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Microfluidic bacterial traps for simultaneous fluorescence and atomic force microscopy

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Nano Research 2017年第11期10卷 3896-3908页

作者： Oliver Peric Melanie Hannebelle jonathan D. adams Georg E. Fantner Laboratory for Bio-and Nano-Instrumentation Institute of Bioengineering School of Engineering EPFL 1015 Lausanne Switzerland

The atomic force microscope has become an established research tool for imaging microorganisms with unprecedented ***,its use in microbiology has been limited by the difficulty of proper bacterial ***,we have developed a microfluidic device that solves the issue of bacterial immobilization for atomic force microscopy under physiological *** device is able to rapidly immobilize bacteria in well-defined positions and subsequently release the cells for quick sample *** developed device also allows simultaneous fluorescence analysis to assess the bacterial viability during atomic force microscope *** demonstrated the potential of our approach for the immobilization of rod-shaped Escherichia coli and Bacillus *** our device,we observed buffer-dependent morphological changes of the bacterial envelope mediated by the antimicrobial peptide *** approach to bacterial immobilization makes sample preparation much simpler and more reliable,thereby accelerating atomic force microscopy studies at the single-cell level.

关键词： atomic force microscope (AFM) microfabrication microfluidics microbiology correlative microscopy physical immobilization

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

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Pedosphere 2023年第6期33卷 819-827页

作者： Dorsaf KERFAHI Yu SHI Baozhan WANG Hokyung SONG Haiyan CHU jonathan M.adams School of Natural Sciences Department of Biological SciencesKeimyung UniversityDaegu 42601Korea State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475001China State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Key Lab of Miboyrgriculural Eonment MintryfgrculureCllege of Life SciencesNanjing Agricultural Univery Nanjing 21008China Department of Earth and Environmental Sciences The University of ManchesterManchester M139PLUK University of Chinese Academy of Sciences Beijing 101408China School of Geography and Oceanography Nanjing UniversityNanjing 210008China

Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.

关键词： amoA gene ammonia-oxidizing bacteria assembly processes beta nearest taxon index community structure operational taxonomic unit

Enduring legacy of coal mining on the fungal community in a High Arctic soil after five decades

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Pedosphere 2022年第5期32卷 698-706页

作者： Dorsaf KERFAHI Kevin K.NEWSHAM Ke DONG Hokyung SONG Mark TIBBETT jonathan M.adams School of Natural Sciences Department of Biological SciencesKeimyung UniversityDaegu 42601(Republic of Korea) NERC British Antarctic Survey Madingley RoadCambridge CB3 OET(UK) Department of Life Science Kyonggi UniversitySuwon-si 16227(Republic of Korea) School of Earth and Environmental Sciences The University of ManchesterManchester M139PL(UK) Department of Sustainable Land Management&Soil Research Center School of AgriculturePolicy and DevelopmentUniversity of ReadingReading RG66AR(UK) School of Geographic and Oceanographic Sciences Nanjing UniversityNanjing 210008(China)

Mineral extraction is known to affect soil fungi in polar environments,but it is unknown how long these effects ***,by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi,we compared soil fungal community in intact natural tundra with that in a nearby former coal mining area,abandoned 52 years previously,on Svalbard in the High *** with those in intact tundra,soils in the former mining area were more acidic and had lower plant *** of similar diversity in the two areas,the fungal community was dominated by Basidiomycota in the intact tundra,but by Ascomycota in the former mining *** genera formed a major part of the tundra community,but were notably less abundant in the mining *** principal variation among samples was soil ***,network connectivity analysis indicated that the fungal community in the former mining area had greater network connectivity than that in the tundra ***,the ecosystem in the former mining area has made only limited recovery towards the natural tundra state even after more than five *** is unclear whether the recovery of the fungal community is limited more by the low primary productivity,slow migration of fungi and plants,or slow changes in soil *** findings emphasize the susceptibility of polar ecosystems to disturbance,given their particularly slow recovery back towards the natural state.

关键词： abandoned mining site ectomycorrhizal fungi intact tundra mine tailings mineral extraction polar ecosystem recovery

Straw biochar strengthens the life strategies and network of rhizosphere fungi in manure fertilized soils

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Soil Ecology Letters 2019年第1期1卷 72-84页

作者： Dandan Wang Na Zhang Haoqi Tang jonathan M.adams Bo Sun Yuting Liang State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China School of Environmental and Safety Engineering Changzhou UniversityChangzhou 213164China University of the Chinese Academy of Sciences No.19A Yuquan RoadBeijing 100049China

Soil fungi have many important ecological functions,however,their life strategies and interactions in manure fertilized soils are not well *** 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 *** 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 *** 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 *** analysis indicated that fungal communities in the biochar amendment enhanced positive correlations compared to the rhizosphere soil and bulk *** equation model indicated that soil pH was the most important factor in altering fungal life strategies and interactions in manure fertilized soils.

