Biology subjects

Lee, C. G.

Publications and source records attributed to Lee, C. G..

At least 19 recordsLinked to original sources

bioRxiv2026

CHARIOT-AAV: Conjugation of diverse vectors to adeno-associated viruses for delivery of large genes

Systemic, tissue-specific delivery of large transgenes exceeding the packaging capacity of adeno-associated viruses (AAVs) remains a key translational challenge for molecular therapeutics. Vectors with larger capacities, such as lentiviral vectors (LVVs) and lipid nanoparticles (LNPs), often lack adjustable, tissue-specific tropisms. Here we report CHARIOT-AAV (Crosslinked Hybrid Architectures for Robust, Interchangeable, and Organ-specific Targeting with AAV), a platform where diverse delivery vectors are conjugated to AAVs, thereby achieving tissue-specific tropism of AAVs and expanded cargo capacity. AAV-AAV conjugates packaging split SpCas9 constructs in AAV.CAP-B10 capsids demonstrate a [~]2-fold increase in brain gene editing efficiency over unconjugated AAV cocktails after intravenous injection. In addition to AAV-AAV conjugates, AAV-LVV and AAV-LNP conjugates achieve AAV-guided delivery of genetic payloads to target cells. Furthermore, AAV-LNP conjugates enable systemic delivery of mRNAs to brain endothelial cells. CHARIOT-AAV thus provides a modular platform for systemic, tissue-specific delivery of diverse therapeutics beyond the limits of individual vectors.

bioengineering↗

bioRxiv2025

Bispecific Targeting of CHI3L1 and PD-1/PD-L1 Axis as a Novel Therapeutic Strategy for Idiopathic Pulmonary Fibrosis

CHI3L1, a chitinase-like protein, plays a key role in the pathogenesis of pulmonary fibrosis, though the precise mechanisms remain unclear. This study explores how CHI3L1 regulates profibrotic macrophage activation and invasive myofibroblast differentiation and their interactions. In vitro, CHI3L1 induced profibrotic M2 macrophage activation and differentiation marked by increased expression of CD163, CD206, and PD-L1. CHI3L1 also enhanced TGF-{beta}1 effects on lung fibroblasts including myofibroblast transformation, migration and tissue invasion. Mechanistically, CHI3L1 increased TGF-{beta}1-stimulation of Smad, Akt and Erk signaling and PD-L1 played a significant role in TGF-{beta}1/CHI3L1-stimulated myofibroblast transformation. Coculture experiment further confirmed the ability of CHI3L1 to induce profibrotic macrophage activation that enhanced myofibroblast transformation mediated via a CD44-PD-L1 axis. Following in vivo bleomycin challenge, CHI3L1 transgenic mice exhibited significantly higher levels of PD-L1+ M2 macrophages, PD-L1+/PDGFR+ fibroblasts and increased numbers of PD-1+ and CD45+/PD-1+ cells compared to wild-type controls. Notably, combined treatment with anti-CHI3L1 and anti-PD-1 antibodies, or a bispecific anti-CHI3L1-anti-PD-1 antibody, resulted in greater inhibition of bleomycin-induced fibrosis than either antibody alone. These findings suggest that there is a stimulatory interaction between CHI3L1 and the PD-1/PD-L1 axis in promoting profibrotic macrophage activation and invasive fibroblast differentiation. The results also highlight the potential of bispecific targeting of CHI3L1 and the PD-1/PD-L1 pathway as an effective therapeutic approach for pulmonary fibrosis.

immunology↗

bioRxiv2025

Kasugamycin inhibits melanoma lung metastasis and regulates CHI3L1-driven M2-like tumor-associated macrophage differentiation

CHI3L1, a chitinase-like protein, is a potent immune modulator involved in various diseases, including lung cancer. While recent studies have demonstrated that kasugamycin (KSM) is a pan-chitinase inhibitor with strong anti-fibrotic activity, its effects on specific chitinase-like proteins remain undefined. This study shows that KSM effectively abrogates CHI3L1-stimulated cellular signaling and bioactivities. In a B16/F10 melanoma lung metastasis model, where CHI3L1 plays a critical role, KSM treatment significantly reduced melanoma lung metastasis dose-dependently. The anti-tumor effect of KSM was found to be CHI3L1-specific, as CHI3L1 overexpression enhanced melanoma lung colony formation, which was effectively blocked by KSM. In melanoma-challenged lungs, KSM treatment significantly reduced the elevation of M2 macrophages expressing CD206, CD163, and PD-L1. In studies using human monocytic THP-1 cells, CHI3L1 promoted M2 macrophage differentiation, which KSM significantly suppressed. Bulk RNA sequencing of differentiated macrophages revealed that CHI3L1 highly induced the expression of epidermal growth factor receptor (EGFR), and this induction was counter-regulated by KSM, and CHI3L1-driven M2 macrophage activation was reduced with EGFR blocker treatment. These findings reveal a novel anti-tumor mechanism of KSM, which inhibits M2-like tumor-associated macrophage differentiation, potentially through the CHI3L1-EGFR axis.

