Binbin Liu

Chinese Academy of Sciences | CAS · Center for Agro-Resources Research

Nitrate (NO3−) accumulation and transport processes in the thick vadose zone affect the evolution of the groundwater NO3− content in intensive agricultural regions. Agricultural land-use change (ALUC), typically accompanied by substantial alterations in nitrogen fertilizer application and irrigation practices, is an important influencing factor. Th...

Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl...

Nitrification, a key step in soil nitrogen cycling, is a biologically mediated process crucial to the ecological environment. However, how nitrifiers drive nitrification under different soil properties and climatic factors at large spatial scales is poorly understood. Here, using metagenomic sequencing and network‐based approaches, we identified ke...

Climate change may lead to adverse effects on agricultural crops, plant microbiomes have the potential to help hosts counteract these effects. While plant–microbe interactions are known to be sensitive to temperature, how warming affects the community composition and functioning of plant microbiomes in most agricultural crops is still unclear. Here...

Nitrous oxide (N2O) pulse emissions are detected in soils subjected to freeze–thaw cycles in both laboratory and field experiments. However, the mechanisms underlying this phenomenon are poorly understood. In this study, a laboratory incubation experiment that included freeze–thaw cycles (FTC), freezing (F) and control (CK) treatments was performed...

Northeast and East China account for ~36% of the Chinese rice cultivation area, yet considerable spatial disparities in nitrogen use efficiency (NUE) existed between these regions. The underlying causes remain poorly understood. Herein, we conducted a case study in two sample sites from the two regions, Wuchang and Changshu, using multi‐scale evide...

Understanding the mechanisms that control seasonal groundwater recharge at local and intermediate scales is critical for understanding contaminant transport. Preferential flow accompanied with intensive and seasonal recharge allows contaminants to migrate rapidly through the unsaturated zones to underlying aquifers. In this study, we investigated t...

• The abundance of N-cycling genes differently responded to NPK application.• Chemical NPK application greatly altered the N-cycling microbial community structure.• Soil acidification was the main driver for the variation in the N-cycling microbial community.• Manure addition was beneficial for stabilizing the N-cycling microbial community.Straw an...

An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant‐soil interactions of the natural mature forest. However, the role of microbial community in tropical AFS remains largely u...

Under the influence of water diversion, the microbial community composition of estuarine waters and sediments might have complex spatiotemporal variations. Microbial interactions with N are significant for lake water quality. Therefore, the largest lake receiving seasonal water diversion in the North China Plain was selected as the study area. Base...

Oxygen (O2) is the most crucial substrate for numerous biochemical processes in plants. Its deprivation is a critical factor that affects plant growth and may lead to death if it lasts for a long time. However, various biotic and abiotic factors cause O2 deprivation, leading to hypoxia and anoxia in plant tissues. To survive under hypoxia and/or an...

Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different...

Concentrated rainfall and water transfer projects result in slight and dramatic increases in flow volume over short periods of time, causing nitrogen recontamination in the water-receiving areas of nitrogen-rich rivers. This study coupled hydrodynamic and biochemical reaction models to construct a model for quantifying diffusive transport and trans...

Denitrifying nitrous oxide (N 2 O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N 2 O emissions in agricultural soils are less understood. Microcosm experiments of two types of Chinese farmland soil were conducted with nitrate (250 mg/kg) and a com...

Globally soil salinity is one of the most devastating environmental stresses affecting agricultural systems and causes huge economic losses each year. High soil salinity causes osmotic stress, nutritional imbalance and ion toxicity to plants and severely affects crop productivity in farming systems. Freezing saline water irrigation and plastic mulc...

Aims The priming effect (PE) on native soil organic matter induced by exogenous carbon addition influences soil carbon and nutrient cycling across the soil depths. Therefore, this study aimed to explore the effects of exogenous glucose-induced PE on native soil organic carbon (SOC) influenced by soil properties across soil depths, weather factors i...

Aims The priming effect (PE) on native soil organic matter induced by exogenous carbon addition influences soil carbon and nutrient cycling across the soil depths. Therefore, this study aimed to explore the effects of exogenous glucose-induced PE on native soil organic carbon (SOC) influenced by soil properties across soil depths, weather factors i...

