Biology subjects

Nie, Y.

Publications and source records attributed to Nie, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Diversity and distribution of viruses inhabiting the oil reservoirs

Oil reservoirs, being one of the most significant subsurface repositories of energy and carbon, have long hosted diverse microorganisms affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assembled an extensive catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7,229 prokaryotic genomes and 6,218 viral genomes from 182 oil reservoir metagenomes, respectively. Based on sequence clustering we identified 3,886 Operational Taxonomic Units (vOTUs) approximately at species level, 94.80% of which were not found in any other environments. The results showed that viruses were widely distributed in oil reservoirs, and oil reservoirs contain a significant number of unique and unexplored viruses. We also constructed a catalogue of 322,060 viral gene clusters including 105 virus-encoded putative auxiliary metabolic genes (AMGs) that participate in host metabolism and adaptation to the environment. Furthermore, our investigation has yielded a total of 7,197 putative virus-host pairs based on CRISPR and tRNA profiles. Viruses within oil reservoirs profoundly infected bacterial Actinobacteriota, Desulfobacterota, as well as archaeal Halobacteriota and Methanobacteriota. Combined microcosm enrichment experiments and bioinformatics analysis, we validated the ecological roles of viruses in regulating the community structure of sulfate reduction microorganisms, primarily through the predation of virulent viruses. Collectively, these findings have unveiled a rich diversity of novel viruses and their ecological functions within oil reservoirs. This study provides a comprehensive understanding of the role of viral communities in the biogeochemical cycle of the deep biosphere. It also facilitates microbial applications aimed at addressing challenges related to fossil-fuel production and carbon emissions in the petroleum industry.

microbiology↗

bioRxiv2023

The evolution of autonomy from two cooperative specialists in the fluctuating environments

From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. For example, it remains unclear whether and how a group of cooperative specialists can evolve into an autonomous organism. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and came to dominate the microbial community. This evolutionary transition was driven by the horizontal gene transfer between the two specialists. However, this evolution was exclusively observed to occur in the fluctuating environment supplied with either naphthalene or pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerts selective pressure that favors the expansion of autonomous genotypes but was associated with both low cell density and low coexistence levels. In contrast, the pyruvate-supplying environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of horizontal gene transfer. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that mutualistic cooperation can evolve into autonomous organisms through direct genetic exchange under specific conditions, including the alternation of mutualism and competition in fluctuating environments in a manner frequently occurring in nature.

evolutionary biology↗

bioRxiv2023

Preserved striatal innervation and motor function despite severe loss of nigral dopamine neurons following mitochondrial dysfunction induced by mtDNA mutations

Degeneration of dopamine neurons in the substantia nigra and their striatal axon terminals causes cardinal motor symptoms of Parkinsons disease (PD). In idiopathic cases, high levels of mitochondrial DNA (mtDNA) mutations associated with mitochondrial dysfunction are a central feature of these vulnerable neurons. Here we present a mouse model expressing the K320E-variant of the mitochondrial helicase Twinkle in dopamine neurons, leading to accelerated mtDNA ageing. K320E-TwinkleDaN mice showed normal motor function at 20 months of age, although already [~]70% of nigral dopamine neurons had perished. The remaining neuron population still preserved [~]75% of axon terminals in the dorsal striatum, which enabled normal dopamine release. Transcriptome analysis and viral tracing confirmed compensatory axonal sprouting of surviving nigral dopamine neurons. We conclude that a small population of substantia nigra neurons can adapt to mtDNA mutations and maintain motor control in mice, holding chances for new treatment strategies in PD patients.

neuroscience↗

bioRxiv2023

Levy statistics define anxiety and depression in mice subjected to chronic stress

