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Ochoa-Hueso R, Eldridge DJ, Berdugo M, Trivedi P, Sokoya B, Cano-Díaz C, Abades S, Alfaro F, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Rios A, Durán J, Geisen S, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Singh BK, Teixido AL, Torres-Díaz C, Wang L, Wang J, Wang J, Zaady E, Zhou X, Zhou XQ, Tedersoo L, Delgado-Baquerizo M. Unearthing the soil-borne microbiome of land plants. GLOBAL CHANGE BIOLOGY 2024; 30:e17295. [PMID: 38804108 DOI: 10.1111/gcb.17295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 05/29/2024]
Abstract
Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.
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Li W, Zhuang Y, Shao SJ, Trivedi P, Zheng B, Huang GL, He Z, Zhang X. Essential contribution of the JAK/STAT pathway to carcinogenesis, lytic infection of herpesviruses and pathogenesis of COVID‑19 (Review). Mol Med Rep 2024; 29:39. [PMID: 38240082 PMCID: PMC10828999 DOI: 10.3892/mmr.2024.13163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
The intracellular pathway of Janus kinase/signal transducer and activator of transcription (JAK/STAT) and modification of nucleosome histone marks regulate the expression of proinflammatory mediators, playing an essential role in carcinogenesis, antiviral immunity and the interaction of host proteins with Herpesviral particles. The pathway has also been suggested to play a vital role in the clinical course of the acute infection caused by severe acute respiratory syndrome coronavirus type 2 (SARS‑CoV‑2; known as coronavirus infection‑2019), a novel human coronavirus initially identified in the central Chinese city Wuhan towards the end of 2019, which evolved into a pandemic affecting nearly two million people worldwide. The infection mainly manifests as fever, cough, myalgia and pulmonary involvement, while it also attacks multiple viscera, such as the liver. The pathogenesis is characterized by a cytokine storm, with an overproduction of proinflammatory mediators. Innate and adaptive host immunity against the viral pathogen is exerted by various effectors and is regulated by different signaling pathways notably the JAK/STAT. The elucidation of the underlying mechanism of the regulation of mediating factors expressed in the viral infection would assist diagnosis and antiviral targeting therapy, which will help overcome the infection caused by SARS‑CoV‑2.
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Leopizzi M, Mundo L, Messina E, Campolo F, Lazzi S, Angeloni A, Marchese C, Leoncini L, Giordano C, Slack F, Trivedi P, Anastasiadou E. Epstein-Barr virus-encoded EBNA2 downregulates ICOSL by inducing miR-24 in B-cell lymphoma. Blood 2024; 143:429-443. [PMID: 37847858 PMCID: PMC10862363 DOI: 10.1182/blood.2023021346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/12/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
ABSTRACT Hematological malignancies such as Burkitt lymphoma (BL), Hodgkin lymphoma (HL), and diffuse large B-cell lymphoma (DLBCL) cause significant morbidity in humans. A substantial number of these lymphomas, particularly HL and DLBCLs have poorer prognosis because of their association with Epstein-Barr virus (EBV). Our earlier studies have shown that EBV-encoded nuclear antigen (EBNA2) upregulates programmed cell death ligand 1 in DLBCL and BLs by downregulating microRNA-34a. Here, we investigated whether EBNA2 affects the inducible costimulator (ICOS) ligand (ICOSL), a molecule required for efficient recognition of tumor cells by T cells through the engagement of ICOS on the latter. In virus-infected and EBNA2-transfected B-lymphoma cells, ICOSL expression was reduced. Our investigation of the molecular mechanisms revealed that this was due to an increase in microRNA-24 (miR-24) by EBNA2. By using ICOSL 3' untranslated region-luciferase reporter system, we validated that ICOSL is an authentic miR-24 target. Transfection of anti-miR-24 molecules in EBNA2-expressing lymphoma cells reconstituted ICOSL expression and increased tumor immunogenicity in mixed lymphocyte reactions. Because miR-24 is known to target c-MYC, an oncoprotein positively regulated by EBNA2, we analyzed its expression in anti-miR-24 transfected lymphoma cells. Indeed, the reduction of miR-24 in EBNA2-expressing DLBCL further elevated c-MYC and increased apoptosis. Consistent with the in vitro data, EBNA2-positive DLBCL biopsies expressed low ICOSL and high miR-24. We suggest that EBV evades host immune responses through EBNA2 by inducing miR-24 to reduce ICOSL expression, and for simultaneous rheostatic maintenance of proproliferative c-MYC levels. Overall, these data identify miR-24 as a potential therapeutically relevant target in EBV-associated lymphomas.