关键词： Rhizosphere Biochar Fungal community Life strategies Network analysis

A biogeographic map of soil bacterial communities in wheats field of the North China Plain

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Soil Ecology Letters 2019年第1期1卷 50-58页

作者： Yu Shi Yuntao Li Meiqing Yuan jonathan M.adams Xianzhang Pan Yunfeng Yang Haiyan Chu State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Forensic Genetics of Ministry of Public Security Institute of Forensic Science of Ministry of Public SecurityBeijing 100038China School of Water Energy and EnvironmentCranfield UniversityCranfield MK460ALUK State Key Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China

The vast diversity of soil bacteria provides essential ecosystem services that support agricultural *** 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 *** North China Plain(NCP)is one of the world’s key agricultural regions,supplying more than 50% of the cereal consumed in ***,it is unknown whether soil microbial diversity is predictable across the *** 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 km^(2).Based on observed bacterial communities and their relationships with environmental factors,we generated a map of bacterial communities across 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 *** findings provide important baseline information for analyzing the relationships between microbial community,soil functionality and crop yields.

关键词： Predicting map Bacteria diversity Actinobacteria Alphaproteobacteria

Soil Metagenome of Tropical White Sand Heath Forests in Borneo:What Functional Traits Are Associated with an Extreme Environment Within the Tropical Rainforest?

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Pedosphere 2019年第1期29卷 12-23页

作者： Dorsaf KERFAHI Binu M.TRIPATHI Johan W.Ferry SLIK Rahayu S.SUKRI Salwana JAAFAR Ke DONG Matthew Chidozie OGWU Hyo-Ki KIM jonathan M.adams Department of Biological Sciences Seoul National University Korea Polar Research Institute Faculty of Science Universiti Brunei Darussalam College of Natural Sciences Kyonggi University Celemics Inc.612 Avison Biomedical Research Center Yonsei Medical Center Division of Agrifood and Environment School of Water Energy and Environment Building 52a Cranfield University

White sand heath forests(WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful lowpH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology(MG-RAST). The results, on one hand, supported our hypothesis(on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference(specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats(CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.

关键词： antibiotic resistance biotic interaction kerangas microbial community microbiota shotgun metagenomics stress tolerance tropical forest

Metagenetics of fairy rings reveals complex and variable soil fungal communities

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Pedosphere 2023年第4期33卷 567-578页

作者： Siyu XU Ke DONG Sangseob LEE Matthew Chidozie OGWU Sainbileg UNDRAKHBOLD Dharmesh SINGH Dagvatseren ARIUNZAYA Orsoo ENKHMANDAL Laura A.SPENCE Anarmaa SHARKHUU Brenda B.CASPER jonathan M.adams Bazartseren BOLDGIV College of Biotechnology Dalian Polytechnic UniversityDalian 116034(China) School of Geographic and Oceanographic Sciences Nanjing UniversityNanjing 210008(China) Department of Life Sciences Kyonggi UniversitySuwon 443-760(Korea) School of Bioscience and Veterinary Medicine University of CamerinoCamerino 62032Marche-Floristic Research Center of the ApenninesGran Sasso and Monti della Laga National ParkSan ColomboBariscianoL'Aquila 67021(Italy) Laboratory of Ecological and Evolutionary Synthesis Department of BiologySchool of Arts and SciencesNational University of MongoliaUlaanbaatar 14201(Mongolia) School of Biological Sciences Seoul National University1 Gwanak-roGwanak-guSeoul 08826(Korea) Sterling College Sterling DriveCraftsbury Common VT 05827(USA) Department of Biology University of PennsylvaniaPhiladelphia PA 19104(USA)

Although fairy rings are widely observed,little is known about the community processes associated with ***,we studied fairy rings in a natural grassland in northern Mongolia by sampling soils outside(future stage),directly under(present stage),and within(past stage)the rings,to represent different time stages during the expansion of fairy *** DNA was extracted for amplicon sequencing of the fungal ITS1 *** present stage had reduced fungal diversity and different fungal communities toward the other *** strikingly,there was an increase in the pathogenic fungus Gibberella baccata in the present stage of most rings and the saprotrophic fairy ring fungus Lepista luscina in ***,no mushrooms of Lepista had been recorded from any of these rings during several years of *** fairy ring fungi were not found in the present stage of every ring,even in some known rings to have previously displayed mushrooms of such *** is possible that these fungi occurred or were more abundant at the unsampled leading edge of the *** increase in *** is intriguing,but its importance,if any,is *** is also unclear whether consortia of fungi or other microbes might be present in these *** absence or low abundance of the previously reported fairy ring fungal species suggests that their presence is transient,with rapid replacement by other *** differences in soil parameters were found between the fairy ring stages,except for *** is a need for broader sampling,including analysis of non-fungal biota,to understand the functional diversity of fairy ring fungi and the consequences for plant communities.