IntroductionAnxiety and depression are recognized as adaptive responses to external stressors in organisms. Current methods for evaluating anxiety and depression in rodents are both burdensome and stressful. The objective of this investigation is to explore a simplified methodology for identifying stress-induced and stress-free states, as well as anxiety and depression levels, by analyzing the movement patterns of rodents. MethodsTo address this issue, we utilized Levy statistics to examine the movement patterns of stressed rodents and compared them to non-stressed controls. We employed the two-dimensional Kolmogorov-Smirnov test to identify significant differences in the {gamma} and parameters derived from Levy flight (LF) between anxiety, depression, and control mice. Additionally, we employed the support vector machine algorithm to optimize the classification of each group. ResultsOur analysis revealed that stressed mice displayed heavy-tailed distributions of movement velocity in open fields, resembling the movement patterns observed in animal predators searching for scarce food sources in nature. In contrast, non-stressed mice exhibited a normal distribution of speed. Notably, the effectiveness of this methodology in the field of drug discovery was confirmed by the response of stressed mice to fluoxetine, a well-established selective serotonin reuptake inhibitor (SSRI). ConclusionThis study unveils a previously unidentified statistical walking pattern in mice experiencing anxiety and depression. These findings offer a novel and accessible approach for distinguishing between anxiety, depression, and healthy mice. This method provides a one-step gentle approach (free walk in an open field) instead of the traditional multi-step stressful tests.

animal behavior and cognition↗

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

The maize PLASTID TERMINAL OXIDASE (PTOX) gene controls the carotenoid content of kernels.

O_LICarotenoids perform a broad range of important functions in humans; therefore, carotenoid biofortification of maize (Zea mays L.), one of the most highly produced cereal crops worldwide, would have a global impact on human health. C_LIO_LIPLASTID TERMINAL OXIDASE (PTOX) genes play an important role in carotenoid metabolism; however, the possible function of PTOX in carotenoid biosynthesis in maize has not yet been explored. In this study, we identified the maize PTOX gene ZmPTOX1 by forward genetic screening. C_LIO_LIWhile most higher plant species possess a single copy of the PTOX gene, maize carries two tandemly duplicated copies of ZmPTOX. Characterization of Zmptox1 mutants revealed that disrupting one copy of ZmPTOX1 was enough to impair carotenoid biosynthesis, indicating that ZmPTOX1 is essential for carotenoid biosynthesis in maize kernels. Remarkably, overexpression of ZmPTOX1 significantly improved the content of carotenoids, especially {beta}-carotene (provitamin A), which was increased by ~3-fold, in maize kernels. C_LIO_LIOverall, our study shows that ZmPTOX1 plays a crucial role in carotenoid biosynthesis in maize kernels and suggests that fine-tuning the expression of this gene could improve the nutritional value of cereal grains. C_LI

plant biology↗

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↗

bioRxiv2023

High immigration rates critical for establishing emigration-driven diversity in microbial communities

Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. While microbial dispersal (including the emigration and immigration process) constitutes an important ecological process, the coupling effects of dispersal and microbial competition in microbial diversity are poorly understood. Here, we investigated how microbial dispersal affects the diversity of microbial communities in the presence of inter-species competition, using a generalized Lotka-Volterra model in combination with experimental investigations. Our model shows that emigration reduces the diversity induced by immigration at low immigration rates. We surprisingly find that it increases the diversity of the community when the immigration rates cross a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species, and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using cocultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral exists over a wide range of species pool sizes, growth rates, and interspecies interactions, and decreases with the increasing of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on diversity of natural communities.

ecology↗

bioRxiv2022

Integrative multispecies omics reveals a hierarchy of cold-responsive network launched by circadian components in rosids