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Liu S, Plaza C, Ochoa-Hueso R, Trivedi C, Wang J, Trivedi P, Zhou G, Piñeiro J, Martins CSC, Singh BK, Delgado-Baquerizo M. Litter and soil biodiversity jointly drive ecosystem functions. GLOBAL CHANGE BIOLOGY 2023; 29:6276-6285. [PMID: 37578170 DOI: 10.1111/gcb.16913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023]
Abstract
The decomposition of litter and the supply of nutrients into and from the soil are two fundamental processes through which the above- and belowground world interact. Microbial biodiversity, and especially that of decomposers, plays a key role in these processes by helping litter decomposition. Yet the relative contribution of litter diversity and soil biodiversity in supporting multiple ecosystem services remains virtually unknown. Here we conducted a mesocosm experiment where leaf litter and soil biodiversity were manipulated to investigate their influence on plant productivity, litter decomposition, soil respiration, and enzymatic activity in the littersphere. We showed that both leaf litter diversity and soil microbial diversity (richness and community composition) independently contributed to explain multiple ecosystem functions. Fungal saprobes community composition was especially important for supporting ecosystem multifunctionality (EMF), plant production, litter decomposition, and activity of soil phosphatase when compared with bacteria or other fungal functional groups and litter species richness. Moreover, leaf litter diversity and soil microbial diversity exerted previously undescribed and significantly interactive effects on EMF and multiple individual ecosystem functions, such as litter decomposition and plant production. Together, our work provides experimental evidence supporting the independent and interactive roles of litter and belowground soil biodiversity to maintain ecosystem functions and multiple services.
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Rani A, Tanwar M, Verma TP, Patra P, Trivedi P, Kumar R, Jha HC. Understanding the role of membrane cholesterol upon Epstein Barr virus infection in astroglial cells. Front Immunol 2023; 14:1192032. [PMID: 37876925 PMCID: PMC10591182 DOI: 10.3389/fimmu.2023.1192032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Background EBV infection has long been postulated to trigger multiple sclerosis (MS) and anti-EBV antibodies showed a consistent presence in MS patients. Previous reports from our group have shown that the EBV infects different brain cells. Entry of the virus in neuronal cells is assisted by several host factors including membrane cholesterol. By using an inhibitor, methyl-β-cyclodextrin (MβCD), we evaluated the role of membrane cholesterol in EBV infection and pathogenesis. Methodology The membrane cholesterol depleted cells were infected with EBV and its latent genes expression were assessed. Further, EBV-mediated downstream signalling molecules namely STAT3, RIP, NF-kB and TNF-α levels was checked at protein level along with spatial (periphery and nucleus) and temporal changes in biomolecular fingerprints with Raman microspectroscopy (RS). Results Upon treatment with MβCD, lmp1 and lmp2a suggested significant downregulation compared to EBV infection. Downstream molecules like STAT3 and RIP, exhibited a decrease in protein levels temporally upon exposure to MβCD while NF-kB levels were found to be increased. Further, the intensity of the Raman spectra exhibited an increase in triglycerides and fatty acids in the cytoplasm of EBV-infected LN-229 cells compared to MβCD+EBV. Likewise, the Raman peak width of cholesterol, lipid and fatty acids were found to be reduced in EBV-infected samples indicates elevation in the cholesterol specific moieties. In contrast, an opposite pattern was observed in the nucleus. Moreover, the ingenuity pathway analysis revealed protein molecules such as VLDLR, MBP and APP that are associated with altered profile of cholesterol, fatty acids and triglycerides with infection-related CNS disorders. Conclusion Taken together, our results underline the important role of membrane cholesterol over EBV entry/pathogenesis in astroglia cells which further trigger/exacerbate virus-associated neuropathologies. These results likely to aid into the prognosis of neurological disease like MS.