immunology↗

bioRxiv2023

Chitinase 3-like-1 (CHI3L1) Inhibits Innate Anti-Tumor and Tissue Remodeling ImmuneResponses by Regulating CD47-SIRPα and CD24-Siglec10-Mediated Phagocytosis

Innate immune responses such as phagocytosis are critically linked to the generation of adaptive immune responses against the neoantigens in cancer and the efferocytosis that is essential for homeostasis in diseases characterized by lung injury, inflammation, and remodeling as in Chronic Obstructive Pulmonary Disease (COPD). Chitinase 3-like-1 (CHI3L1) is induced in many cancers where it inhibits adaptive immune responses by stimulating immune checkpoint molecules (ICPs) and portends a poor prognosis. CHI3L1 is also induced in COPD where it regulates epithelial cell death. Here we demonstrate that pulmonary melanoma metastasis inhibits macrophage phagocytosis by stimulating the CD47-SIRP and CD24-Siglec10 phagocytosis checkpoint pathways while inhibiting macrophage "eat me" signals from calreticulin and HMGB1. We also demonstrate that these effects on macrophage phagocytosis are mediated by CHI3L1 stimulation of the SHP-1 and SHP-2 phosphatases and the inhibition of the accumulation and phosphorylation of cytoskeleton-regulating non-muscle myosin IIa. This inhibition of innate immune responses like phagocytosis provides a mechanistic explanation for the ability of CHI3L1 to stimulate ICPs and inhibit adaptive immune responses in cancer and diseases like COPD. The ability of CHI3L1 to simultaneously inhibit innate immune responses, stimulate ICPs, inhibit T cell co-stimulation, and regulate a number of other oncogenic and inflammation pathways suggest that CHI3L1-targeted therapeutics are promising interventions in cancer, COPD and other disorders.

immunology↗

bioRxiv2023

Chitinase 3-like-1 (CHI3L1) in the Pathogenesis of Epidermal Growth Factor Receptor Mutant Non-Small Cell Lung Cancer

Non-small cell lung cancer (NSCLC) accounts for 85% of all lung cancers. In NSCLC, 10-20% of Caucasian patients and 30-50% of Asian patients have tumors with activating mutations in the Epidermal Growth Factor Receptor (EGFR). A high percentage of these patients exhibit favorable responses to treatment with tyrosine kinase inhibitors (TKI). Unfortunately, a majority of these patients develop therapeutic resistance with progression free survival lasting 9-18 months. The mechanisms that underlie the tumorigenic effects of EGFR and the ability of NSCLC to develop resistance to TKI therapies, however, are poorly understood. Here we demonstrate that CHI3L1 is produced by EGFR activation of normal epithelial cells, transformed epithelial cells with wild type EGFR and cells with cancer-associated, activating EGFR mutations. We also demonstrate that CHI3L1 auto-induces itself and feeds back to stimulate EGFR and its ligands. Highly specific antibodies against CHI3L1 (anti-CHI3L1/FRG) and TKI, individually and in combination, abrogated the effects of EGFR activation on CHI3L1 and the ability of CHI3L1 to stimulate the EGFR axis. Anti-CHI3L1 also interacted with osimertinib to reverse TKI therapeutic resistance and induce tumor cell death and inhibit pulmonary metastasis while stimulating tumor suppressor genes including KEAP1. CHI3L1 is a downstream target of EGFR that feeds back to stimulate and activate the EGFR axis. Anti-CHI3L1 is an exciting potential therapeutic for EGFR mutant NSCLC, alone and in combination with osimertinib or other TKIs.

cancer biology↗

bioRxiv2022

CHI3L1 Enhances Melanoma Lung Metastasis via Regulation of T cell Co-stimulators and CTLA-4/B7 Axis

