Pub Date : 2023-03-10DOI: 10.1186/s12302-023-00724-5
Yang Yang, Weiguo Liu, Tingwen Huang, Yaru Yang
Background
The interactions between rhizosphere microbial community and ephemeral desert plants strongly affect the ecological protection, restoration and reconstruction in deserts. Ephemeral desert plants as the pioneer plants in the succession are widely distributed in deserts. However, how the ephemeral desert plants assemble their rhizosphere microbiota to adapt to arid and semi-arid environments has been little explored. Here, we used high-throughput sequencing techniques to compare rhizosphere bacterial communities and functions with different ephemeral desert plants composition from Gurbantünggüt Desert in western China.
Results
These plants had the same dominant bacterial phyla, which approximately counted 98% of the total bacterial communities. But the bacterial communities had significant differences (P < 0.05) in the composition, structure, diversity and functions of all groups. When comparing every two groups, similarities appeared in the composition, structure and functions of rhizosphere microbiota, and within each group, it is more likely that the rhizosphere bacterial communities of closely related ephemeral desert plants tend to be consistent. Additionally, the rhizosphere bacterial taxa had more similarities in predicted functions. And the predicted functions were correlated with the dominant bacterial phyla.
Conclusions
Overall, to adapt to the arid and semi-arid environments, the rhizosphere bacterial communities of ephemeral desert plants appear similarities based on having differences. This finding will help to understand the importance of how plants and soil microorganisms cooperate in the process of adaption to arid and semi-arid environments.
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Pub Date : 2023-02-21DOI: 10.1186/s12302-023-00715-6
Rafael Fonseca Benevenuto, Caroline Bedin Zanatta, Friedrich Waßmann, Michael F. Eckerstorfer, Sarah Zanon Agapito-Tenfen
In Europe, genetically modified organisms (GMOs) are subject to an authorization process including a mandatory risk assessment. According to the respective guidance by the European Food Safety Authority (EFSA), one of the pillars of this GMO risk assessment is a comparative analysis of the compositional and agronomic characteristics. This targeted approach has been criticized for its limitations, as it only considers pre-determined compounds, being insufficient to assess a comprehensive range of relevant compounds, including toxins and anti-nutrients, on a case-specific basis. Strategies based on advanced untargeted omics technologies have been proposed as a potential broader approach to be implemented into the initial step of the risk assessment framework. Here, we provide an example of a step-by-step omics analysis based on systems biology approach to fit into the context of European GMO regulation. We have performed field trial experiments with genetically modified (GM) Intacta™ Roundup Ready™ 2 Pro soybean containing both cry1Ac and cp4epsps transgenic inserts and analyzed its proteomic profile against the non-GM counterpart and reference varieties. Based on EFSA’s comparative endpoint-by-endpoint approach, the proteomics analysis revealed six proteins from the GMO outside the 99% tolerance intervals of reference varieties (RVs) in the equivalence test. Interestingly, from the near-isogenic (non-GM) comparator we found as many as ten proteins to be outside of the said RVs’ equivalence limits. According to EFSA’s statistical guidelines, differences found in metabolite abundance between a GMO and its non-GM comparator would not be considered biologically relevant as all compounds of concern remained within the equivalence limits of commercial RVs. By assessing the proteomic and metabolomic data through our proposed systems biology approach, we found 70 proteins, and the metabolite xylobiose as differentially expressed between the GMO and its non-GM comparator. Biological relevance of such results was revealed through a functional biological network analysis, where we found alterations in several metabolic pathways related to protein synthesis and protein processing. Moreover, the allergenicity analysis identified 43 proteins with allergenic potential being differentially expressed in the GM soybean variety. Our results demonstrate that implementation of advanced untargeted omics technologies in the risk assessment of GMOs will enable early and holistic assessment of possible adverse effects. The proposed approach can provide a better understanding of the specific unintended effects of the genetic modification on the plant’s metabolism, the involved biological networks, and their interactions, and allows to formulate and investigate dedicated risk hypotheses in the first place. We draw conclusions on a detailed comparison with the comparative assessment according to EFSA and provide scientific arguments and examples on how the current co
