103
Microbial ecology, 32, 55
Microbial fingerprinting technique, 26
Microbially assisted bioremediation, 20–21
Microbial world, 3
Microorganisms, 73
Molecular-based methodologies, 31
Multiple displacement amplification, 35
Multiple sequence alignment (MSA), 42
N
Next-generation sequencing (NGS), 35, 42
technologies, 73
N-fixation, 10
Nuclear isolation, 36
O
Operational taxonomic unit (OTU), 28, 75
Orphelia, 65
P
PaPaRa, 67
Phospholipid fatty acid analysis (PLFA), 24
attribute, 24
difference, 25
lipids, 24
SOM, 25
Phylogenetic analysis, 42
Phymm, 67
Phyto-bioremediation, 72
Plant growth-promoting microorganisms
(PGPMs), 6
Plant–microbe interactions, 17
Predicted-Relative-Metabolic-Turnover, 68
Prokaryotes, 53
Protein microarray, 58
Proteofingerprint, 57
Pyrosequencing, 52
Q
Quality-control analysis, 66
Quantitative real-time PCR (qPCR), 30
R
RAIphy, 67
RAMMCAP, 68
Rapid annotation by subsystem technology, 46
Restriction enzyme (RE), 27
Rhizospheric microorganisms, 15
Ribosomal RNA (rRNA) genes
sequencing, 65
Ribosomal-Database-Project, 42, 66
Rice production, 11
S
Sanger sequencing data, 41
Sequence binning, 42
Sequencing single bacterial cells, 35
ShotgunFunctionalizeR, 69
SILVA, 65
Simulators tools, 69
Single-cell genomics (SCG), 36
advantages, 34
algorithms and software, 38
characteristics, 38
development, 34
isolation, 36
metagenomics, 34
WGA, 37
Single-cell sequencing analysis, 69
Single-strand conformation polymorphism
(SSCP)
DGGE/TGGE, 29
PCR, 29
16S–23S rRNA, 29
SmashCell, 69
Smash-Community, 70
Soil function, 2
Soil metatranscriptomics, 52
Soil microbial communities, 24, 54, 60, 71
Soil microbial community analysis, 62–64
Soil microorganisms, 3, 6
Soil organic matter (SOM), 25
SOrt-ITEMS, 67
SourceTracker, 69
Spar-CC, 68
SPHINX, 67
Stable isotope probing (SIP), 30
STAMP, 70
Stress tolerance, 7
Suppressive soils, 39
Sustainable development goals (SDGs), 2, 72
T
TACOA, 67
Taxonomic binning, 42, 46
Taxonomic profiling
AMPHORA2, 66
CARMA3, 66
ClaMS, 66
Index