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Yuan J, Zhao K, Tan X, Xue R, Zeng Y, Ratti C, Trivedi P. Perspective on the development of synthetic microbial community (SynCom) biosensors. Trends Biotechnol 2023; 41:1227-1236. [PMID: 37183053 DOI: 10.1016/j.tibtech.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Synthetic microbial community (SynCom) biosensors are a promising technology for detecting and responding to environmental cues and target molecules. SynCom biosensors use engineered microorganisms to create a more complex and diverse sensing system, enabling them to respond to stimuli with enhanced sensitivity and accuracy. Here, we give a definition of SynCom biosensors, outline their construction workflow, and discuss current biosensing technology. We also highlight the challenges and future for developing and optimizing SynCom biosensors and the potential applications in agriculture and food management, biotherapeutic development, home sensing, urban and environmental monitoring, and the One Health foundation. We believe SynCom biosensors could be used in a real-time and remote-controlled manner to sense the chaos of constantly dynamic environments.
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Correction: Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2023; 14:50. [PMID: 37099064 PMCID: PMC10133421 DOI: 10.1007/s12672-023-00640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
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Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, Bastida F, Moreno-Jiménez E, Zhou XQ, Hu HW, He JZ, Moreno JL, Abades S, Alfaro F, Bamigboye AR, Berdugo M, Blanco-Pastor JL, de Los Ríos A, Duran J, Grebenc T, Illán JG, Makhalanyane TP, Molina-Montenegro MA, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Teixido AL, Casado-Coy N, Trivedi P, Torres-Díaz C, Verma JP, Mukherjee A, Zeng XM, Wang L, Wang J, Zaady E, Zhou X, Huang Q, Tan W, Zhu YG, Rillig MC, Delgado-Baquerizo M. Publisher Correction: Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat Commun 2023; 14:2405. [PMID: 37100778 PMCID: PMC10133300 DOI: 10.1038/s41467-023-37920-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
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Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, Bastida F, Moreno-Jiménez E, Zhou XQ, Hu HW, He JZ, Moreno JL, Abades S, Alfaro F, Bamigboye AR, Berdugo M, Blanco-Pastor JL, de Los Ríos A, Duran J, Grebenc T, Illán JG, Makhalanyane TP, Molina-Montenegro MA, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Teixido AL, Casado-Coy N, Trivedi P, Torres-Díaz C, Verma JP, Mukherjee A, Zeng XM, Wang L, Wang J, Zaady E, Zhou X, Huang Q, Tan W, Zhu YG, Rillig MC, Delgado-Baquerizo M. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat Commun 2023; 14:1706. [PMID: 36973286 PMCID: PMC10042830 DOI: 10.1038/s41467-023-37428-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.