{"title":"Integration of omics analyses into GMO risk assessment in Europe: a case study from soybean field trials","authors":"Rafael Fonseca Benevenuto, Caroline Bedin Zanatta, Friedrich Waßmann, Michael F. Eckerstorfer, Sarah Zanon Agapito-Tenfen","doi":"10.1186/s12302-023-00715-6","DOIUrl":"10.1186/s12302-023-00715-6","url":null,"abstract":"<div><p>In Europe, genetically modified organisms (GMOs) are subject to an authorization process including a mandatory risk assessment. According to the respective guidance by the European Food Safety Authority (EFSA), one of the pillars of this GMO risk assessment is a comparative analysis of the compositional and agronomic characteristics. This targeted approach has been criticized for its limitations, as it only considers pre-determined compounds, being insufficient to assess a comprehensive range of relevant compounds, including toxins and anti-nutrients, on a case-specific basis. Strategies based on advanced untargeted omics technologies have been proposed as a potential broader approach to be implemented into the initial step of the risk assessment framework. Here, we provide an example of a step-by-step omics analysis based on systems biology approach to fit into the context of European GMO regulation. We have performed field trial experiments with genetically modified (GM) Intacta™ Roundup Ready™ 2 Pro soybean containing both cry1Ac and cp4epsps transgenic inserts and analyzed its proteomic profile against the non-GM counterpart and reference varieties. Based on EFSA’s comparative endpoint-by-endpoint approach, the proteomics analysis revealed six proteins from the GMO outside the 99% tolerance intervals of reference varieties (RVs) in the equivalence test. Interestingly, from the near-isogenic (non-GM) comparator we found as many as ten proteins to be outside of the said RVs’ equivalence limits. According to EFSA’s statistical guidelines, differences found in metabolite abundance between a GMO and its non-GM comparator would not be considered biologically relevant as all compounds of concern remained within the equivalence limits of commercial RVs. By assessing the proteomic and metabolomic data through our proposed systems biology approach, we found 70 proteins, and the metabolite xylobiose as differentially expressed between the GMO and its non-GM comparator. Biological relevance of such results was revealed through a functional biological network analysis, where we found alterations in several metabolic pathways related to protein synthesis and protein processing. Moreover, the allergenicity analysis identified 43 proteins with allergenic potential being differentially expressed in the GM soybean variety. Our results demonstrate that implementation of advanced untargeted omics technologies in the risk assessment of GMOs will enable early and holistic assessment of possible adverse effects. The proposed approach can provide a better understanding of the specific unintended effects of the genetic modification on the plant’s metabolism, the involved biological networks, and their interactions, and allows to formulate and investigate dedicated risk hypotheses in the first place. We draw conclusions on a detailed comparison with the comparative assessment according to EFSA and provide scientific arguments and examples on how the current co","PeriodicalId":54293,"journal":{"name":"Environmental Sciences Europe","volume":"35 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2023-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enveurope.springeropen.com/counter/pdf/10.1186/s12302-023-00715-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4819902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-17DOI: 10.1186/s12302-023-00720-9
Ibrahim Sa’adu, Andrea Farsang
Researchers are focused on the global issue of plastic contamination in agricultural soils because of the known effects of plastics on the soil ecosystem. Previous reviews did not pay attention to plastic sources, standardized extraction methods, soil characterization, and the abundance of plastics in agricultural soils. This study aims to review up-to-the-minute knowledge about plastic contamination studies, suggest the best method for microplastic studies, and propose future research areas. The research about plastic contamination in agricultural soils published from January 2018 to March 2022 was reviewed for this review article. Studies focusing on microplastics in soils other than agricultural soils were not considered in the present review. The data were acquired from several databases, namely Web of Science and Google Scholar. The keywords used to search these databases were "microplastics AND agricultural soils" and "macroplastics AND agricultural soils". Other literature sources were obtained from the reference lists of downloaded articles, and other pieces of literature that directly dealt with macroplastic and microplastic contamination in agricultural soils were obtained from relevant journals and books. Overall, 120 sources of literature, including 102 original research articles, 13 review articles, and five books, were selected, reviewed, and synthesized. As expected, agricultural soils, including arable lands, paddy lands, uplands, irrigation, and greenhouse soils, receive plastic contaminants. The contaminants of different sizes and forms are distributed spatially and temporally in the surface, subsurface, and profiles of the agricultural soils. Unlike previous studies that reported many studies on sewage sludge, the significant sources of plastic contamination in the agricultural soils included mulching, sludge and compost placement, and greenhouses abandonment. The distribution of plastic contamination studies in the agricultural lands is Asia: 60%; Europe: 29%; Africa: 4%; North America: 4%; Latin America: 3%; and Australia: 0%. After careful analysis of the methods used for the plastics contamination studies, the study concluded that floatations with low-density solutions such as distilled water and NaCl are efficient in separating light-density microplastics. In contrast, ZnCl and NaI are incredibly efficient in separating the heavy-density microplastics. Moreover, this review provides insight for future research in the field.
