Biology subjects

Zhao, H.-P.

Publications and source records attributed to Zhao, H.-P..

3 recordsLinked to original sources

bioRxiv2025

Metagenomics and qPCR analysis of aerobic metabolic TCE degrading bacteria

Chloroethenes are common groundwater contaminants. While they were initially considered non-biodegradable, different pathways for both, anaerobic and aerobic degradation have been discovered over the last 40 years. Anaerobic reductive dechlorination of tetrachloroethene and trichloroethene (TCE) leads to the formation and possible accumulation of the toxic intermediate products, dichloroethene (DCE) and vinyl chloride (VC). In contrast, aerobic metabolic processes result in mineralization of the contaminants without the formation of stable intermediates. Therefore, productive aerobic degradation processes can have a considerable advantage, depending on site conditions and chloroethene molecule. The potential for aerobic degradation processes can be assessed by molecular biological analysis. In our study, aerobic metabolic TCE enrichment cultures, bioaugmented groundwater, and a microcosm with intrinsic aerobic TCE degradation potential were analyzed. Amplicon sequencing and shotgun metagenomics were used to identify the Rhodocyclaceae bacterial family in all samples, as well as functional gene sequences, which were relatives of monooxygenases and dehalogenases. Based on these sequencing data, qPCR detection methods for TCE assimilating Rhodocyclaceae (Rho) as well as for different functional genes that were associated with monooxygenases (moABC) and haloacid dehalogenases like hydrolases (hdlh) have been established. The specificity of the qPCR methods was demonstrated with a variety of environmental samples and different chloroethene degrading bacterial cultures. The new metagenomic insights and qPCR methods facilitate the assessment of biodegradation potential and monitoring of aerobic metabolic TCE degradation at contaminated sites. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/667672v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@10b51feorg.highwire.dtl.DTLVardef@3414e0org.highwire.dtl.DTLVardef@14694ccorg.highwire.dtl.DTLVardef@d2e4e9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIRhodocyclaceae bacteria were identified in all aerobic TCE degrading samples C_LIO_LIFunctional monooxygenase and dehalogenase like genes were detected C_LIO_LIqPCR methods for monitoring of aerobic metabolic TCE degradation were developed C_LIO_LISpecificity of qPCR methods was shown with different aerobic chloroethene degrading cultures and environmental samples C_LI

microbiology↗

bioRxiv2023

Host signature as major driver of root and rhizosphere core microbiomes that differently affect plant functional traits

BackgroundPlant can evolve with a core root microbiome that maintains essential functions for host performance. However, the relative importance of plant traits and soil factors on the structure, assembly, co-occurrence networks of the core root microbiomes and their relevance for plant characteristics remain elusive. Here, we investigated how plant species identity and soil environment affect the core bacterial communities in the bulk soil, rhizosphere and root endosphere of four plants with a gradient of Cd/Zn accumulation capacity under controlled and field environments. We further tested on the role of the core bacterial isolates in plant growth and accumulation of metal and nutrients. ResultsWe identified root compartment and plant species rather than environmental parameters as the primary driver of Cd-accumulator root microbiome. Stochastic processes were more important for the assembly of endosphere generalists (58.5%) than rhizosphere counterparts (45.2%), indicating that generalists were more robust to environmental changes. Increasing host selection from epiphytes to endophytes resulted in the existence of the endosphere and rhizosphere generalist core microbiota common to different plants under varying growth environments, highlighting that shared environmental and physiological features of host plants are decisive for core microbiome establishment. Further, endophytic core microbiota conferred greater biotic connectivity within networks and was more important predictors of plant metal accumulation, whereas the rhizosphere cores were more closely linked to plant biomass and nutrient status. The divergent functions of rhizosphere and endosphere core microbes on plant characteristics were also validated by inoculating the synthetic communities comprising bacterial isolates belonging to the core microbiota. ConclusionThis study indicated the pivotal role of plant trait in the assembly of conserved and functionally important core microbiome common to different Cd-accumulators, which brings us closer to manipulating the persistent root microbial associations to accelerate the rejuvenation of metal-disturbed soils through host genetics.

microbiology↗

bioRxiv2021

A mixed blessing of viruses in wastewater treatment plants

Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. in silico Predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The former group of virus-encoded genes (i.e. AMGs) may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, the latter group (i.e. ARGs) would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.

microbiology↗