Jul 2019, Volume 1 Issue 1-2

Cover illustration

  • Antimicrobial resistance is already considered to be a major threat to human health, and its emergence and dissemination have caused widespread public concern. Soils have became an important sink for antibiotic resistance genes (ARGs) because of the influence of human activities such as the application of manures and wastewater irrigation. To better understand the impacts of ARGs on the soil ecosystem, the transport of ARGs is a basic question. So far, however, the role of so [Detail] ...

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    James I. Prosser
    Qing-Lin Chen, Xin-Li An, Bang-Xiao Zheng, Michael Gillings, Josep Peñuelas, Li Cui, Jian-Qiang Su, Yong-Guan Zhu

    Loss of biodiversity is a major threat to the ecosystem processes upon which society depends. Natural ecosystems differ in their resistance to invasion by alien species, and this resistance can depend on the diversity in the system. Little is known, however, about the barriers that microbial diversity provides against microbial invasion. The increasing prevalence of antibiotic-resistant bacteria is a serious threat to public health in the 21st century. We explored the consequences of the reduction in soil microbial diversity for the dissemination of antibiotic resistance. The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR. Microbial diversity was negatively correlated with the abundance of antibiotic-resistance genes, and this correlation was maintained after accounting for other potential drivers such as incubation time and microbial abundance. Our results demonstrate that high microbial diversity can act as a biological barrier resist the spread of antibiotic resistance. These results fill a critical gap in our understanding of the role of soil microbial diversity in the health of ecosystems.

    Dong Zhu, Hong-Tao Wang, Fei Zheng, Xiao-Ru Yang, Peter Christie, Yong-Guan Zhu

    Soils have become an important sink for antibiotic resistance genes (ARGs). To better understand the impacts of ARGs on the soil ecosystem, the transport of ARGs is a basic question. So far, however, the role of soil animals in the dispersal of ARGs is not understood. Here, two treatments (without collembolans and with collembolans) were established, each treatment included unamended and manure-amended soil, and soil samples were collected at 14, 28 and 56 days after incubation. The effects of the collembolan Folsomia candida on dispersal of ARGs in the soil ecosystem were explored using high-throughput qPCR combined with Illumina sequencing. As the culture time increased, more shared ARGs and OTUs were detected between the unamended and manured soil, especially in the treatment with collembolans. Vancomycin, aminoglycoside and MLSB genes may have been more readily transported by the collembolan. On the 28th day after incubation, a high abundance of mobile genetic elements (MGEs) was found in the treatment with collembolans. These results clearly reveal that collembolans can accelerate the dispersal of ARGs in the soil ecosystem. Procrustes analysis and the Mantel test both indicate that soil bacterial communities were significantly correlated with ARG profiles. Furthermore, partial redundancy analysis indicates that soil bacterial communities can explain 41.28% of the variation in ARGs. These results suggest that the change of soil microbial community have an important contribution to the dispersal of ARGs by the collembolan.

    Teri C. Balser, Chao Liang, Jessica L. M. Gutknecht

    During the past two decades interest in linking soil microbial community composition and activity with ecosystem scale field studies of nutrient cycling or plant community response to disturbances has grown. Despite its importance there are challenges in making this linkage. Foremost is the question of analytical feasibility. In general, microbiological community-level methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. Soil lipid analysis shows potential as a middle ground between simple biomass measures and molecular profiling. However, the two protocols that have most often been followed are either rapid but indiscriminate (total lipid analysis or fatty acid methyl ester analysis; FAME), or precise but time consuming (phospholipid fatty acid analysis; PLFA). In this paper we report results from a standardized soil used test a modified extraction method (the ‘hybrid’ method) developed to balance the speed of FAME and the precision of PLFA in order to increase sample throughput. In comparing the three methods, we find that FAME and PLFA are qualitatively and quantitatively distinct. The FAME method yielded the highest fatty acid abundance, but also had high variance resulting in low precision. The PLFA method had precision, but low yield. The ‘hybrid’ method fell midway between FAME and PLFA for quantitative fatty acid yield. In addition, the hybrid extraction can be completed in a fraction of the time it takes for PLFA. The hybrid protocol appears to provide an optimal balance between effort and accuracy and therefore is a good choice for large-scale ecosystem studies.

    Li Kui, Hui Sun, Qian Lei, Wei Gao, Lijun Bao, Yuexi Chen, Zhongjun Jia

    The alpine treeline ecotone is characterized as the upper limit of the forest in the high-mountain ecosystem. Due to the freeze–thaw cycles, the soil organism community, such as microbial communities are expected to change between seasons. However, there are limited microbial-community studies focused on the high altitude alpine ecosystem. We conducted a study in the alpine treeline ecotone on the eastern Qinghai–Tibet Plateau, China, and investigated the seasonal variability of the soil microbial community. We collected all soil samples within the alpine treeline ecotone, between the treeline and timberline in the high-mountain region. The 16S rRNA genes of the microbial communities (bacterial and archaeal) were analyzed by high-throughput sequencing to the genus level. The results showed that soil microbial community in the alpine treeline ecotone was consistently dominated by eight phyla which consisted of 95% of the total microbial community, including Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, Bacteroidetes, and Verrucomicrobia. The overall diversity and evenness of the community were relatively stable, with an average of 0.5% difference between seasons. The highest seasonal variability occurred at the upper boundary of the alpine treeline ecotone, and few or almost no seasonal change was observed at lower elevations, indicating dense forest cover and litter deposition might have created a local micro-climate that reduced seasonal variation among the surrounding environmental conditions. Our study was one of the first group that documented the microbial community assemblage in the treeline ecotone on the Qinghai-Tibet Plateau.