由于塑料对土壤生态系统的已知影响,研究人员一直关注农业土壤中塑料污染的全球问题。以往的综述没有关注塑料来源、标准化提取方法、土壤特征以及农业土壤中塑料的丰度。本研究旨在回顾塑料污染研究的最新进展,提出微塑料研究的最佳方法,并提出未来的研究方向。本文回顾了2018年1月至2022年3月发表的农业土壤塑料污染研究成果。本综述未考虑农业土壤以外土壤中微塑料的研究。这些数据来自几个数据库,即Web of Science和Google Scholar。用于检索这些数据库的关键词是“微塑料和农业土壤”和“宏观塑料和农业土壤”。其他文献来源来自下载文章的参考文献列表,其他直接涉及农业土壤宏塑性和微塑性污染的文献来自相关期刊和书籍。总的来说,120个文献来源,包括102篇原创研究文章,13篇综述文章和5本书,被选择,审查和综合。不出所料,农业土壤,包括耕地、稻田、高地、灌溉和温室土壤,都会受到塑料污染。不同大小和形式的污染物在空间和时间上分布在农业土壤的表层、地下和剖面中。与以往对污水污泥的研究不同,农业土壤中塑料污染的主要来源包括覆盖、污泥和堆肥的放置以及温室的废弃。农业用地塑料污染研究分布在亚洲:60%;欧洲:29%;非洲:4%;北美:4%;拉丁美洲:3%;澳大利亚:0%。在仔细分析了塑料污染研究中使用的方法后,该研究得出结论,用蒸馏水和NaCl等低密度溶液进行浮选,可以有效分离轻密度微塑料。相比之下,ZnCl和NaI在分离高密度微塑料方面非常有效。同时,本文也为该领域未来的研究提供了思路。
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Pub Date : 2023-02-15DOI: 10.1186/s12302-023-00716-5
Marcel Riegel, Brigitte Haist-Gulde, Frank Sacher
Laboratory tests and column tests were carried out in a waterwoks to investigate the removal of short- and long-chain PFAS using activated carbon filtration and ion exchange treatment. For all adsorbents, the sorption affinity of short-chain per- and polyfluoroalkyl carboxylic acids (PFCA) was significantly lower than that of long-chain PFAS or short-chain per- and polyfluoroalkyl sulfonic acids (PFSA). In the PFAS-polluted groundwater matrix, the short-chain PFCA PFBA and PFPeA could only be sufficiently removed with activated carbon over short run times of 6000 and 11,000 bed volumes (BV), respectively. Longer PFCA with a chain length of C6 or more were removed over longer run times.
The removal of short-chain PFCA using ion exchange media could also only be achieved over relatively short run times of 5000 BV for PFBA, 10,000BV for PFPeA and 18,000 BV for PFHxA. These are sometimes significantly longer than those of activated carbon. Due to the higher material costs for ion exchange media, there are nevertheless no lower operating costs when the ion exchangers are used in single-use mode. However, ion exchangers can be regenerated and then reused which can result in economic advantages compared to activated carbon filtration. However, for the extensive regeneration, especially for the elution of the long-chain PFAS, the additional use of ethanol is needed in the process. In contrast, the short-chain PFBA and PFPeA can be extracted without organic solvent from a weakly basic ion exchanger.
{"title":"Sorptive removal of short-chain perfluoroalkyl substances (PFAS) during drinking water treatment using activated carbon and anion exchanger","authors":"Marcel Riegel, Brigitte Haist-Gulde, Frank Sacher","doi":"10.1186/s12302-023-00716-5","DOIUrl":"10.1186/s12302-023-00716-5","url":null,"abstract":"<div><p>Laboratory tests and column tests were carried out in a waterwoks to investigate the removal of short- and long-chain PFAS using activated carbon filtration and ion exchange treatment. For all adsorbents, the sorption affinity of short-chain per- and polyfluoroalkyl carboxylic acids (PFCA) was significantly lower than that of long-chain PFAS or short-chain per- and polyfluoroalkyl sulfonic acids (PFSA). In the PFAS-polluted groundwater matrix, the short-chain PFCA PFBA and PFPeA could only be sufficiently removed with activated carbon over short run times of 6000 and 11,000 bed volumes (BV), respectively. Longer PFCA with a chain length of C6 or more were removed over longer run times.</p><p>The removal of short-chain PFCA using ion exchange media could also only be achieved over relatively short run times of 5000 BV for PFBA, 10,000BV for PFPeA and 18,000 BV for PFHxA. These are sometimes significantly longer than those of activated carbon. Due to the higher material costs for ion exchange media, there are nevertheless no lower operating costs when the ion exchangers are used in single-use mode. However, ion exchangers can be regenerated and then reused which can result in economic advantages compared to activated carbon filtration. However, for the extensive regeneration, especially for the elution of the long-chain PFAS, the additional use of ethanol is needed in the process. In contrast, the short-chain PFBA and PFPeA can be extracted without organic solvent from a weakly basic ion exchanger.</p></div>","PeriodicalId":54293,"journal":{"name":"Environmental Sciences Europe","volume":"35 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://enveurope.springeropen.com/counter/pdf/10.1186/s12302-023-00716-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4608220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}