Legume-rhizobia interactions in a complex microbiome
Date
2018
Authors
Chia, Ming-Dao
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Abstract
Biological nitrogen fixation is important for agriculture, carbon
sequestration, and ecosystem restoration. This is primarily
conducted by rhizobia (nitrogen fixing bacteria) in association
with legume plants.
Most research in improving rhizobial strains involves single
strain experiments. However, improved metagenomics methods have
demonstrated considerable differences between single strain
inoculations and strain behaviour when exposed to a complex
microbiome.
To identify some these differences, this experiment applies two
treatment factors in a controlled environment of containers with
autoclaved sand. All main experimental containers were inoculated
with several strains of Bradyrhizobia japonicum. The first
treatment factor was the planting of surface-sterilised seedlings
of host plant Acacia acuminata; the second treatment factor was
inoculation with an external soil microbiome. Several negative
controls without planting or inoculation were also present.
A novel method of whole genome metagenomic sequencing to observe
known strain abundance, without amplification or culturing, was
developed. Using this method, abundance patterns of these B.
japonicum strains were compared between initial inoculation and
the end of a growth period of several weeks. Analysis reveals a
single strain as the preferred nodulation strain within this
experiment, but also shows that all strains inoculated continued
to persist in the substrate at detectable levels.
The use of long reads with the MinION DNA sequencer also allowed
the potential of identification of horizontal gene transfer
events. None were detected in an initial screen, but a framework
for further inspection of this dataset for such events is
described.
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Acacia, bacteria, biological nitrogen fixation, DNA sequencing, genomics, legumes, metagenomics, microbiome, nanopore sequencing, rhizobia
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