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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

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Decreased soil pH weakens the positive rhizosphere effect on denitrification capacity

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Pedosphere 2024年第5期34卷 905-915页

作者： Jun WANG Zongxiang ZHANG Fei LIANG Zhao CHE Yongkang WEN Manyu ZHANG Wenjun JIN Zhaorong DONG He SONG College of Agronomy Anhui Agricultural UniversityHefei 230036China Key Laboratory of Arable Land Quality Monitoring and Evaluation Ministry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China College of Resources and Environmental Sciences China Agricultural UniversityBeijing 100193China

The stimulating effect of rhizosphere on denitrification is considered to be an unavoidable loss of soil nitrogen(N)and detrimental to crop N use efficiency,which is regulated by crop growth and soil *** acidification,occurring rapidly in many intensive farming lands,affects both crop growth and soil properties,thereby altering rhizosphere effect on ***,the mechanism by which soil acidification regulates rhizosphere denitrification still remains ***,we determined the denitrification capacity(DC)and associated community compositions of nirK-and nirS-type denitrifiers in maize rhizosphere and bulk soils at four acidity gradients(pH=6.8,6.1,5.2,and 4.2).Results showed that the stimulating effect of rhizosphere on DC strongly depended on soil *** to bulk soil,rhizosphere soil had significantly higher DC at pH 5.2,but not at pH of *** increasing soil acidity,the stimulation of rhizosphere on DC(calculated as the difference in DC between rhizosphere and bulk soils)decreased from 8.01 to 0.01 mg N ***,soil acidification significantly reduced the differences in dissolved organic carbon(DOC)and abundance of key nirK-type denitrifier taxa between rhizosphere and bulk soils,both of which were positively related to the stimulation of rhizosphere on *** findings demonstrated that soil acidification could weaken the positive rhizosphere effect on denitrification via regulated C availability and associated nirK-type denitrifier community,potentially reducing N loss risk in rhizosphere *** independent role of soil p H should be fully considered when modelling N behaviour in plant-soil systems.

关键词： bacterial abundance denitrifier community dissolved organic carbon operational taxonomic unit soil acidification

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Abiotic and biotic drivers of struvite solubilization in contrasting soils

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Pedosphere 2023年第6期33卷 828-837页

作者： Antonio RUIZ-NAVARRO Manuel DELGADO-BAQUERIZO Concha CANO-DíAZ Carlos GARCíA Felipe BASTIDA Centro de Edafologia y Biologia Aplicada del Segura Consejo Superior de Investigaciones Cientificas(CEBAS-CSIC)Department of Soil and Water ConservationEspinardoMurcia E-30100Spain ICL Specialty Fertilizers Iberia TotanaMurcia E-30850Spain Laboratorio de Biodiversidad y Funcionamiento Ecosistemico Instituto de Recursos Naturales y Agrobiologia de Sevilla(IRNAS)CSICAv.Reina Mercedes 10Sevilla E-41012Spain IRNAS-CSIC Unidad Asociada Universidad Pablo de OlavideUniversidad Pablo de Olavide(UPO)Sevilla 41013Spain Centre for Research and Development in Agrifood Systems and Sustainability(CISAS) Instituto Politecnico de Viana do Castelo(IPVC)Rua Escola Industrial e Comercial Nun'Alvares 34Viana do Castelo 4900-347Portugal

Phosphorus(P) limitation in the coming decades calls for the utilization of alternative fertilizers in agriculture. Struvite is a promising P source, but its potential role as a fertilizer is dependent on different physical, chemical, and biological properties, which are very heterogeneous in soil, complicating the prediction of the best soil conditions for its application. Here, we evaluated the solubility of struvite in soil, its redistribution into P fractions, and its potential abiotic and biotic drivers in 62 globally distributed soils with contrasting properties through an incubation assay. We found that after 40 d, about 35% of struvite P was redistributed into soil fractions more accessible to plants and microbes. Phosphorus redistribution from struvite was driven by a complex suite of soil physical, chemical, and microbial properties as well as environmental factors that varied across soils. Soil texture played a critical role in determining the redistribution of P in struvite-amended soils in soluble(H2O extraction), labile(NaHCO3 extraction), and moderately labile(NaOH extraction) *** addition, the soil solution cation concentration was one of the most important drivers of available struvite-derived P fractions. The great importance of texture and cations in determining struvite-derived P fractions in soil was contrasted with the relatively minor role of pH. At the microbial level, the number of bacterial operational taxonomic units(OTUs) from the unfertilized soils that correlated with struvite-derived P fractions was higher than that of fungi. The number of OTUs that correlated with the struvite-derived soluble P fraction was dominated by fungi, whereas the number of OTUs that correlated with the struvite-derived labile P fraction was dominated by bacteria. Overall, this study provided a predictive framework for the potential use of struvite as a P fertilizer in contrasting soils.