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Malavia M, Lindquist J, Marchak K, Trivedi P, Casadaban L. Abstract No. 268 Modified Radiation Lobectomy as Bridge to Liver Resection: A Single-Center Experience. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Roy Choudhury A, Trivedi P, Choi J, Madhaiyan M, Park JH, Choi W, Walitang DI, Sa T. Inoculation of ACC deaminase-producing endophytic bacteria down-regulates ethylene-induced pathogenesis-related signaling in red pepper (Capsicum annuum L.) under salt stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13909. [PMID: 37026423 DOI: 10.1111/ppl.13909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 05/22/2023]
Abstract
Pathogenesis-related (PR) signaling plays multiple roles in plant development under abiotic and biotic stress conditions and is regulated by a plethora of plant physiological as well as external factors. Here, our study was conducted to evaluate the role of an ACC deaminase-producing endophytic bacteria in regulating ethylene-induced PR signaling in red pepper plants under salt stress. We also evaluated the efficiency of the bacteria in down-regulating the PR signaling for efficient colonization and persistence in the plant endosphere. We used a characteristic endophyte, Methylobacterium oryzae CBMB20 and its ACC deaminase knockdown mutant (acdS- ). The wild-type M. oryzae CBMB20 was able to decrease ethylene emission by 23% compared to the noninoculated and acdS- M. oryzae CBMB20 inoculated plants under salt stress. The increase in ethylene emission resulted in enhanced hydrogen peroxide concentration, phenylalanine ammonia-lyase activity, β-1,3 glucanase activity, and expression profiles of WRKY, CaPR1, and CaPTI1 genes that are typical salt stress and PR signaling factors. Furthermore, the inoculation of both the bacterial strains had shown induction of PR signaling under normal conditions during the initial inoculation period. However, wild-type M. oryzae CBMB20 was able to down-regulate the ethylene-induced PR signaling under salt stress and enhance plant growth and stress tolerance. Collectively, ACC deaminase-producing endophytic bacteria down-regulate the salt stress-mediated PR signaling in plants by regulating the stress ethylene emission levels and this suggests a new paradigm in efficient colonization and persistence of ACC deaminase-producing endophytic bacteria for better plant growth and productivity.
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Arena A, Romeo MA, Focaccetti C, Anastasiadou E, Trivedi P, Cifaldi L, Gilardini Montani MS, Benedetti R, Santarelli R, Gonnella R, Benvenuto M, Marchese C, Masuelli L, Bei R, Cirone M. Different outcome of targeting ERN1/IRE1 alpha and EIF2AK3/PERK in NSG mice engrafted with primary effusion lymphoma. Br J Haematol 2023; 201:e12-e15. [PMID: 36775956 DOI: 10.1111/bjh.18688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/14/2023]
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Manimaran P, Shah R, Trivedi P, Mehta S. Primary cutaneous neuroendocrine tumor with axillary lymph node metastasis: A clinical masquerade. J Postgrad Med 2023; 69:118-119. [PMID: 36751760 DOI: 10.4103/jpgm.jpgm_254_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Nguyen BT, Dumack K, Trivedi P, Islam Z, Hu H. Plant associated protists-Untapped promising candidates for agrifood tools. Environ Microbiol 2023; 25:229-240. [PMID: 36482161 PMCID: PMC10108267 DOI: 10.1111/1462-2920.16303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.
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Fan K, Chu H, Eldridge DJ, Gaitan JJ, Liu YR, Sokoya B, Wang JT, Hu HW, He JZ, Sun W, Cui H, Alfaro FD, Abades S, Bastida F, Díaz-López M, Bamigboye AR, Berdugo M, Blanco-Pastor JL, Grebenc T, Duran J, Illán JG, Makhalanyane TP, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Verma JP, Rey A, Rodríguez A, Siebe C, Teixido AL, Trivedi P, Wang L, Wang J, Yang T, Zhou XQ, Zhou X, Zaady E, Tedersoo L, Delgado-Baquerizo M. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat Ecol Evol 2023; 7:113-126. [PMID: 36631668 DOI: 10.1038/s41559-022-01935-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023]
Abstract
While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant-soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2022; 13:139. [PMID: 36520265 PMCID: PMC9755447 DOI: 10.1007/s12672-022-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morphogenesis and organogenesis in the low organisms have been found to be modulated by a number of proteins, and one of such factor, deformed epidermal auto-regulatory factor-1 (DEAF-1) has been initially identified in Drosophila. The mammalian homologue of DEAF-1 and structurally related proteins have been identified, and they formed a family with over 20 members. The factors regulate gene expression through association with co-repressors, recognition of genomic marker, to exert histone modification by catalyze addition of some chemical groups to certain amino acid residues on histone and non-histone proteins, and degradation host proteins, so as to regulate cell cycle progression and execution of cell death. The formation of fused genes during chromosomal translocation, exemplified with myeloid transforming gene on chromosome 8 (MTG8)/eight-to-twenty one translocation (ETO) /ZMYND2, MTG receptor 1 (MTGR1)/ZMYND3, MTG on chromosome 16/MTGR2/ZMYND4 and BS69/ZMYND11 contributes to malignant transformation. Other anomaly like copy number variation (CNV) of BS69/ZMYND11 and promoter hyper methylation of BLU/ZMYND10 has been noted in malignancies. It has been reported that when fusing with Runt-related transcription factor 1 (RUNX1), the binding of MTG8/ZMYND2 with co-repressors is disturbed, and silencing of BLU/ZMYND10 abrogates its ability to inhibition of cell cycle and promotion of apoptotic death. Further characterization of the implication of ZMYND proteins in carcinogenesis would enhance understanding of the mechanisms of occurrence and early diagnosis of tumors, and effective antitumor efficacy.