Plants are either recognized to produce nitrous oxide (N2O) or considered as a medium to transport soil-produced N2O. To date, it is not clear whether in their habitat plants conduit N2O produced in soil or are a natural source. We aimed to understand role of plants in N2O emissions in field conditions. Therefore, rubber plants (Ficus elastica) wer...

PurposeThe excessive use of nitrogen (N) fertilizer in intensive agriculture has increased nitrate leaching into groundwater, but its impacts on N transformation processes and the associated microbial communities in the deep vadose zone remain unclear.Materials and methodsSoil samples from 0–1050 cm depth were collected from a 20-year field experim...

Excessive nitrogen (N) fertilization in agricultural ecosystems strongly affects microbial N-cycling processes in soil. However, a comprehensive understanding of how microorganisms involved in each N transformation process respond to long-term elevated N inputs is lacking. Here, using metagenomic sequencing combined with the direct assembly of N-cy...

Biofilms are the slimy cities some microbes form when they invade a surface. Conventional cleaning products are generally good at breaking up biofilms. But they tend to be harsh on the environment. And while natural products are a good alternative, it takes multiple enzymes to break up the strong polymers that make bacteria stick. But researchers a...

Impacts of manure application on the soil fungal community in agricultural systems have been extensively explored. However, the contribution of manure-sourced exogenous species in shaping soil fungal diversity and community assemblage are still open questions. In this study, fungal communities in soils that received manure with or without chemical...

Soil salinity is one of the most important abiotic stresses limiting plant growth and productivity. The breeding of salt-tolerant wheat cultivars has substantially relieved the adverse effects of salt stress. Complementing these cultivars with growth-promoting microbes has the potential to stimulate and further enhance their salt tolerance. In this...

Background: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms a...

Despite knowing that phytoremediation by salt-tolerant plants is an effective technology for ameliorating saline soils and that microorganisms contribute significantly to plant stress tolerance and soil fertility, we still lack a comprehensive understanding of how microbes respond to the growth of salt-tolerant plants and the subsequent decline in...

Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one...

Background: Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but a...

Pseudomonas songnenensis strain L103 was isolated from a 100-m-deep aquifer in the North China Plain, a heavily nitrogen-fertilized agricultural area. The genome is 4.8 Mb and contains 4,409 protein-coding genes, including a full set of genes ( nar , nir , nor , and nos ) for complete denitrification.

Urease inhibitors are widely used in agricultural soils to reduce nitrogen loss, but their effects on soil microbial communities remain largely unknown. In a microcosm incubation experiment the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) was more effective than hydroquinone (HQ) in inhibiting urease in the studied soil, although both...

Urea is a widely used nitrogen (N) fertilizer in agriculture, but considerable amounts of urea are lost through ammonia volatilization. Soil microbes are major urease producers; however, the impact of urea application on the soil ureolytic microbial community is poorly understood. In this study, the urease activity and the abundance and composition...

Microbial strains and indigenous microbiota in soil slurries have been reported to use electrons from electrodes for nitrate (NO3−) reduction. However, there are few studies confirming this in a soil matrix hitherto. This study investigated if, and how, an electric potential affected NO3− reduction in a soil matrix. The results showed that, compare...

Denitrification allows sustained respiratory metabolism during periods of anoxia, an advantage in soils with frequent anoxic spells. However, the gains may be more than evened out by the energy cost of producing the denitrification machinery, particularly if the anoxic spell is short. This dilemma could explain the evolution of different regulatory...

The continuous use of nitrogen (N) fertilizers to increase soil fertility and crop productivity often results in unexpected environmental effects and N losses through biological processes, such as nitrification and denitrification. In this study, multidisciplinary approaches were employed to assess the effects of N fertilization in a long-term (~20...

Tillage can strongly affect the long-term productivity of an agricultural system by altering the composition and spatial distribution of nutrients and microbial communities. The impact of tillage methods on the vertical distribution of soil microbial communities is not well understood, and the correlation between microbial communities and soil nutr...

Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participa...

Soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, the response of the soil nitrifier and denitrifier communities to climate warming is poorly understood. A long-term field warming experiment has been conducted for 8 years at Luancheng Experimental Farm Station on the North China Plain; we used thi...

Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. Af...

Unlabelled: Accumulating empirical evidence over the last 60 years has shown that the reduction of N2O to N2 is impaired by low soil pH, suggesting that liming of acid soils may reduce N2O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N2O...

