Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge

Abstract

Pre-treatment of waste activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, impacts of WAS pre-treatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pre-treatment improve digestion performance, remain elusive. In this study, genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different feeding sludge: APAD, WAS pre-treated with 0.25 mol/L alkaline/acid; HS-APAD, WAS pre-treated with 0.8 mol/L alkaline/acid; Thermal-AD, thermal pre-treated WAS; Control-AD, fresh WAS. We retrieved 254 metagenomic-assembled genomes (MAGs) to identify the key functional populations involved in methanogenic digestion process. These MAGs span 28 phyla with 69 of them as yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in Thermal-AD, corroborating different substrates released from alkaline/acid and thermal pre-treatments. Of the major functional populations (i.e., fermenters, syntrophic acetogens and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in the APAD and HS-APAD with improved digestion performance. IMPORTANCE Wastewater treatment generates large amounts of waste activated sludge (WAS), which mainly consist of recalcitrant microbial cells and particulate organic matter. Though WAS pre-treatment is an effective way to release sludge organic matter for subsequent digestion, information on detailed impacts of the sludge pre-treatment on digestion sludge microbiome remain scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pre-treatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiome could be a unique source to explore microbial dark matter. These results may shed light on future optimization of methanogenic sludge digestion and resource recovery.

Meta-omics analysis revealed structural and metabolic shifts of acidification communities after feeding with thermal hydrolysis pretreated food waste

“…Those compounds reduce the feedstock biodegradability and correspondingly impact microbial communities [11,12]. It was found that the Shannon diversity of microbial communities was significantly decreased after the inclusion of THP during anaerobic digestion [12,19,20], which was potentially due to the sterilization effect of THP on indigenous microbes [21]. The structure of the methanogens' community also showed adaptation to TH pretreated substrate during biogas production.…”

Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT

“…Genome-resolved metagenomics was firstly applied in 2004 from low microbial diversity environment (Tyson et al 2004), followed by a series of initiations such as Earth Microbiome Project (EMP) and the European Nucleotide Archive (ENA) which enabled us to unravel the microorganisms on a global scale (Thompson et al 2017). For example, the latest report from EMP projects revealed more than 52,000 Metagenomic Assembled Genomes (MAGs) on species level (Amid et al 2020, Nayfach et al 2020), consisting a wide range of samples from environments with medium to high level of microbial complexities, such as human (Pasolli et al 2019, Almeida et al 2021), freshwater (Ali et al 2020), marine (Tully et al 2018, Reji et al 2020), engineered environment (Ransom-Jones et al 2017, Liang et al 2020) and soil (Kroeger et al 2018, Nascimento Lemos et al 2020), etc. Such studies implementing genome-resolved metagenomic approaches have largely expanded branches of microorganisms on tree of life (Hug et al 2016).…”

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

“…Shotgun metagenomic sequencing has helped to reveal the diversity of microbial communities in natural habitats [ 15 ] and in engineered environments such as composting [ 1 , 16 ] or sludge digesters [ 17 ]. New methods and computational tools now allow the recovery of metagenome-assembled genomes (MAGs) from complex ecosystems [ 18 – 23 ].…”