Elucidating regulators and molecular mechanisms underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold-stress responses. Previous studies were mainly conducted on single species and whether the regulators and mechanisms are conserved across different species remains elusive. Here, we selected three species that diverged at early evolution of rosids (93-115 million years ago) and integrated phylotranscriptome and ChIP/DAP-seq datasets to identify cold-responsive regulators and their regulatory networks. First, we found over ten thousand cold-responsive genes including differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, genes encoding a set of transcription factors (TFs) (AP2/ERF, MYB, WRKY, NAC, etc.) and RNA binding proteins (RBPs) (Ribosomal, RRM, DEAD, Helicase_C, etc.) are conserved in cold responses in rosids. Compared to TFs, RBPs show a delayed cold-responsive pattern, likely suggesting a hierarchical regulation of DEGs and DASGs. Between DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups and interestingly, pathway analysis on each dataset of DEGs, DASGs, and DE-DASGs coincidently shows an enrichment of circadian rhythm. Evidentially, many circadian components are cold-regulated at both transcriptional and post-transcriptional levels. Moreover, we reasoned 226 cold-responsive genes regulated by at least two of five circadian components (CCA1, LHY, RV4, RVE8, and RVE7) in rosids. Finally, we unveiled a conserved hierarchical network in dynamic transcriptional and post-transcriptional regulation of cold-responsive genes launched by circadian components in rosids. Together, our results provide insights into core regulators and mechanisms underlying cold-responsive regulatory network across rosids, despite a long evolutionary history.

plant biology↗

bioRxiv2022

Optical Metabolic Imaging Uncovers Sex- and Diet-dependent Lipid Changes in Aging Drosophila Brain

Aging is associated with progressive declines in physiological integrity and functions alongside increases in vulnerability to develop a number of diseases. The brain regulates sensory and motor functions as well as endocrine functions, and age-associated changes in brain are likely prerequisite for the organismal aging. Lipid metabolism has been associated with brain aging, which could be easily intervened by diets and lifestyles. However, the underlying mechanism through which brain lipid metabolism is regulated by diet during aging is elusive. Using stimulated Raman scattering (SRS) imaging combined with deuterium water (D2O) labeling, we visualized that lipid metabolic activities were changed by diet manipulation in aging Drosophila brain. Furthermore, we illuminated that insulin/IGF-1 signaling (IIS) pathway mediates the transformation of brain lipid metabolic changes in both an aging- and a diet-dependent manner. The lipid droplets (LDs) in the brain gradually became inert in both activities of lipid synthesis and mobilization with aging. High sugar diets enhanced the metabolic activity through promoting lipogenesis while dietary restriction increased the metabolic activity in both lipogenesis and lipolysis in brain LDs. However, these effects were impaired in both chico1/+ and dfoxo Drosophila mutants. We also observed that old chico1/+ brains maintained high metabolic activities, whilst the aged dfoxo brains acted exactly the opposite. More interestingly, the sexual dimorphism in brain lipid metabolism was impaired under diet regulation in both chico1/+ and dfoxo mutants. Locally reduced IIS activity in glial cells can mimic the systemic changes in systematic IIS mutants to maintain lipogenesis and lipolysis in aged brains, providing mechanistic insight into the anti-aging effects of IIS pathway. Our results highlight the manipulation of glia-specific IIS activity as a promising strategy in anti-aging treatments.

bioengineering↗

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↗

bioRxiv2022

lncRNA-WAL Promotes Aggressiveness of Triple-Negative Breast Cancer via inducing β-Catenin nuclear translocation.

Because of its insensitive to existing radiotherapy, chemotherapy and targeted treatments, Triple-negative breast cancer (TNBC) remains a great challenge to overcome. More and more evidence has indicated abnormal wnt/{beta}-catenin pathway activation in TNBC but not luminal or her2+ breast cancer, and lncRNAs play a key role in a variety of cancers. Through lncRNA microarray profiling between Activated and inactivated Wnt/{beta}-catenin pathway of TNBC tissues, lnc-WAL (Wnt/{beta}-catenin associated lncRNA; WAL) was selected as the top up-regulated lncRNA in Wnt/{beta}-catenin pathway activation compared with the inactivation group. RIP-seq was analyzed between {beta}-catenin and IgG groups of, where lnc-WAL could interact with {beta}-catenin. Clinically, increased lnc-WAL in the TNBC tumor tissue was associated with shorter survival. lnc-WAL promoted the EMT, the ability of breast cancer stem cells (BCSC), proliferation, migration and invasion of TNBC cells. Mechanistically, lnc-WAL inhibited {beta}-catenin protein degradation via Axin-mediated phosphorylation at serine 45. Subsequently, {beta}-catenin was accumulated in nuclear and activated the target genes. Importantly, Wnt/{beta}-catenin pathway activation stimulated the transcription of lnc-WAL. These results pointed to a master regulatory role of lnc-WAL/Axin/{beta}-catenin in the malignant progression of TNBC. Our findings provide important clinical translational evidence that lnc-WAL maybe as potential therapeutic target against TNBC.

