Li-Li Han

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia ☆

UNLABELLED The effluents from wastewater treatment plants have been recognized as a significant environmental reservoir of antibiotics and antibiotic resistance genes (ARGs). Reclaimed water irrigation (RWI) is increasingly used as a practical solution for combating water scarcity in arid and semiarid regions, however, impacts of RWI on the patterns of ARGs and the soil bacterial community remain unclear. Here, we used high-throughput quantitative PCR and terminal restriction fragment length polymorphism techniques to compare the diversity, abundance and composition of a broad-spectrum of ARGs and total bacteria in 12 urban parks with and without RWI in Victoria, Australia. A total of 40 unique ARGs were detected across all park soils, with genes conferring resistance to β-lactam being the most prevalent ARG type. The total numbers and the fold changes of the detected ARGs were significantly increased by RWI, and marked shifts in ARG patterns were also observed in urban parks with RWI compared to those without RWI. The changes in ARG patterns were paralleled by a significant effect of RWI on the bacterial community structure and a co-occurrence pattern of the detected ARG types. There were significant and positive correlations between the fold changes of the integrase intI1 gene and two β-lactam resistance genes (KPC and IMP-2 groups), but no significant impacts of RWI on the abundances of intI1 and the transposase tnpA gene were found, indicating that RWI did not improve the potential for horizontal gene transfer of soil ARGs. Taken together, our findings suggested that irrigation of urban parks with reclaimed water could influence the abundance, diversity, and compositions of a wide variety of soil ARGs of clinical relevance. ONE-SENTENCE SUMMARY Irrigation of urban parks with treated wastewater significantly increased the abundance and diversity of various antibiotic resistance genes, but did not significantly enhance their potential for horizontal gene transfer.

Influence of rice straw amendment on mercury methylation and nitrification in paddy soils.

UNLABELLED Currently, rice straw return in place of burning is becoming more intensive in China than observed previously. However, little is known on the effect of returned rice straw on mercury (Hg) methylation and microbial activity in contaminated paddy fields. Here, we conduct a microcosm experiment to evaluate the effect of rice straw amendment on the Hg methylation and potential nitrification in two paddy soils with distinct Hg levels. Our results show that amended rice straw enhanced Hg methylation for relatively high Hg content soil, but not for low Hg soil, spiking the same additional fresh Hg. methylmercury (MeHg) concentration was significantly correlated to the dissolved organic carbon (DOC) content and relative abundance of dominant microbes associated with Hg methylation. Similarly, amended rice straw was found to only enhance the potential nitrification rate in soil with relatively high Hg content. These findings provide evidence that amended rice straw differentially modulates Hg methylation and nitrification in Hg contaminated soils possibly resulting from different characteristics in the soil microbial community. This highlights that caution should be taken when returning rice straw to contaminated paddy fields, as this practice may increase the risk of more MeHg production. MAIN FINDING Rice straw amendment enhanced both Hg methylation and nitrification potential in the relatively high, but not low, Hg soil.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N2O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N2O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N2O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N2O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N2O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N2O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.

Temporal dynamics of fungal communities in soybean rhizosphere

PurposeMany biotic and abiotic factors influence the structural and functional diversity of microbial communities in the rhizosphere. This study aimed to understand the dynamics of fungal community in the soybean rhizosphere during soybean growth and directly compare the influence of abiotic and biotic factors in shaping the fungal communities across different growth periods.Materials and methodsHigh-throughput sequencing based on internal transcribed spacer (ITS) region, quantitative PCR, and statistical analysis approaches were used to measure the fungal community structure, abundance, and dynamic changes of 63 rhizosphere soil samples which were taken from different fertilization regimes and rhizobium inoculation treatments during three soybean growth stages.Results and discussionAmong the taxa examined, more than 16 fungal classes were detected from the 21 soil samples. Sordariomycetes was the most abundant class, followed by Dothideomycetes, Agaricomycetes, and Eurotiomycetes. Soybean growth stage was the most important factor determining the diversity patterns of the fungal communities. Fungal community diversity was closely related to the base-fertilizer application, and fungal community richness was associated with rhizobium inoculation. Beta diversity of the fungal community based on the Bray-Curtis distance was significantly related to plant growth stage. Network analysis showed that mutual cooperation among fungal taxa became more intimate during the plant growth.ConclusionsCompared with edaphic properties, plant growth stage was the dominant factor in determining soil fungal community dynamics. Base-fertilizer and rhizobium inoculation affected the alpha diversity of the soil fungi.

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.

Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China

A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China

PurposeViruses are the most abundant biological entities and play significant biological roles in marine system. However, little is known about their biodiversity in mud volcanic soil, which is salty and covered with emitting sludge. In this study, we report metagenomic analysis results of viral community composition and function from the Dushanzi mud volcanic soil (named NHS) in Xinjiang, China, and provide a comparative analysis with other environmental types.Materials and methodsWe utilized metagenomes to obtain the virus data and carried out viral automatic phylogenetic and functional analyses by the metagenomics analysis server. After assembling by metaSPAdes, scaffolds were rapidly identified and annotated with the PHAge Search Tool in order to identify new phage genomes.Results and discussionFor the ssDNA viral group, Microviridae were the most abundant viral family, which were above 95%. Other plant viruses (Geminiviridae, Nanoviridae) and animal viruses (Circoviridae, Parvoviridae) were also detected. The majority of viral significant hits belonged to Siphoviridae (80.36%). Phages, which infect bacteria, were widely distributed in the soil sample. There were eight novel viral genomes identified in the NHS virome. The two longest scaffolds were annotated to Pseudomonas aeruginosa phage YMC11 and Acinetobacter baumannii phage LZ35, respectively. Other six new viral genomes were identified as Microviridae. Comparisons of NHS virome with other published viromes revealed that the type of ecosystem mainly drove the viral community structure.ConclusionsThis work provided detailed viral community composition and function information, which supplemented microbial community research on mud volcanoes. Importantly, we also identified eight complete viral genomes in the NHS virome which were obviously different from known viruses.

Unique community structure of viruses in a glacier soil of the Tianshan Mountains, China

PurposeGlaciers of the Tianshan Mountains have been geographically isolated for a long time with little human interference. This study aimed to understand the viral community structures and their ecological functions in a unique glacier soil.Materials and methodsThe abundances of purified virus particles and bacteria in the glacier soil were examined using epifluorescence microscopy and quantitative PCR of the 16S rRNA gene, respectively. Metagenomic analysis was employed to investigate the taxonomic and functional compositions as well as the phylogenetic relationship of the functional genes of the viruses in the glacier soil.Results and discussionA total of eight double-stranded DNA (dsDNA) virus families were identified in the glacier soil, with Siphoviridae, Podoviridae, and Myoviridae being the more abundant families. The diverse dsDNA viruses and few ssDNA and other types of viruses formed the unique community structure of viruses in the Tianshan Mountains glacier soil. The functional genes identified from the virome mainly belonged to phage-related proteins. The phage terminase of Caudovirales presented high diversity, and its amino acid sequences were different from those in other environments.ConclusionsThe results showed a unique viral diversity and taxonomic composition in the glacier soil, which suggests the significant ecological role of Caudovirales in this environment.

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China.

Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0–44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8–93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (≥17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0–5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities.