizing bacteria (AOB) and archaea (AOA), and nitrite-oxidizing bacteria (NOB).

Main Results:

  • Urea addition significantly increased soil nitrate and the abundance of bacterial/archaeal amoA genes.
  • Nitrification activity correlated positively with specific Nitrosospira-like AOB, soil group 1.1b-like AOA, and Nitrospira-like NOB.
  • Pyrosequencing revealed assimilation of 13C-labeled CO2 by distinct AOA and NOB lineages, including 'Candidatus Nitrososphaera gargensis' and 'Candidatus Nitrosotalea devanaterra'.

Conclusions:

  • Paddy field nitrification involves a diverse range of microbial phylotypes, including previously underappreciated groups.
  • Active ammonia-oxidizing bacteria and archaea are closely affiliated with specific lineages, suggesting specialized roles.
  • The findings imply significant physiological diversification within soil nitrifying communities adapting to fluctuating paddy field conditions.