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Delgado-Baquerizo M, Hu HW, Maestre FT, Guerra CA, Eisenhauer N, Eldridge DJ, Zhu YG, Chen QL, Trivedi P, Du S, Makhalanyane TP, Verma JP, Gozalo B, Ochoa V, Asensio S, Wang L, Zaady E, Illán JG, Siebe C, Grebenc T, Zhou X, Liu YR, Bamigboye AR, Blanco-Pastor JL, Duran J, Rodríguez A, Mamet S, Alfaro F, Abades S, Teixido AL, Peñaloza-Bojacá GF, Molina-Montenegro MA, Torres-Díaz C, Perez C, Gallardo A, García-Velázquez L, Hayes PE, Neuhauser S, He JZ. The global distribution and environmental drivers of the soil antibiotic resistome. MICROBIOME 2022; 10:219. [PMID: 36503688 PMCID: PMC9743735 DOI: 10.1186/s40168-022-01405-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 10/31/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. RESULTS We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. CONCLUSIONS Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.
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Guerra CA, Berdugo M, Eldridge DJ, Eisenhauer N, Singh BK, Cui H, Abades S, Alfaro FD, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Ríos A, Durán J, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Picó S, Verma JP, Rey A, Rodríguez A, Tedersoo L, Teixido AL, Torres-Díaz C, Trivedi P, Wang J, Wang L, Wang J, Zaady E, Zhou X, Zhou XQ, Delgado-Baquerizo M. Global hotspots for soil nature conservation. Nature 2022; 610:693-698. [PMID: 36224389 DOI: 10.1038/s41586-022-05292-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/30/2022] [Indexed: 11/09/2022]
Abstract
Soils are the foundation of all terrestrial ecosystems1. However, unlike for plants and animals, a global assessment of hotspots for soil nature conservation is still lacking2. This hampers our ability to establish nature conservation priorities for the multiple dimensions that support the soil system: from soil biodiversity to ecosystem services. Here, to identify global hotspots for soil nature conservation, we performed a global field survey that includes observations of biodiversity (archaea, bacteria, fungi, protists and invertebrates) and functions (critical for six ecosystem services) in 615 composite samples of topsoil from a standardized survey in all continents. We found that each of the different ecological dimensions of soils-that is, species richness (alpha diversity, measured as amplicon sequence variants), community dissimilarity and ecosystem services-peaked in contrasting regions of the planet, and were associated with different environmental factors. Temperate ecosystems showed the highest species richness, whereas community dissimilarity peaked in the tropics, and colder high-latitudinal ecosystems were identified as hotspots of ecosystem services. These findings highlight the complexities that are involved in simultaneously protecting multiple ecological dimensions of soil. We further show that most of these hotspots are not adequately covered by protected areas (more than 70%), and are vulnerable in the context of several scenarios of global change. Our global estimation of priorities for soil nature conservation highlights the importance of accounting for the multidimensionality of soil biodiversity and ecosystem services to conserve soils for future generations.