    Mengru Wang, Shenglei Fu, Hongzhi Zhang, Meina Wang, Haixiang Xu, Leilei Shi

    Atmospheric nitrogen (N) deposition has increased dramatically since the industrial revolution due to human activities. In terrestrial ecosystems, excess nitrogen inputs can greatly affect soil chemical properties, plant growth, and activities of soil microbes and fauna. Millipedes can fragment and consume large quantities of litter, and they regulate nutrient cycling and affect soil fertility through excretion of faeces. Many soil fauna graze on the faeces of millipedes as a part of the soil food web. The decomposition and stabilization of these millipede faeces are especially important in soil carbon dynamics and nutrient cycling, and these processes rely heavily upon microbial activity. However, very few studies have investigated how microbial community structure and oxidase activity of millipede faeces respond to climate change, especially N deposition. Therefore, we designed a microcosm study to investigate this question, which included two treatments, N addition treatment and control (without N addition).We found that: (i) microbial community structure in millipede faeces was altered and the biomass of fungi and actinomycetes in faecal pellets were significantly reduced after N addition, but bacteria still dominated in millipede faeces after N addition, (ii) oxidase activity was suppressed in response to N addition, and (iii) microbial community structure and oxidase activities were significantly correlated to organic carbon and dissolved total nitrogen of faeces. All these changes suggest that millipede excretion activities under nitrogen deposition contribute to carbon stabilization and reduction in greenhouse gas emission owing to the significant role of fungi and associated oxidase in carbon mineralization. It is noteworthy to pay more attention to the function of saprotrophic invertebrates in future N deposition studies.

    Yu Shi, Yuntao Li, Meiqing Yuan, Jonathan M. Adams, Xianzhang Pan, Yunfeng Yang, Haiyan Chu

    The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production. Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services, thus providing valuable insights to improve food production. The North China Plain (NCP) is one of the world’s key agricultural regions, supplying more than 50% of the cereal consumed in Asia. However, it is unknown whether soil microbial diversity is predictable across the NCP. Using the MiSeq Illumina platform, we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP, which cover nearly 0.3 million KM2. Based on observed bacterial communities and their relationships with environmental factors, we generated a map of bacterial communities across the NCP. The highest bacterial diversity was found in the middle part of the NCP, with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria. These findings provide important baseline information for analyzing the relationships between microbial community, soil functionality and crop yields.

    Yangying Liu, Shang Wang, Zhujun Wang, Zhaojing Zhang, Huayu Qin, Ziyan Wei, Kai Feng, Shuzhen Li, Yueni Wu, Huaqun Yin, Hui Li, Ye Deng

    Degradation succession in forests is an important and serious land use/cover change problem in ecology, and during these processes soil microbial communities mediate the recycling of most important nutrients. To reveal the effect of degradation succession processes on soil microbial community diversity, structure, and species interrelationships, we collected abundant samples (21 per vegetation type) in broad-leaved forest, coniferous forest, and meadow to observe the microbial community dynamics. The results showed that diversity and structure of soil prokaryotic and fungal communities responded differently to different forest degradation processes, diversity of soil microbial communities increased during degradation processes. Soil microbial communities abundance changes may indicate that prokaryotic communities showed a living strategies change as an ecological adaption to harsh conditions during forest degradation process. While for fungal communities, their abundance changes may indicate that environmental selection pressure and plant selectivity during forest degradation process. Changes in soil prokaryotic communities and fungal communities were both correlated with soil carbon and nitrogen loss. The soil microbial interaction network analysis indicated more complex species interrelationships formed due to the loss of soil nutrients during degradation succession processes, suggesting soil microbial communities might form more complex and stable networks to resist the external disturbance of soil nutrient loss. All results suggested soil microorganisms, including bacteria, archaea and fungi, all involved in the soil nutrient decline during the forest degradation process.

    Dandan Wang, Na Zhang, Haoqi Tang, Jonathan M. Adams, Bo Sun, Yuting Liang

    Soil fungi have many important ecological functions, however, their life strategies and interactions in manure fertilized soils are not well understood. The aim of this study was to investigate the effects of biochar amendment on the fungal life strategies and species interactions in ryegrass (Lolium perenne L.) rhizosphere soil by high-throughput sequencing. Three soil treatments were evaluated: soil and pig manure mixture without planting ryegrass and biochar application (bulk soil), mixture with ryegrass planting (rhizosphere soil (RS)), and addition of 2% (w/w) biochar with ryegrass (RS+ biochar). Our results indicated that temporal turnover, defined as the slope of linear regression between community similarity and time, was significantly higher in the biochar amendment (slope= -0.2689, p<0.0001) relative to the rhizosphere soil. Following biochar addition, the percentage of species employing slow acclimation ecological strategies decreased (from 27% to 17%) and the percentage of sensitive species increased (from 40% to 50%) in comparison to the rhizosphere soil. Network analysis indicated that fungal communities in the biochar amendment enhanced positive correlations compared to the rhizosphere soil and bulk soil. Structural equation model indicated that soil pH was the most important factor in altering fungal life strategies and interactions in manure fertilized soils.