ICOS/ICOSL and CD28/B7-1/B7-2 are T cell co-stimulators and CTLA-4 is an immune checkpoint inhibitor that play critical roles in the pathogenesis of neoplasia. Chitinase 3-like-1 (CHI3L1) is induced in many cancers where it portends a poor prognosis and contributes to tumor metastasis. Here we demonstrate that CHI3L1 inhibits the expression of ICOS, ICOSL and CD28 while stimulating CTLA-4 and the B7 moieties in melanoma lung metastasis. We also demonstrate that RIG-like helicase innate immune activation augments T cell co-stimulation, inhibits CTLA-4 and suppresses pulmonary metastasis. At least additive antitumor responses were seen in melanoma lung metastasis treated with anti-CTLA-4 and anti-CHI3L1 antibodies in combination. Synergistic cytotoxic T cell-induced tumor cell death and the heightened induction of the tumor suppressor PTEN were seen in co-cultures of T and tumor cells treated with bispecific antibodies that target both CHI3L1 and CTLA-4. Thus, CHI3L1 contributes to pulmonary metastasis by inhibiting T cell co-stimulation and stimulating CTLA-4. The simultaneous targeting of CHI3L1 and the CTLA-4 axis with individual and, more powerfully with bispecific antibodies, represent promising therapeutic strategies for pulmonary metastasis.

immunology↗

bioRxiv2022

Host Chitinase 3-like-1 is a Universal Therapeutic Target for the Delta, Omicron and Other SARS-CoV-2 Viral Variants in COVID 19

COVID 19 is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2) which has caused a world-wide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics and or the ability to induce severe disease. Currently, the delta ({delta}) and omicron (o) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause break through infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.

immunology↗

bioRxiv2021

Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma

Chi3l1 (Chitinase 3-like 1) is a secreted protein highly expressed in glioblastoma. Here, we show that exposure of glioma stem cells (GSCs) to Chi3l1 reduces the CD133+/SOX2+ cells and increases the CD44+/Chi3l1+ cells. Chi3l1 binds to CD44 and induces phosphorylation and nuclear translocation of beta-catenin, Akt and STAT3. Single cell RNA-seq and RNA velocity following incubation of GSCs with Chi3l1 show significant changes in GSC state dynamics driving GSCs towards a mesenchymal expression profile and reducing transition probabilities towards terminal cellular states. ATAC-seq reveals that Chi3l1 increases accessibility of promoters containing MAZ transcription factor footprint. Inhibition of MAZ directly regulates genes with highest expression in cellular clusters exhibiting significant cell state transitions. Finally, targeting Chi3l1 in vivo with a blocking antibody, resets the transcriptomic profile of glioblastoma and inhibits tumor growth. Our work implicates Chi3l1 as modulator of GSC cellular states and demonstrates pre-clinical efficacy of anti-Chi3l1 antibody treatment.

cancer biology↗

bioRxiv2021

Dysregulated myogenesis and autophagy in genetically induced pulmonary emphysema

Patients with chronic obstructive pulmonary disease (COPD)-pulmonary emphysema often develop locomotor muscle dysfunction, which is independently associated with disability and higher mortality in that population. Muscle dysfunction entails reduced muscle mass and force-generation capacity, which are influenced by fibers integrity. Myogenesis, which is muscle turnover driven by progenitor cells such as satellite cells, contributes to the maintenance of muscle integrity in the context of organ development and injury-repair cycles. Injurious events crucially occur in COPD patients skeletal muscles in the setting of exacerbations and infections which lead to acute decompensations for limited periods of time after which, patients typically fail to recover the baseline status they had before the acute event. Autophagy, which is dysregulated in muscles from COPD patients, is a key regulator of satellite cells activation and myogenesis, yet very little research has so far investigated the mechanistic role of autophagy dysregulation in COPD muscles. Using a genetically inducible murine model of COPD-driven muscle dysfunction and confirmed with a second genetic animal model, we found a significant myogenic dysfunction associated with a reduced proliferative capacity of freshly isolated satellite cells. Transplantation experiments followed by lineage tracing suggest that an intrinsic defect in satellite cells, and not in the COPD environment, plays a dominant role in the observed myogenic dysfunction. RNA sequencing analysis of freshly isolated satellite cells suggests dysregulation of transcripts associated with control of cell cycle and autophagy, which is confirmed by a direct observation of COPD mice satellite cells fluorescent-tracked autophagosome formation. Moreover, spermidine-induced autophagy stimulation leads to improved satellite cells autophagosome turnover, replication rate and myogenesis. Our data suggests that pulmonary emphysema causes a disrupted myogenesis, which could be improved with stimulation of autophagy and satellite cells activation, leading to an attenuated muscle dysfunction in this context.

physiology↗

bioRxiv2021

Chitinase 3-like-1 Contributes to Acetaminophen-induced Liver Injury by Promoting Hepatic Platelet Recruitment