Many denitrifying organisms contain the norEF gene cluster, which codes for two proteins that are thought to be involved in denitrification because they are expressed during the reduction of nitrite and nitric oxide. The products of both genes are predicted to be membrane associated, and the norE product is a member of the cytochrome c oxidase subu...

Reactive nitrogen species (RNS), in particular nitric oxide (NO), are toxic to bacteria, and bacteria have mechanisms to allow growth despite this stress. Understanding how bacteria interact with NO is essential to understanding bacterial physiology in many habitats, including pathogenesis; however, many targets of NO and enzymes involved in NO res...

Denitrifiers differ in how they handle the transition from oxic to anoxic respiration, with consequences for NO and N2 O emissions. To enable stringent comparisons we defined parameters to describe denitrification regulatory phenotype (DRP) based on accumulation of NO2 (-) , NO and N2 O, oxic/anoxic growth and transcription of functional genes. Eig...

Thauera species are members of the betaproteobacteria and are most noted for their ability to metabolize aromatic compounds under anoxic conditions. Here, we announce the draft genome sequences of five Thauera strains in an effort to provide further genetic information as a resource for understanding the ecological function of this environmentally...

Eighteen Mesorhizobium strains, obtained from root nodules of woody legumes growing in Ethiopia, were previously shown by multilocus sequence analysis of five housekeeping genes to form three novel genospecies (Degefu et al., 2011). In the present study, the phylogenetic relationship between representative strains of these three genospecies and the...

Denitrifying prokaryotes use NO(x) as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2). Cultured denitrifying prokaryotes show characteristic transient accumulati...

Nitrous oxide (N2O), which is to a large part derived from denitrification in soil, is a major greenhouse gas and was also recently shown to be the single most important ozone-depleting substance. Previous studies demonstrate that the N2O/N2 product ratio of denitrification is strongly dependent on pH, increasing with decreasing soil pH. The mechan...

The acclimated, anaerobic microbial community is an efficient method for indole-containing wastewater treatment. However, our understanding of the diversity of indole-degrading communities is still limited. We investigated two anaerobic, indole-decomposing microbial communities under both denitrifying and sulfate-reducing conditions. Utilizing a ne...

Denitrification, the reduction of nitrogen oxides (NO(3)(-) and NO(2)(-)) to N(2) via the intermediates NO and N(2)O, is crucial for nitrogen turnover in soils. Cultivation-independent approaches that applied nitrite reductase genes (nirK/nirS) as marker genes to detect denitrifiers showed a predominance of genes presumably derived from as yet uncu...

The N(2)O : N(2) product ratio of denitrification is negatively correlated with soil pH, but the mechanisms involved are not clear. We compared soils from field experiments where the pH had been maintained at different levels (pH 4.0-8.0) by liming (> or = 20 years), and quantified functional gene pools (nirS, nirK and nosZ), their transcription an...

This study developed a new statistical strategy for analyzing clone library data to observe whether there is a defined pattern in structural responses of gut microbiota to environmental perturbations. A large clone library of genus Bacteroides was constructed with fecal samples for each subject in rotavirus-infected (Group R) and healthy children (...

A Thauera-specific nested-PCR denaturing gradient gel electrophoresis (DGGE) method was developed, and its usefulness was demonstrated by monitoring the structural shifts of Thauera spp. in an anaerobic-anoxic-oxic fixed-biofilm coking wastewater treatment plant (WWTP) responding to operational perturbations. The specificity of the PCR method was c...

We compared the microbial communities of two denitrifying bioreactors acclimated by quinoline and indole under identical condition. We acclimated two reactors by using the same seeding sludge and acclimating conditions. When both reactors reached steady stage with a high pollutant removal capacity after 6 weeks adaptation, we constructed the 16S rD...

To characterize the heterotrophic nitrifying bacteria. The bacteria were isolated from membrane bioreactor for treating synthetic wastewater using the method newly introduced in this study. Fluorescence in situ hybridization (FISH) was used to validate the nonexistence of autotrophic ammonia oxidizers and nitrite oxidizers. Batch tests were carried...

Molecular analysis of community structure can help diagnose problems in malfunctioning full-scale wastewater treatment system. A lab-scale A1-A2-O fixed biofilm system with highly efficient nitrification (NH3-N removal at 95. 2%) was set up as a reference for an industrial system with poor performance of nitrification (NH3-N removal efficiency at -...