Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance th...Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.展开更多
Microplastics(MPs)and phthalate acid esters(PAEs)co-occur as emerging contaminants of global importance.Their abundance in soil is of increasing concern as plastic-intensive practices continue.Mulching with plastic fi...Microplastics(MPs)and phthalate acid esters(PAEs)co-occur as emerging contaminants of global importance.Their abundance in soil is of increasing concern as plastic-intensive practices continue.Mulching with plastic films,inclusion in fertilizers,composts,sludge application,and wastewater irrigation are all major and common sources of MPs and PAEs in soil.Here,we review studies on the concentration and effects of MPs and PAEs in soil.While there is limited research on the interactions between MPs and PAEs in agroecosystems,there is evidence to suggest they could mutually affect soil ecology and plant growth.Therefore,we propose new research into 1)establishing an efficient,accurate,and simple method to quantify different types of microplastics in soils and plants;2)exploring the behavior and understanding the mechanisms of co-transfer,transformation,and interactions with soil biota(especially in vegetable production systems);3)assessing the risk and consequences of combined and discreet impacts of MPs and PAEs on plants and soil biota,and 4)preventing or reducing the transfer of MPs and PAEs into-and within-the food chain.展开更多
Thank you for the interest in the article of soil biofilms.We are happy to discuss this topic.Firstly,we should clarify something crucial:at no point has the term“soil biofilm”been used to describe the soil microbia...Thank you for the interest in the article of soil biofilms.We are happy to discuss this topic.Firstly,we should clarify something crucial:at no point has the term“soil biofilm”been used to describe the soil microbial biomass.We have always maintained that biofilms comprise microbial biomass and EPS as distinct pools.Therefore,the title of the above article,“Soil biofilms”:Misleading description of microbial biomass,is itself misleading.展开更多
Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observab...Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://unite.ut.ee),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.展开更多
基金supported by the National Natural Science Foundation of China(41877029)the National Basic Research Program of China(2016YFD0800206)the Fundamental Research Funds for the Central Universities(2662017JC008).
文摘Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.
基金This research was funded by the National Key Research and Development Program of China(2016YFD0800204)the Outstanding Youth Fund of Natural Science Foundation of Jiangsu,China(BK20150050)+2 种基金the National Natural Science Foundation of China(41977137,42007145,41977356)the Key Program of Frontier Sciences,Chinese Academy of Sciences(QYZDJ-SSWDQC035)the Natural Science Foundation of Jiangsu,China(BK20201106).
文摘Microplastics(MPs)and phthalate acid esters(PAEs)co-occur as emerging contaminants of global importance.Their abundance in soil is of increasing concern as plastic-intensive practices continue.Mulching with plastic films,inclusion in fertilizers,composts,sludge application,and wastewater irrigation are all major and common sources of MPs and PAEs in soil.Here,we review studies on the concentration and effects of MPs and PAEs in soil.While there is limited research on the interactions between MPs and PAEs in agroecosystems,there is evidence to suggest they could mutually affect soil ecology and plant growth.Therefore,we propose new research into 1)establishing an efficient,accurate,and simple method to quantify different types of microplastics in soils and plants;2)exploring the behavior and understanding the mechanisms of co-transfer,transformation,and interactions with soil biota(especially in vegetable production systems);3)assessing the risk and consequences of combined and discreet impacts of MPs and PAEs on plants and soil biota,and 4)preventing or reducing the transfer of MPs and PAEs into-and within-the food chain.
文摘Thank you for the interest in the article of soil biofilms.We are happy to discuss this topic.Firstly,we should clarify something crucial:at no point has the term“soil biofilm”been used to describe the soil microbial biomass.We have always maintained that biofilms comprise microbial biomass and EPS as distinct pools.Therefore,the title of the above article,“Soil biofilms”:Misleading description of microbial biomass,is itself misleading.
基金financial support from European Funds through COMPETENational Funds through the Portuguese Foundation for Science and Technology(FCT)within projects PTDC/AGR-FOR/3807/2012-FCOMP-01-0124-FEDER-027979 and PEst-C/MAR/LA0017/2013+4 种基金supported by National Science Foundation Grant DBI 1046115supported by FFG,BMWFJ,BMVIT,ZIT,Zukunftsstiftung Tirol,and Land Steiermark within the Austrian COMET program FFG Grant 824186Financial support to JP was partially provided by the Polish Ministry of Science and Higher Education(MNiSW),grant no.NN303_548839financial support from FAPEMIG and CNPqfunded by the Government of Canada through Genome Canada and the Ontario Genomics Institute through the Biomonitoring 2.0 project(OGI-050).
文摘Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://unite.ut.ee),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.