Biology subjects

Wu, X.-L.

Publications and source records attributed to Wu, X.-L..

10 recordsLinked to original sources

bioRxiv2025

Metagenomics reveals potential interactions between CPR bacteria and their phages in groundwater ecosystems

Candidate phyla radiation (CPR) is a vast lineage composed of bacteria with ultra-small size, streamlined genomes, notable defects in core metabolic potential and symbiotic lifestyle, which are widely detected in groundwater ecosystems. Increasing attention has focused on the physiological and ecological significance of CPR bacteria, while the potential interactions between CPR bacteria and their phages still need more exploration. Here, we collected 82 groundwater metagenomic datasets and further derived 1,162 phages with the potential to infect 2,439 groundwater CPR metagenome-assembled genomes (MAGs). Notably, the groundwater CPR MAGs were predominantly infected by temperate phages, and the abundance profiles of phage-CPR interactions in groundwater ecosystems supported the Piggybacking the Winner (PtW) hypothesis, suggesting that lysogenic infection was a strategy co-evolved by CPR bacteria and their phages in groundwater ecosystems. Intriguingly, the groundwater CPR phages encoded various auxiliary metabolic genes (AMGs) that might promote symbiotic lifestyle and metabolic potential of host CPR MAGs. These included AMGs associated with concanavalin A-like lectin/glucanases superfamily and O-Antigen nucleotide sugar biosynthesis, which could enhance surface adhesion of host CPR MAGs. Moreover, AMGs related to ABC transport system and P-type transporter could strengthen metabolic exchange and uptake of essential nutrients from surroundings. Additionally, AMGs involved in various metabolic pathways might alleviate metabolic deficiencies in host CPR MAGs. This study elucidated the mechanisms of phage-CPR interactions and the potential roles of phages in modulating the physiology and ecology of CPR bacteria within groundwater ecosystems.

microbiology↗

bioRxiv2023

The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities

In microbial systems, a metabolic pathway can be either completed by one autonomous population or alternatively be distributed among a consortium performing metabolic division of labor (MDOL), where several specialized populations cooperate to complete the pathway. MDOL facilitates the systems function by reducing the metabolic burden; however, it may also hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the metabolic efficiency of a community is influenced by trade-offs between the metabolic specialization and versatility of individuals, with the latter potentially introducing metabolic redundancy into the community. However, it remains unclear how metabolic specialization and versatility of the individuals involved can be controlled in order to optimize the function of the community. In this study, we deconstructed the metabolic pathway of naphthalene degradation into four specialized steps and introduced them individually or combinatorically into different strains, with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia with varying levels of metabolic redundancy and tested their naphthalene degradation efficiency. We found that 74 consortia possessing metabolic redundancy exhibited higher degradation efficiency than both the autonomous population and the rigorous MDOL community. Quantitative modeling derived from our experiments provides general strategies for identifying the most effective MDOL consortium with functional redundancy (MCFR) from a range of possible MCFRs. Our large-scale genomic analysis suggests that natural communities for hydrocarbon degradation are mostly functionally redundant. In summary, our study provides critical insights into the engineering of high-performance microbial systems and explains why functional redundancy is prevalent in natural microbial communities.

microbiology↗

bioRxiv2023

Keystone taxa responsible for the microbial community stability and performance of activated sludges

BackgroundThe functions and stability of a community depend on its species, which form complex interaction networks. The keystone taxa identified by network analysis are generally considered to play a vital role in the structure and function of microbial communities, but there is no uniformly accepted operational definition of such taxa. Further, what species and how they affect the communitys stability and function are still poorly understood. MethodsTo solve this problem, we performed a large-scale network analysis of the microbial communities residing in 1186 activated sludge (AS) samples. ResultsWe found that the AS co-occurrence network is a typical scale-free network. While most taxa in the AS co-occurrence network have little association, there are still a small number of taxa that are strongly interconnected. We defined a group of keystone taxa that have an important impact on network stability. Further analysis results indicate that the communities harboring the keystone taxa maintain higher stability, but these communities possess lower pollutant removal rates. In addition, we found that keystone taxa were more likely to appear in samples with lower sludge load. ConclusionsOur work identified the keystone taxa that maintain the stability of microbial communities in the AS systems but at the cost of reducing their function. This finding shed light on the relationship between composition, stability, and function within microbial communities. It also provides novel insights into manipulating the function of microbial communities by modifying their composition.

