High-Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology

Area of Science:

• Microbial Ecology
• Environmental Microbiology
• Molecular Ecology

Background:

• High-throughput sequencing commonly yields relative microbial abundance data, with known discrepancies compared to absolute abundances.
• Previous studies have recognized but rarely explored the ecological implications of these abundance data discrepancies.

Purpose of the Study:

• To investigate microbial community dynamics, co-occurrence patterns, and assembly processes in Lake Dongting using both relative and absolute abundance data.
• To highlight the importance of absolute quantification for accurate microbial ecological interpretations.

Main Methods:

• Quantified microbial absolute abundances using spike-in based 16S absolute quantification sequencing.
• Analyzed microbial community dynamics and co-occurrence networks using both relative and absolute abundance data.
• Compared ecological assembly processes and environmental drivers between the two abundance measures.

Main Results:

• Absolute and relative abundances showed comparable community-level results but differed significantly at the population level.
• Relative abundance data masked individual taxa dynamics, especially for abundant taxa.
• Correlation-based co-occurrence networks from relative abundance underestimated rare taxa and were less stable than those from absolute abundance.
• Temperature was the primary driver of microbial community composition and assembly, irrespective of abundance data type.
• Relative abundance data suggested stronger environmental and deterministic effects on microbial assembly.

Conclusions:

• Absolute quantification is crucial for uncovering microbial ecological patterns obscured by relative abundance data.
• The study underscores the need to incorporate absolute abundance measurements for a comprehensive understanding of microbial communities.
• Findings emphasize the impact of abundance data choice on ecological interpretations, particularly concerning rare taxa and community interactions.