关键词： community process functional guilds Gibberella baccata grassland ITS1 region network analysis soil fungus

Stochasticity dominates assembly processes of soil nematode metacommunities on three Asian mountains

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Pedosphere 2023年第2期33卷 331-342页

作者： Shuqi ZOU jonathan adams Zhi YU Nan LI Dorsaf KERFAHI Binu TRIPATHI Changbae LEE Teng YANG Itumeleng MOROENYANE Xing CHEN Jinsoo KIM Hyun Jeong KWAK Matthew Chidozie OGWU Sang-Seob LEE Ke DONG Department of Integrative Biotechnology Sungkyunkwan University300 Chuncheon-DongSuwon 16419(Korea) School of Geographic and Oceanographic Sciences Nanjing UniversityNanjing 210008(China) Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf Guangxi Key Laboratory of Earth Surface Processes and Intelligent SimulationNanning Normal University175 East Mingxiu RoadNanning 530001(China) School of Natural Sciences Department of Biological SciencesKeimyung UniversityDaegu 42601(Korea) Korea Polar Research Institute Incheon 21990(Korea) Department of Forestry Environment and SystemsKookmin UniversitySeoul 02707(Korea) State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of Sciences71 East Beijing RoadNanjing 210008(China) Institut National Recherche Scientifique Institut Armand-Frappier SantéBiotechnologie531 Boulevard des PrairiesLaval H7V1B7(Canada) College of Life Science and Technology Guangxi University100 Daxue RoadNanning 530004(China) Department of Biological Sciences Kyonggi University154-42 Gwanggyosan-roYeongtong-guSuwon-siGyeonggi-do 16227(Korea) School of Biological Sciences Seoul National University1 Gwanak-roSeoul 08826(Korea)

Nematodes play an important role in ecosystems;however,very little is known about their assembly processes and the factors influencing *** studied nematode communities in bulk soils from three Asian mountain ecosystems to determine the assembly processes of free-living nematode metacommunities and their driving *** each mountain,elevations span a range of climatic conditions with the potential to reveal assembly processes that predominate across multiple biomes.A phylogenetic null modeling framework was used to analyze 18S rRNA gene amplicons to quantify various assembly *** found that phylogenetic turnover between nematode communities on all mountains was dominated by stochastic processes,with“undominated processes”being the most predominant stochastic *** has a significant impact on the relative importance of deterministic and stochastic processes.A variety of climatic and edaphic variables significantly influenced the variations in community assembly processes with elevation,even though their impacts were not consistent between the ***,our results indicate that free-living nematode metacommunities in a wide range of environments are largely structured by stochastic processes rather than by niche-based deterministic processes,suggesting that metacommunities of soil free-living nematodes may respond to climate change in a largely unpredictable way.

关键词： climate change ecological drift elevation gradient environmental stress stochastic process

Effects of Slope Aspects on Soil Bacterial and Arbuscular Fungal Communities in a Boreal Forest in China

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Pedosphere 2016年第2期26卷 226-234页

作者： CHU Haiyan XIANG Xingjia YANG Jian jonathan M. adams ZHANG Kaoping LI Yuntao SHI Yu State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China State Key Laboratory of Forest and Soil Ecology Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110164 China Department of Biological Sciences Seoul National University Seoul 151 Korea University of Chinese Academy of Sciences Beijing 100049 China

The effects of slope aspects on soil biogeochemical properties and plant communities in forested environments have been studied extensively; however, slope aspect influence on soil microbial communities remains largely unexamined, despite the central role of soil biota in ecosystem functioning. In this study, the communities of both soil bacteria and arbuscular mycorrhizal fungi （AMF） were investigated using tagged pyrosequencing for three types of slope aspects （south-facing aspect, north-facing aspect and flat area） in a boreal forest of the Greater Khingan Mountains, China. The bacterial and AMF community composition differed with slope aspects. Bacterial diversity was the lowest on the north-facing aspect, and AMF diversity was the lowest on the flat area. Aspects also had a significant impact on soil pH and available phosphorus （P） and shrubby biomass. Soil pH and understory shrub biomass were significantly correlated with bacterial communities, and soil available P and shrub biomass showed significant correlations with AMF communities. Our results suggested that slope aspects affected bacterial and AMF communities, mediated by aspect-induced changes in plant community and soil chemical properties （e.g., pH and available P）, which improved the knowledge on the effects of forest slope aspects on aboveground and belowground communities.

关键词： available P plant communities pyrosequencing shrubby biomass soil chemical properties soil microbial communities soil pH