关键词： bacteria fungi environmental factor operational taxonomic unit phosphorus fertilizer phosphorus fraction phosphorus solubilization soil fertility soil property

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Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

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Pedosphere 2021年第4期31卷 521-530页

作者： Songjuan GAO Weidong CAO Guopeng ZHOU Robert M.REES College of Resources and Environmental Sciences Nanjing Agricultural UniversityNanjing 210095(China) Key Laboratory of Plant Nutrition and Fertilizer Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081(China) Scotland’s Rural College(SRUC) West Mains RoadEdinburgh EH93JG(UK)

The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at

关键词： alpha diversity bacterial composition functional group operational taxonomic unit soil fertility Weighted UniFrac distance

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Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

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Pedosphere 2020年第6期30卷 778-790页

作者： Casparus J.BRINK Anneke POSTMA Etienne SLABBERT Ferdinand POSTMA A.Muthama MUASYA Karin JACOBS Department of Microbiology University of StellenboschPrivate Bag X1Stellenbosch 7600South Africa Central Analytical Facility University of StellenboschPrivate Bag X1Stellenbosch 7602South Africa Department of Biological Sciences University of Cape TownPrivate Bag X3Rondebosch 7701South Africa

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos *** interactions between *** and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos *** aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown ***,as well as the effect of seasonal changes on these *** communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were *** N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain ***,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this *** similar bacterial communities were associated with natural and commercially grown *** differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet *** study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important ***.

关键词： bulk soil fynbos N-fixing bacterial community operational taxonomic unit rhizosphere soil 16S rRNA sequencing

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Exploring the interaction patterns among taxa and environments from marine metagenomic data

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Frontiers of Electrical and Electronic Engineering in China 2016年第2期4卷 84-91页

作者： Ze-Gang Wei Shao-Wu Zhang Fang Jing Key Laboratory of Information Fusion Technology of Ministry of Education College of Automation Northwestern PolytechnicalUniversity Xi'an 710072 China

The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring these patterns is helpful for exploiting the marine resources. In this paper, we use the complex network approach to mine and analyze the interaction patterns of marine taxa and environments in spring, summer, fall and winter seasons. With the 16S rRNA pyrosequencing data of 76 time point taken monthly over 6 years, we first use our MtHc clustering algorithm to generate the operational taxonomic units （OTUs）. Then, employ the k-means method to divide 76 time point samples into four seasonal groups, and utilize mutual information （MI） to construct the four correlation networks among microbial species and environment factors. Finally, we adopt the symmetrical non-negative matrix factorization method to detect the interaction patterns, and analysis the relationship between marine species and environment factors. The results show that the four seasonal microbial interaction networks have the characters of complex networks, and interaction patterns are related with the seasonal variability; the same environmental factor influences different species in the four seasons; the four environmental factors of day length, photosynthetically active radiation, NO2＋ NO3 and silicate may have stronger influences on microbes than other environment factors.

关键词： marine microbe operational taxonomic unit interaction pattern network clustering

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Metagenomic Surveys of Gut Microbiota

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Genomics, Proteomics & Bioinformatics 2015年第3期13卷 148-158页

作者： Rahul Shubhra Mandal Sudipto Saha Santasabuj Das Biomedical Informatics Centre National Institute of Cholera and Enteric Diseases Bioinformatics Centre Bose Institute Division of Clinical Medicine National Institute of Cholera and Enteric Diseases

Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax- onomic unit （OTU） levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti- mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac- tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe-microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe-microbe inter- action networks.

关键词： Disease Sequencing 16S rRNA operational taxonomic unit Microbial interactionnetwork

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