Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation.

Yu Xia,Yi Wang,Yubo Wang,Francis Y L Chin,Tong Zhang

doi:10.1186/s13068-016-0524-z

Abstract

BackgroundThe Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; however, the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. Our previous metatranscriptional analysis revealed this prevalent population that showed minimum involvement in the main pathways of cellulose hydrolysis and subsequent methanogenesis in the thermophilic cellulose fermentative consortium (TCF).ResultsIn further pursuit, five high-quality curated draft genomes (>98 % completeness) of this population, including two affiliated with the inaccessible lineage of SBR1031, were retrieved by sequence-based multi-dimensional coverage binning. Comparative genomic analyses revealed versatile genetic capabilities for carbohydrate-based fermentative lifestyle including key genes catalyzing cellulose hydrolysis in Anaerolinea phylotypes. However, the low transcriptional activities of carbohydrate-active genes (CAGs) excluded cellulolytic capability as the selective advantage for their prevalence in the community. Instead, a substantially active type VI pili (Tfp) assembly was observed. Expression of the tight adherence protein on the Tfp indicated its function for cellular attachment which was further testified to be more likely related to cell aggregation other than cellulose surface adhesion. Meanwhile, this Tfp structure was found not contributing to syntrophic methanogenesis. Members of the SBR1031 encoded key genes for acetogenic dehydrogenation that may allow ethanol to be used as a carbon source.ConclusionThe common prevalence of Anaerolineae in anaerobic digesters should be originated from advantageous cellular adhesiveness enabled by Tfp assembly other than its potential as cellulose degrader or anaerobic syntrophs.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0524-z) contains supplementary material, which is available to authorized users.

Highlights

The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences
Tetranucleotide frequency (TNF) was used to filter out possible contamination at hierarchy distance of 0.1 [20]. The quality of these six primary Chloroflexi genome bins was evaluated in terms of genome completeness and contamination, respectively based on the occupation and duplication of the 107 essential single-copy genes (ESCGs) shared >95 % of all bacteria (Additional file 1: Tables S3, S4)
Being commonly regarded as aerobic, strains of Sphingomonas and Pseudomonas had been reported to be tolerant to anaerobic environment [32,33,34,35]. The overgrowth of these two genera in the attached community after 24 h of incubation may be originated from a combination of their ability to utilize beta-linked monosaccharides released from the hydrolysis process [36] as well as their extraordinary ability to grow in biofilm [37, 38]. These results indicated the accumulation of Anaerolinales took place other than directly on the surface of cellulose, we speculate, instead of initiating the attachment on substrate surface, the adhesive feature of Anaerolineae enabled by active pilA expression might serve as the adhesive matrix for the aggregation of fermentative population in the liquid phase

Summary

Introduction

The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. A series of metabolic reactions such as hydrolysis, acidogenesis (fermentation), acetogenesis, and methanogenesis are involved in the process of anaerobic digestion. The flow velocity within the digester, especially in upflow anaerobic sludge blanket reactor (UASB), may select organisms which can adhere to each other to form well-settling granular sludge. This widely distributed Anaerolineae population had been reported as both the backbone of sludge granules [6] and the causative agent of filamentous bulking in UASB [2, 7]

Methods

Results

Conclusion