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| 1 | Soil Organic Carbon in a Changing World显示文摘Soil contains more than three times as much carbon (C) as either the atmosphere or terrestrial vegetation.Soil organic C (SOC) is essentially derived from inputs of plant and animal residues,which are processed by the microbiota (bacteria,archaea,protists,fungi and viruses) that dominates SOC transformation and turnover in complex terrestrial environments.A | JIA Zhongjun Yakov KUZYAKOV David MYROLD James TIEDJE | 2017 | Pedosphere2017，27，5： | 7 |
| 2 | Soil biodiversity in a rapidly changing world显示文摘Microbes are simple single-cell organisms,but have an enormous practical significance for human kind.Soil microbes make our planet habitable,and the planet's rapidly changing environments in turn have a profound impact on the soil microbial communities,both positively and negatively.It is thus crucial to better understand how abiotic and biotic factors interact to assemble microbiomes under the given environmental conditions,and how they modulate the intrinsic link between microbial diversity and ecosystem function.From a functional viewpoint. | Zhongjun JIA David D.MYROLD Ralf CONRAD | 2020 | Pedosphere2020，30，1： | 4 |
| 3 | Hierarchical Micropore/Nanorod Apatite Hybrids In-Situ Grown from 3-D Printed Macroporous Ti6Al4V Implants with Improved Bioactivity and Osseointegration显示文摘The advent of three-dimensional(3-D) printed technique provides great possibility in the fabrication of customized porous titanium(Ti) implant. However, the bioinert property of the printed Ti poses an outstanding problem. Hybrid micro-arc oxidation and hydrothermal(MAO–HT) treatment on porous metals is able to produce multi-scaled hierarchical orthopedic implant, showing great potential for surface modification of 3-D printed implant. In this study, cylindrical porous Ti6Al4V(Ti64) scaffolds with pore size of 640 μm, porosity of 73% were 3-D printed by electron beam melting process, and their surfaces were left untreated or treated by a combined MAO–HT procedure. In vitro bioactivity was tested by immersion in simulated body fluid for different time points. Then, 12 scaffolds in each group were implanted into the femoral condyles of New Zealand rabbit for 8 weeks. Osseointegration was evaluated by qualitative and quantitative histological analysis, and the bone ingrowth features were probed by sequential fluorescent labeling at 3 and 6 weeks post-surgery. Following the MAO–HT treatment, the porous Ti64 scaffold was endowed with multi-scaled micro/nano-topographies and high amounts of Ca P on its surface.The treated scaffold exhibited drastically enhanced apatite forming ability compared with the untreated one. In vivo test revealed significantly that a higher amount of bone ingrowth and bone implant contact at the treated scaffold. The 2 types of scaffolds had different patterns of bone ingrowth: the treated scaffold exhibited a pattern of contact osteogenesis, by which bone formed directly on the treated implant surface, whereas bone formed distal to the implant surface of the untreated scaffold. MAO–HT treatment can significantly enhance the in vitro apatite-inducing ability and in vivo osseointegration capacity of 3-D porous Ti64 scaffold and may provide as a viable approach for the fabrication of bioactive 3-D printed porous implant for orthopedic applications. | Peng Xiu Zhaojun Jia Jia Lv Chuan Yin Hong Cai Chunli Song Huijie Leng Yufeng Zheng Zhongjun Liu Yan Cheng | 2017 | Journal of Materials Science & Technology2017，33，2： | 2 |
| 4 | Soil microbial community assemblage and its seasonal variability in alpine treeline ecotone on the eastern Qinghai-Tibet Plateau显示文摘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 microbialcommunity 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 highthroughput 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 microclimate 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. | Li Kui Hui Sun Qian Lei Wei Gao Lijun Bao Yuexi Chen Zhongjun Jia | 2019 | Soil Ecology Letters2019，1，1： | 2 |
| 5 | Effect of rice plants on CI-h production, transport, oxidation and emission in rice paddy soil 显示文摘 | Zhongjun Jia Zucong Cai Hua Xu | 2001 | Plant and Soil2001，230，2： | 1 |
