Biology subjects

Tang, Y.-Q.

Publications and source records attributed to Tang, Y.-Q..

3 recordsLinked to original sources

bioRxiv2024

Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoates-producing mixed microbial cultures via meta-omics study

The dynamics of the structure of polyhydroxyalkanoates-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, we enriched five PHA-MMCs and sampled temporally to study the interactions between phage and prokaryotic members by combining metagenomics and metatranscriptomics. 963 metagenome-assemble genomes and 4294 phage operational taxonomic units were assembled from bulk metagenomic data. There were complex interactions between the phages in Casadabanvirus and Unclassified Hendrixvirinae and the dominant species in Azomonas, Paracoccus, Thauera and Breundimonas. The dynamic change of the structure of phage and prokaryotic communities were remarkably consistent. Further structural equation modeling analysis showed that phage communities could significantly affect the activity and community structure of prokaryotic microorganisms. In addition, seven key auxiliary metabolic genes (phaC, fadJ, acs, ackA, phbB, acdAB and fadD) in the PHA synthesis pathway were identified from phage sequences. Importantly, these auxiliary metabolic genes were expressed at the transcriptional level, indicating that they were in an active functional state. This meta-analysis provides the first catalog of phages in PHA-MMCs and the auxiliary metabolic genes they carry, as well as how they play a role in the dynamic changes of prokaryotic communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of artificial open microbial systems. ImportanceThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (MMCs), with extremely low cost, has the potential for expanded production. However, there is a gap of understanding of the dynamics of dominant species in MMCs to better control community structure. Our results demonstrate for the first time the impact of phages on the structure of prokaryotic communities in the MMCs. There are complex interactions between the PHA producers (Azomonas, Paracoccus, Thauera) and phages (Casadabanvirus and Unclassified Hendrixvirinae). Phage communities can negatively regulate the activity and structure of prokaryotic communities. In addition, the auxiliary metabolic genes in the PHA synthesis pathways carried by phages may promote the PHA synthesis ability of prokaryotic members. This study highlights the impact of phages on prokaryotic community structure, suggesting that phages have the potential to become a tool for better controlling the microbial community structure of PHA-MMCs.

microbiology↗

bioRxiv2021

Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor

Metabolic division of labor (MDOL) is commonly observed in microbial communities, where a metabolic pathway is sequentially implemented by several members similar to an assembly line. Uncovering the assembly rules of the community engaged in MDOL is crucial for understanding its ecological contribution, as well as for engineering high-performance microbial communities. To investigate the assembly of the community engaged in MDOL, we combined mathematical modelling with experimentations using synthetic microbial consortia. We built a theoretical framework predict the assembly of MDOL system, and derived a simple rule: to maintain co-existence of the MDOL members, the populations responsible for former steps should hold a growth advantage (m) over the private benefit (n) of the population responsible for last step, and the steady-state frequency of the last population is determined by the quotient of n and m. Our experiments further indicated that our theoretical framework accurately predicted the stability and assembly of our engineered synthetic consortia that degrade naphthalene through two-step or multi-step MDOL. Our results demonstrate that the assembly of microbial community engaged in MDOL is determined by a limited number of parameters. This quantitative understanding provides novel insights on designing and managing stable microbial systems to address grand challenges facing human society in agriculture, degradation of the environment, and human health.

microbiology↗

bioRxiv2021

Chasing the metabolism of novel syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats

BackgroundAcetate is the major intermediate of anaerobic digestion of organic waste to CH4. In anaerobic methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or a syntrophic degradation by a syntrophy of acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB, as well as the mechanisms of their interactions with methanogenic partners remain poorly understood. ResultsIn this study, we successfully enriched previously unknown SAOB by operating continuous thermophilic anaerobic chemostats fed with acetate, propionate, butyrate, or isovalerate as the sole carbon and energy source. They represent novel clades belonging to Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. In these SAOB, acetate is degraded through reverse Wood-Ljungdahl pathway or an alternative pathway mediated by the glycine cleavage system, while the SAOB possessing the latter pathway dominated the bacterial community. Moreover, H2 is the major product of the acetate degradation by these SAOB, which is mediated by [FeFe]-type electron-confurcating hydrogenases, formate dehydrogenases, and NADPH reoxidation complexes. We also identified the methanogen partner of these SAOB in acetate-fed chemostat, Methanosarcina thermophila, which highly expressed genes for CO2-reducing methanogenesis and hydrogenases to supportively consuming H2 at transcriptional level. Finally, our bioinformatical analyses further suggested that these previously unknown syntrophic lineages were prevalent and might play critical roles in thermophilic methanogenic reactors. ConclusionThis study expands our understanding on the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders, and presents novel insights on how they interact with their methanogens partner. These knowledges strengthen our awareness on the important role of SAO in thermophilic methanogenesis and may be applied to manage microbial community to improve the performance and efficiency of anaerobic digestion.

microbiology↗