genetics↗

bioRxiv2022

Neural signals encoded by specific frequencies of closed-loop electrical stimulation structurally and functionally reconstruct spinal sensorimotor circuits after spinal cord injury

Epidural electrical stimulation restores locomotion in animals and humans with spinal cord injury (SCI). However, the coding rules underlying electrical stimulation remain poorly understood, which has greatly limited the application of such electrical neuromodulation techniques in SCI clinical treatment. To elucidate the coding rules of electrical stimulation on spinal sensorimotor circuit reconstruction after complete SCI, we initially developed a spinal-muscle closed-loop stimulation protocol to mimic feedforward and feedback electrical signals in spinal sensorimotor circuits. Afterwards, using methods of sensorimotor function evaluation, neural circuit tracing and neural signal recording, we discovered a unique stimulus frequency of 10-20 Hz under closed-loop conditions was required for structural and functional reconstruction of spinal sensorimotor circuits. The single-cell transcriptome analysis of activated motoneurons characterized molecular networks involved in spinal sensorimotor circuit reconstruction. This study provides insights into neural signal decoding during spinal sensorimotor circuit reconstruction, and indicates a technological approach for the clinical treatment of SCI.

neuroscience↗

bioRxiv2022

Single-agent Foxo1 inhibition normalizes glycemia and induces gut β-like cells in streptozotocin-diabetic mice

Insulin treatment remains the sole effective intervention for Type 1 Diabetes. Here, we investigated the therapeutic potential of converting intestinal epithelial cells to insulin-producing, glucose-responsive {beta}-like cells by targeted inhibition of Foxo1. We have shown that this can be achieved by genetic ablation in gut Neurogenin3 progenitors, adenoviral or shRNA-mediated inhibition in human gut organoids, and chemical inhibition in Akita mice, a model of insulin-deficient diabetes. In the present study, we provide evidence that two novel Foxo1 inhibitors, FBT432 and FBT374 have glucose-lowering and gut {beta}-like cell-inducing properties in mice rendered insulin-deficient by administration of streptozotocin. FBT432 is also highly effective in combination with a Notch inhibitor in this model. The data add to a growing body of evidence suggesting that Foxo1 inhibition be pursued as an alternative treatment to insulin administration in diabetes.

pharmacology and toxicology↗

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↗

bioRxiv2021

EpicPCR-Directed Cultivation of a Candidatus Saccharibacteria Symbiont Reveals a Type IV Pili-dependent Epibiotic Lifestyle

Candidate phyla radiations (CPR), accounting for a major microbial supergroup with remarkably small genomes and reduced sizes, are widely distributed yet mostly uncultured. Limited culture and its obligate reliance upon other bacteria hindered investigation of their lifestyles. In this work we isolated a CPR bacterium, TM7i, with its host Leucobacter aridocollis J1, by combination of Emulsion, Paired Isolation and Concatenation PCR (epicPCR) detection and filtrate co-culture. Genomic profiling of TM7 genomes and microscopic investigation of TM7i-J1 symbiosis suggest the conservation of type IV pili and a pili-dependent lifestyle of TM7. Further, we observed twitching motility of TM7i mediated by pili and its role played in the interaction with its host. Our results shed a light on the lifestyle about this enigmatic bacterial radiation, which may also be adopted by other CPR organisms. The epicPCR-directed isolation method underlines high efficiency of CPR bacteria isolation and thus may be used in other symbiotic or epibiotic microorganisms.

microbiology↗