| 6 | Heterotrophy-coordinated diazotrophy is associated with significant changes of rare taxa in soil microbiome显示文摘Soil heterotrophic respiration during decomposition of carbon(C)-rich organic matter plays a vital role in sustaining soil fertility.However,it remains poorly understood whether dinitrogen(N_(2))fixation occurs in support of soil heterotrophic respiration.In this study,^(15)N_(2)-tracing indicated that strong N_(2)fixation occurred during heterotrophic respiration of carbon-rich glucose.Soil organic ^(15)N increased from 0.37 atom%to 2.50 atom%under aerobic conditions and to 4.23 atom%under anaerobic conditions,while the concomitant CO_(2)flux increased by 12.0-fold under aerobic conditions and 5.18-fold under anaerobic conditions.Soil N_(2)fixation was completely absent in soils replete with inorganic N,although soil N bioavailability did not alter soil respiration.High-throughput sequencing of the 16S rRNA gene further indicated that:i)under aerobic conditions,only 15.2%of soil microbiome responded positively to glucose addition,and these responses were significantly associated with soil respiration and N_(2)fixation and ii)under anaerobic conditions,the percentage of responses was even lower at 5.70%.Intriguingly,more than 95%of these responses were originally rare with<0.5%relative abundance in background soils,including typical N_(2)-fixing heterotrophs such as Azotobacter and Clostridium and well-recognized non-N_(2)-fixing heterotrophs such as Sporosarcina,Agromyces,and Sedimentibacter.These results suggest that only a small portion of the soil microbiome could respond quickly to the amendment of readily accessible organic C in a fluvo-aquic soil and highlighted that rare phylotypes might have played more important roles than previously appreciated in catalyzing soil C and nitrogen turnovers.Our study indicates that N_(2)fixation could be closely associated with microbial turnover of soil organic C when available in excess. | Wei GAO Lianfeng WANG Zhongjun JIA | 2022 | Pedosphere2022，32，3： | 1 |
| 7 | Effect of soil water contents in the non-rice growth season on CH4 emission during the following rice-growing period显示文摘 | Hua Xu Zucong Cai Zhongjun Jia | 2002 | Nutrient Cycling in Agroecosystems (-)2002，，1： | 1 |
| 8 | Methanotrophy-driven accumulation of organic carbon in four paddy soils of Bangladesh显示文摘Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associated with microbial methane oxidation is poorly understood.Therefore,to investigate methane-derived carbon incorporation into soil organic matter,paddy soils originated from different parent materials(Inceptisol,Entisol,and Alfisol) were collected after rice harvesting from four major rice-producing regions in Bangladesh.Following microcosm incubation with 5%(volume/volume)^(13) CH_(4),soil^(13) C-atom abundances significantly increased from background level of 1.08% to 1.88%–2.78%,leading to a net methane-derived accumulation of soil organic carbon ranging from 120 to 307 mg kg^(-1).Approximately 23.6%–60.0% of the methane consumed was converted to soil organic carbon during microbial methane oxidation.The phylogeny of^(13) C-labeled pmoA(enconding the alpha subunit of the particulate methane monooxygenase) and 16 S rRNA genes further revealed that canonical α(type II) and γ(type I) Proteobacteria were active methane oxidizers.Members within the Methylobacter-and Methylosarcina-affiliated type Ia lineages dominated active methane-oxidizing communities that were responsible for the majority of methane-derived carbon accumulation in all three paddy soils,while Methylocystis-affiliated type IIa lineage was the key contributor in one paddy soil of Inceptisol origin.These results suggest that methanotroph-mediated synthesis of biomass plays an important role in soil organic matter accumulation.This study thus supports the concept that methanotrophs not only consume the greenhouse gas methane but also serve as a key biotic factor in maintaining soil fertility. | Nasrin SULTANA Jun ZHAO Yuanfeng CAI G.K.M.Mustafizur RAHMAN Mohammad Saiful ALAM Mohammad FAHEEM Adrian HO Zhongjun JIA | 2022 | Pedosphere2022，32，2： | 1 |
| 9 | OPPORTUNITIES AND APPROACHES FOR MANIPULATING SOIL-PLANT MICROBIOMES FOR EFFECTIVE CROP NITROGEN USE IN AGROECOSYSTEMS显示文摘Soil microbiomes drive the biogeochemical cycling of nitrogen and regulate soil N supply and loss,thus,pivotal nitrogen use efficiency(NUE).Meanwhile,there is an increasing awareness that plant associated microbiomes and soil food web interactions is vital for modulating crop productivity and N uptake.The rapid advances in modern omics-based techniques and biotechnologies make it possible to manipulate soil-plant microbiomes for improving NUE and reducing N environmental impacts.This paper summarizes current progress in research on regulating soil microbial N cycle processes for NUE improvement,plant-microbe interactions benefiting plant N uptake,and the importance of soil microbiomes in promoting soil health and crop productivity.We also proposes a potential holistic(rhizosphere-root-phyllosphere)microbe-based approach to improve NUE and reduce dependence on mineral N fertilizer in agroecosystems,toward nature-based solution for nutrient management in intensive cropping systems. | Jingjing PENG Olatunde OLADELE Xiaotong SONG Xiaotang JU Zhongjun JIA Hangwei HU Xuejun LIU Shuikuan BEI Anhui GE Limei ZHANG Zhenling CUI | 2022 | Frontiers of Agricultural Science and Engineering2022，9，3： | 1 |