ecology↗

bioRxiv2022

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks

Activated sludge (AS) of wastewater treatment plants (WWTP) is one of the worlds largest artificial microbial ecosystems and the microbial community of the AS system is closely related to WWTP performance. However, how to predict its community structure is still unclear. Here, we used artificial neural networks (ANN) to predict the microbial compositions of AS systems collected from WWTPs located worldwide. We demonstrated that the microbial compositions of AS systems are predictable using our approach. The predictive accuracy R21:1 of Shannon-Wiener index reached 60.42%, and the average R21:1 of ASVs appearing in at least 10% of samples (ASVs>10%) and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs>10% was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using an ANN model, with the R21:1 ranging from 32.62% to 56.81%. Furthermore, we found that industry wastewater source (IndConInf) had good predictive abilities, although its correlation with ASVs>10% in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlight by the ANN model. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure.

bioinformatics↗

bioRxiv2021

Type IV pilus shapes a "bubble-jet" pattern opposing spatial intermixing of two interacting bacterial populations

Microbes are social organisms that commonly live in sessile biofilms. Spatial patterns of populations within biofilms can be an important determinant of community-level properties. The best-studied characteristics of spatial patterns is spatial intermixing of different populations. The specific levels of spatial intermixing critically contribute to how the dynamics and functioning of such communities are governed. However, the precise factors that determine spatial patterns and intermixing remain unclear. Here, we investigated the spatial patterning and intermixing of an engineered synthetic consortium composed of two Pseudomonas stutzeri strains that degrade salicylate via metabolic cross-feeding. We found that the consortium self-organizes across space to form a previously unreported spatial pattern (referred to here as a bubble-jet pattern) that exhibits a low level of intermixing. Interestingly, when the genes encoding for type IV pili were deleted from both strains, a highly intermixed spatial pattern developed and increased the productivity of the entire community. The intermixed pattern was maintained in a robust manner across a wide range of initial ratios between the two strains. Our findings show that the type IV pilus plays a role in mitigating spatial intermixing of different populations in surface-attached microbial communities, with consequences for governing community-level properties. These insights provide tangible clues for the engineering of synthetic microbial systems that perform highly in spatially structured environments. ImportanceWhen growing on surfaces, multi-species microbial communities form biofilms that exhibit intriguing spatial patterns. These patterns can significantly affect the overall properties of the community, such as enabling otherwise impermissible metabolic functions to occur, as well as driving the evolutionary and ecological processes acting on communities. The development of these patterns is affected by several drivers, including cell-cell interactions, nutrient levels, density of founding cells and surface properties. The type IV pilus is commonly found to mediate surface-associated behaviors of microorganism, but its role on pattern formation within microbial communities is unclear. Here we report that in a cross-feeding consortium, the type IV pilus affects the spatial intermixing of interacting populations involved in pattern formation, and ultimately influences overall community productivity and robustness. This novel insight assists our understanding of the ecological processes of surface-attached microbial communities and suggests a potential strategy to engineer high-performance synthetic microbial communities.

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

Successful microbial colonization of space using an anti-aggregation strategy

Many organisms live in habitats with limited nutrients or space, competition for these resources is ubiquitous. Although spatial factors related to populations manner of colonizing space influences its success in spatial competition, what these factors are and to what extent they influence the outcome remains under-explored. Here, we applied a simulated competitive model to explore the spatial factors affecting outcomes of competition for space. By quantifying spatial factors using Space Accessibility, we show that colonizing space in an anti-aggregation manner contributes to microbial competitive success. We also find that the competitive edge derived from being anti-aggregation in colonizing space, which results in a higher Space Accessibility, neutralizes the disadvantage arising from either lower growth rate or lower initial abundance. These findings shed light on the role of space colonization manners on maintaining biodiversity within ecosystems and provide novel insights critical for understanding how competition for space drives evolutionary innovation.

ecology↗

bioRxiv2020

Substrate traits govern the assembly and spatial organization of microbial community engaged in metabolic division of labor