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Torkington J, Harries R, O'Connell S, Knight L, Islam S, Bashir N, Watkins A, Fegan G, Cornish J, Rees B, Cole H, Jarvis H, Jones S, Russell I, Bosanquet D, Cleves A, Sewell B, Farr A, Zbrzyzna N, Fiera N, Ellis-Owen R, Hilton Z, Parry C, Bradbury A, Wall P, Hill J, Winter D, Cocks K, Harris D, Hilton J, Vakis S, Hanratty D, Rajagopal R, Akbar F, Ben-Sassi A, Francis N, Jones L, Williamson M, Lindsey I, West R, Smart C, Ziprin P, Agarwal T, Faulkner G, Pinkney T, Vimalachandran D, Lawes D, Faiz O, Nisar P, Smart N, Wilson T, Myers A, Lund J, Smolarek S, Acheson A, Horwood J, Ansell J, Phillips S, Davies M, Davies L, Bird S, Palmer N, Williams M, Galanopoulos G, Rao PD, Jones D, Barnett R, Tate S, Wheat J, Patel N, Rahmani S, Toynton E, Smith L, Reeves N, Kealaher E, Williams G, Sekaran C, Evans M, Beynon J, Egan R, Qasem E, Khot U, Ather S, Mummigati P, Taylor G, Williamson J, Lim J, Powell A, Nageswaran H, Williams A, Padmanabhan J, Phillips K, Ford T, Edwards J, Varney N, Hicks L, Greenway C, Chesters K, Jones H, Blake P, Brown C, Roche L, Jones D, Feeney M, Shah P, Rutter C, McGrath C, Curtis N, Pippard L, Perry J, Allison J, Ockrim J, Dalton R, Allison A, Rendell J, Howard L, Beesley K, Dennison G, Burton J, Bowen G, Duberley S, Richards L, Giles J, Katebe J, Dalton S, Wood J, Courtney E, Hompes R, Poole A, Ward S, Wilkinson L, Hardstaff L, Bogden M, Al-Rashedy M, Fensom C, Lunt N, McCurrie M, Peacock R, Malik K, Burns H, Townley B, Hill P, Sadat M, Khan U, Wignall C, Murati D, Dhanaratne M, Quaid S, Gurram S, Smith D, Harris P, Pollard J, DiBenedetto G, Chadwick J, Hull R, Bach S, Morton D, Hollier K, Hardy V, Ghods M, Tyrrell D, Ashraf S, Glasbey J, Ashraf M, Garner S, Whitehouse A, Yeung D, Mohamed SN, Wilkin R, Suggett N, Lee C, Bagul A, McNeill C, Eardley N, Mahapatra R, Gabriel C, Datt P, Mahmud S, Daniels I, McDermott F, Nodolsk M, Park L, Scott H, Trickett J, Bearn P, Trivedi P, Frost V, Gray C, Croft M, Beral D, Osborne J, Pugh R, Herdman G, George R, Howell AM, Al-Shahaby S, Narendrakumar B, Mohsen Y, Ijaz S, Nasseri M, Herrod P, Brear T, Reilly JJ, Sohal A, Otieno C, Lai W, Coleman M, Platt E, Patrick A, Pitman C, Balasubramanya S, Dickson E, Warman R, Newton C, Tani S, Simpson J, Banerjee A, Siddika A, Campion D, Humes D, Randhawa N, Saunders J, Bharathan B, Hay O. Incisional hernia following colorectal cancer surgery according to suture technique: Hughes Abdominal Repair Randomized Trial (HART). Br J Surg 2022; 109:943-950. [PMID: 35979802 PMCID: PMC10364691 DOI: 10.1093/bjs/znac198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Incisional hernias cause morbidity and may require further surgery. HART (Hughes Abdominal Repair Trial) assessed the effect of an alternative suture method on the incidence of incisional hernia following colorectal cancer surgery. METHODS A pragmatic multicentre single-blind RCT allocated patients undergoing midline incision for colorectal cancer to either Hughes closure (double far-near-near-far sutures of 1 nylon suture at 2-cm intervals along the fascia combined with conventional mass closure) or the surgeon's standard closure. The primary outcome was the incidence of incisional hernia at 1 year assessed by clinical examination. An intention-to-treat analysis was performed. RESULTS Between August 2014 and February 2018, 802 patients were randomized to either Hughes closure (401) or the standard mass closure group (401). At 1 year after surgery, 672 patients (83.7 per cent) were included in the primary outcome analysis; 50 of 339 patients (14.8 per cent) in the Hughes group and 57 of 333 (17.1 per cent) in the standard closure group had incisional hernia (OR 0.84, 95 