| 10 | Stable-isotope probing of bacterial community for dissolved inorganic carbon utilization in Microcystis aeruginosa-dominated eutrophic water显示文摘Dissolved inorganic carbon(DIC) is an important source of carbon in aquatic ecosystems,especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing(SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria(Microcystis aeruginosa). Our 16 S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H^(13)CO^(3-) into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H^(13)CO^(3-) metabolized by Microcystis as organic matter, e.g. Bacteroidetes(Cytophagales, Sphingobacteriales), and microcystindegrading bacteria Betaproteobacteria(Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater. | Weiguo Zhang Jiangye Li Chengcheng Wang Xue Zhou Yan Gao Zhongjun Jia | 2019 | Journal of Environmental Sciences2019，31，5： | 1 |
| 11 | Urease gene‐containing A rchaea dominate autotrophic ammonia oxidation in two acid soils显示文摘 | Lu Lu Zhongjun Jia | 2013 | Environ Microbiol2013，，： | 1 |
| 12 | Simvastatin induces osteoblastic differentiation and inhibits adipocytic differentiation in mouse bone marrow stromal cells显示文摘 | Chunli Song Zhaoqing Guo Qingjun Ma Zhongqiang Chen Zhongjun Liu Hongti Jia Gengting Dang | 2003 | Biochemical and Biophysical Research Communications2003，，3： | 1 |
| 13 | Interplay between collective behavior and spreading dynamics on complex networks显示文摘 | Li Kezan Ma Zhongjun Jia Zhen | 2012 | Chaos2012，22，04： | 1 |
| 14 | Chronic Nitrogen Fertilization Modulates Competitive Interactions Among Microbial Ammonia Oxidizers in a Loess Soil显示文摘Nitrogen(N) application may lead to niche segregation of soil ammonia-oxidizing archaea(AOA) and bacteria(AOB), thereby reducing the competitive interactions between AOA and AOB due to higher ammonium substrate availability. However, the adaptive mechanisms of AOA and AOB under N enrichment remain poorly understood. Stable isotope probing(SIP) microcosm incubation was employed to reveal community changes of active AOA and AOB in a loess soil from a field experiment growing potatoes that received no N(control, CK), low N(LN, 75 kg N ha^(-1)), and high N(HN, 375 kg N ha^(-1)). The results showed that the soil potential nitrification rate(PNR) was measured by culturing of the soil samples from the field experiment. Soil PNR was significantly increased in HN by87.5% and 67.5% compared with CK and LN, respectively. Compared with CK, the^(13)C-amoA genes of soil AOA and AOB in HN had 2.58 × 10~4 and 1.55 × 10~6 copies, representing 1.6-and 16.2-fold increase respectively. It was indicated that AOB dominated soil ammonia oxidation. A phylogenetic analysis of the^(13)C-amoA gene showed that N application significantly increased the proportion of54 d9-like AOA up to 90% in HN, while the Nitrososphaera gargensis-like and Nitrososphaera viennensis-like AOA were inhibited and completely disappeared. Nitrogen application also resulted in the community shift of active AOB-dominant group from Nitrosospira briensis-like to Nitrosospira sp. TCH711-like. Our study provides compelling evidence for the emergence and maintenance of active nitrifying communities under the intensified N input to an agricultural ecosystem. | DONG Xingchen ZHANG Jian QIU Huizhen ZHANG He LUO Chaoyue DENG Delei SHEN Qirong JIA Zhongjun | 2019 | Pedosphere2019，29，1： | 0 |
| 15 | Determination of carbon-fixing potential of Bathyarchaeota in marine sediment by DNA stable isotope probing analysis显示文摘Bathyarchaeota is believed to play a crucial role in the global carbon cycle due to its vast biomass,broad distribution,and diverse habitat.However,its physiological and metabolic features are hard to determine without pure culture.While metagenomic analyses have shown that Bathyarchaeota has a complete inorganic carbon fixation(Wood-Ljungdahl,WL)pathway,no direct functional confirmation has been reported.To explore the inorganic carbon fixation ability of Bathyarchaeota,we used lignin and sodium bicarbonate-^(13)C(NaH^(13)CO_(3))in the long-term incubation of marine sediment samples.We found that Bathyarchaeota grew continuously in the cultivation system with lignin,and its abundance increased up to 15.3 times after10 months,increasing its fraction of all archaea from 30%to 80%.We monitored theδ^(13)C