Metabolic division of labor (MDOL) is widespread in nature, whereby a complex metabolic pathway is shared between different strains within a community for mutual benefit. However, little is known about how the mutual interactions in the microbial community engaged in MDOL are regulated. We hypothesized that when degradation of an organic compound is carried out via MDOL, the substrate traits (i.e., concentration and its toxicity) modulate the benefit allocation between the two microbial populations, thus affecting the structure of this community. We tested this hypothesis by combining mathematical modelling with experiments using engineered synthetic microbial consortia. Numerous modelling analyses suggested that the proportion of the population executing the first metabolic step can be simply estimated by Monod-like formulas governed by substrate traits. The model and the proposed formula quantitatively predicted the structure of our synthetic consortia composed of two strains degrading salicylate through MDOL. Individual-based modelling and colony pattern formation assays further indicated that our rule is also applicable to estimating community structure in spatially structured environments. Our results demonstrate that the structure of the microbial communities can be quantitatively predicted from simple environmental factors, such as substrate concentration and its toxicity, which provides novel perspectives on understanding the assembly of natural communities, as well as insights into how to manage artificial microbial systems.

microbiology↗

bioRxiv2020

Sessile bacterium unlocks ability of surface motility through mutualistic interspecies interaction

In addition to their common planktonic lifestyle, bacteria frequently live in surface-associated habitats. Surface motility is essential for exploring these habitats for food sources. However, many bacteria are found on surfaces, even though they lack features required for migrating along surfaces. How these canonical non-motile bacteria adapt to the environmental fluctuations on surfaces remains unknown. Recently, several cases of interspecies interaction were reported that induce surface motility of non-motile bacteria either by using hitchhiking strategies or through social spreading mechanisms. Here, we report a previously unknown mechanism for interaction-dependent surface motility of the canonical non-motile bacterium, Dietzia sp. DQ12-45-1b, which is induced by interaction with a dimorphic prosthecate bacterium, Glycocaulis alkaliphilus 6B-8T. Dietzia cells exhibits "sliding"-like motility in an area where the strain Glycocaulis cells was pre-colonized with a sufficient density. Furthermore, we show that biosurfactants play a critical role in inducing the surface motility of Dietzia cells. Our analysis also demonstrates that Dietzia degrade n-alkanes and provide Glycocaulis with the resulting metabolites for survival, which in turn enabled directional migration of Dietzia towards nutrients in the environment. Such interaction-dependent migration was also found between Dietzia and Glycocaulis strains isolated from other habitats, suggesting that this mutualistic relationship ubiquitously occurs in natural environments. In conclusion, we propose a novel model for such a win-win strategy, whereby non-motile bacteria pay metabolites to dimorphic prosthecate bacteria in return for migrating to reach environments otherwise inaccessible. We propose that this mechanism represents a common strategy for canonically non-motile bacteria living on a surface. ImportanceCell motility provides a selective advantage for bacteria searching for nutrients. While a large body of evidence exists for how motile bacteria migrate on surface by virtue of different ways of motility, fewer studies concerned about how canonical non-motile bacteria adapted to those surface-associated habitats. Recent reports have proposed that interactions with other bacteria trigger the movement of those sessile bacteria. However, these interactions are limited to hitchhiking or social spreading modes. Here, we characterized a previously unknown interaction mode between Dietzia and Glycocaulis. This interaction differs from previously described modes, thus advance our limited understanding of how sessile bacteria move on surfaces. We propose that this interaction mode represents a win-win strategy for both strains, and this mode might be widely distributed across diverse environments. These novel insights should greatly assist in understanding the mechanisms responsible for the cellular interplay between microbes in complex microbiomes.

microbiology↗

bioRxiv2018

Mono-homologous linear DNA recombination by the non-homologous end-joining pathway as a novel and simple gene inactivation method: a proof of concept study in Dietzia sp. DQ12-45-1b

Non-homologous end-joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo. Herein, we established a proof-of-concept mono-homologous linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate non-replicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA mono homolog to the sequence in chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, the Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for non-model microorganisms.\n\nIMPORTANCEThe non-model gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knockout eleven genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the mono-homologous linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse non-model prokaryotic organisms.

microbiology↗