per cent c.i. 0.55 to 1.27; P = 0.402). At 2 years, 78 patients (28.7 per cent) in the Hughes repair group and 84 (31.8 per cent) in the standard closure group had incisional hernia (OR 0.86, 0.59 to 1.25; P = 0.429). Adverse events were similar in the two groups, apart from the rate of surgical-site infection, which was higher in the Hughes group (13.2 versus 7.7 per cent; OR 1.82, 1.14 to 2.91; P = 0.011). CONCLUSION The incidence of incisional hernia after colorectal cancer surgery is high. There was no statistical difference in incidence between Hughes closure and mass closure at 1 or 2 years. REGISTRATION NUMBER ISRCTN25616490 (http://www.controlled-trials.com).
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Qiu Z, Verma JP, Liu H, Wang J, Batista BD, Kaur S, de Araujo Pereira AP, Macdonald CA, Trivedi P, Weaver T, Conaty WC, Tissue DT, Singh BK. Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome. Environ Microbiol 2022; 24:4652-4669. [PMID: 36059126 DOI: 10.1111/1462-2920.16194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022]
Abstract
Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen, Fusarium oxysporum f. sp. vasinfectum (FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings. This article is protected by copyright. All rights reserved.
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Liu L, Trivedi P, Ho B, Selph C, Hughes M, Casadaban L. Abstract No. 397 Adrenal vein sampling with slow infusion of Cosyntropin for identifying surgically curable cases. J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Trivedi P, Batista BD, Bazany KE, Singh BK. Plant-microbiome interactions under a changing world: responses, consequences and perspectives. THE NEW PHYTOLOGIST 2022; 234:1951-1959. [PMID: 35118660 DOI: 10.1111/nph.18016] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/19/2022] [Indexed: 05/07/2023]
Abstract
Climate change is increasing global temperatures and the frequency and severity of droughts in many regions. These anthropogenic stresses pose a significant threat to plant performance and crop production. The plant-associated microbiome modulates the impacts of biotic and abiotic stresses on plant fitness. However, climate change-induced alteration in composition and activities of plant microbiomes can affect host functions. Here, we highlight recent advancements in our understanding of the impact of climate change (warming and drought) on plant-microbiome interactions and on their ecological functions from genome to ecosystem scales. We identify knowledge gaps, propose new concepts and make recommendations for future research directions. It is proposed that in the short term (years to decades), the adaptation of plants to climate change is mainly driven by the plant microbiome, whereas in the long term (century to millennia), the adaptation of plants will be driven equally by eco-evolutionary interactions between the plant microbiome and its host. A better understanding of the response of the plant and its microbiome interactions to climate change and the ways in which microbiomes can mitigate the negative impacts will better inform predictions of climate change impacts on primary productivity and aid in developing management and policy tools to improve the resilience of plant systems.
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Musa A, Afify O, Al-Hihi M, Anavim A, Holton J, Azar S, Kumar V, Cassella K, Ledbetter K, Trivedi P, Arnold E, Ter-Oganesyan R. Abstract No. 526 How do interventional radiology residency program directors prefer to increase female and under-represented minority (URM) representation? J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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