of total organic carbon to identify microbial carbon fixation in the cultivation systems,finding that it increased in the first month while NaH^(13)CO_(3)was present but only increased continuously afterward when lignin was also present.Furthermore,ultracentrifugation was performed on DNA extracted from samples at different cultivation stages to separate DNA of different buoyant densities,and bathyarchaeotal and bacterial 16S ribosomal RNA(r RNA)gene abundance were quantified using qPCR.Compared to bacteria,bathyarchaeotal 16S rRNA tended to be concentrated in heavy layers after 4 months of incubation with lignin and NaH^(13)CO_(3),indicating that Bathyarchaeota DNA contained^(13)C through proliferation based on lignin utilization and NaH^(13)CO_(3)assimilation,proving the carbon fixation capacity of Bathyarchaeota. | Wenyue LIANG Tiantian YU Liang DONG Zhongjun JIA Fengping WANG | 2023 | Science China Earth Sciences2023，66，4： | 0 |
| 16 | In Memoriam:David D.Myrold(1955–2021)显示文摘David D.Myrold,65,Professor of Soil Microbiology in the Department of Crop and Soil Science at Oregon State University,passed away in Corvallis,Oregon,USA on July 15,2021.Dave was well known to many soil scientists for his work on soil nitrogen cycling,a career of research work that was summarized in his latest 2021 publication—Transformation of Nitrogen. | Zhongjun JIA Jeanette M.NORTON Joshua P.SCHIMEL James M.TIEDJE | 2022 | Pedosphere2022，32，1： | 0 |
| 17 | Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios显示文摘Long-term nitrogen(N)fertilization imposes strong selection on nitrifying communities in agricultural soil,but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood.Using a 44-year grassland fertilization experiment,we investigated community shifts of active nitrifiers by DNA-based stable isotope probing(SIP)of field soils that received no fertilization(CK),high levels of organic cattle manure(HC),and chemical N fertilization(CF).Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils,whereas no activity occurred in CK soils.The 44 years of inorganic N fertilization selected only 13C-ammonia-oxidizing bacteria(AOB),whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea(AOA)and AOB could be actively13C-labeled.Phylogenetic analysis indicated that Nitrosospira sp.62-like AOB dominated inorganically fertilized CF soils,while Nitrosospira sp.41-like AOB were abundant in organically fertilized HC soils.The 13C-AOA in HC soils were affiliated with the 29i4 lineage.The 13C-nitrite-oxidizing bacteria(NOB)were dominated by both Nitrospira-and Nitrobacter-like communities in CF soils,and the latter was overwhelmingly abundant in HC soils.The 13C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions.These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field.Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field,where distinct nitrifiers have been shaped by intensified anthropogenic N input. | Zhongjun JIA Xue ZHOU Weiwei XIA Dario FORNARA Baozhan WANG Elizabeth Anne WASSON Peter CHRISTIE Martin F.POLZ David D.MYROLD | 2020 | Pedosphere2020，30，1： | 0 |
| 18 | Elevated and atmospheric-level methane consumption by soil methanotrophs of three grasslands in China显示文摘Background:Methane(CH4)oxidation driven by soil aerobic methanotrophs demonstrates the capacity of grassland as a CH4 sink.Methods:In this study,we compared the oxidation characteristics of atmospheric-level and elevated concentration(10%)CH4 in a typical grassland(steppe)on the Loess Plateau,an alpine meadow(meadow)on the Qinghai-Tibet Plateau,and an inland arid-area artificial grassland(pasture)in northwest China and investigated the communities of active methanotrophs and their contribution to CH4 oxidation using DNA-based stable-isotope probing and Illumina Miseq sequencing.Results:The results showed that the oxidation of atmospheric CH4 only occurred in steppe and meadow soils where the USCγgroup of methanotrophs was numerically dominant in the methanotroph community.Pasture soils,with their very low relative abundance of USCγ,did not show atmospheric CH4 oxidation.However,a DNA-stable isotope probing experiment with 10%CH4 indicated that conventional CH4 oxidizers(Methylocaldum and Methylocystis)rather than USCγcommunities assimilated significant amounts of 13CH4 for growth.Conclusions:The CH4 oxidation mechanisms in the three experimental grassland soils varied significantly.The USCγgroup may be obligate oligotrophic microorganisms or their growth requires specific unknown conditions. | Yufang Wang Yuanfeng Cai Fujiang Hou Saman Bowatte Zhongjun Jia | 2023 | Grassland Research2023，2，2： | 0 |
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