Hepatic platelet accumulation contributes to acetaminophen (APAP)-induced liver injury (AILI). However, little is known about the molecular pathways involved in platelet recruitment to the liver and whether targeting such pathways could attenuate AILI. The present study unveiled a critical role of chitinase 3-like-1 (Chi3l1) in hepatic platelet recruitment during AILI. Increased Chi3l1 and platelets in the liver were observed in patients and mice overdosed with APAP. Compared to wild-type (WT) mice, Chi3l1-/- mice developed attenuated AILI with markedly reduced hepatic platelet accumulation. Mechanistic studies revealed that Chi3l1 signaled through CD44 on macrophages to induce podoplanin expression, which mediated platelet recruitment through C-type lectin-like receptor 2. Moreover, APAP treatment of CD44-/- mice resulted in much lower numbers of hepatic platelets and liver injury than WT mice, a phenotype similar to that in Chi3l1-/- mice. Recombinant Chi3l1 could restore hepatic platelet accumulation and AILI in Chi3l1-/- mice, but not in CD44-/- mice. Importantly, we generated anti-Chi3l1 monoclonal antibodies and demonstrated that they could effectively inhibit hepatic platelet accumulation and AILI. Overall, we uncovered the Chi3l1/CD44 axis as a critical pathway mediating APAP-induced hepatic platelet recruitment and tissue injury. We demonstrated the feasibility and potential of targeting Chi3l1 to treat AILI.

pharmacology and toxicology↗

bioRxiv2021

Effects of green manure application on soil microbial communities and activities in the decontaminated sandy soil paddy field in Fukushima, Japan

On March 11, 2011, Japan experienced an unprecedented earthquake off the Pacific coast of Tohoku, and suffered the direct and long-term effects of the earthquake and tsunami in the area. In Fukushima prefecture, agricultural land contaminated with radioactive Cesium from the Fukushima Daiichi Nuclear Power Plant. Therefore, surface soil were removed for deconamination, and low fertility sandy soil was covered. Organic matter input is necessary to increase soil organic matter and green manure application is an effective method to improve soil fertility in the paddy field. Soil microbes and enzyme activities are sensitively responded to organic matter addition, but their dynamics on the dressed field are not well investigated. In this study, we focused on changing the microbial community, diversity and enzyme activities along with the green manure decomposition process in the sandy soil dressed paddy field in Japan. The green manure of hairy vetch and oat were harvested and incorporated in May 2020 and their decomposition process as cellulose and hemicellulose contents were determined. Soil bacterial communities were analyzed using 16S amplicon sequencing. The green manure was rapidly decomposed within the first 13 days, and they did not remain 50 days after green manure incorporation. Soil microbial biomass carbon was higher in the M treatment after GM treatment, but was not significant between treatments after 50 days. Dehydrogenase and {beta}-glucosidase activities changed during the harvesting period, but did not correlate with GM decomposition. Microbial diversity (OTU numbers and Shannon index) also changed with GM application, but they were not associated with GM decomposition. Soil prokaryotic communities and some bacteria (Baciili and Chlorolfexi) are significantly influenced by GM treatment. However, Clostrida was not affected by GM. Mixed green manure treatment showed significantly rapid hemicellulose decomposition than other treatments. In this process, Anaerolineae were negatively correlated with the decreasing of hemicellulose in this treatment. These results showed that GM treatment affected microbial communities, and their response was active during the decomposition process.

microbiology↗

bioRxiv2021

Kasugamycin is a novel chitinase 1 inhibitor with strong antifibrotic effects on pulmonary fibrosis

RationalePulmonary fibrosis is a devastating lung disease with few therapeutic options. Chitinase 1 (CHIT1), an 18 glycosyl hydrolase family member, contributes to the pathogenesis of pulmonary fibrosis through regulation of Transforming Growth Factor (TGF)-{beta} signaling and effector function. Therefore, CHIT1 is a potential therapeutic target of pulmonary fibrosis. ObjectivesThis study aimed to identify and characterize a druggable CHIT1 inhibitor with strong antifibrotic activity and minimal toxicity for therapeutic application to pulmonary fibrosis. MethodsExtensive screening of small molecule libraries identified the aminoglycoside antibiotic Kasugamycin as a potent CHIT1 inhibitor. Measurements and Main ResultsElevated levels of CHIT1 were detected in the lungs of patients with pulmonary fibrosis. In vivo bleomycin- and TGF-{beta}-stimulated murine models of pulmonary fibrosis, Kasugamycin showed impressive anti-fibrotic effects in both preventive and therapeutic conditions. In vitro studies also demonstrated that Kasugamycin inhibits fibrotic macrophage activation, fibroblast proliferation and myofibroblast transformation. Null mutation of transforming growth factor beta associated protein 1 (TGFBRAP1), a recently identified CHIT1 interacting signaling molecule, phenocopied antifibrotic effects of Kasugamycin in in vivo lungs and in vitro fibroblasts responses. Kasugamycin inhibits physical association between CHIT1 and TGFBRAP1, suggesting that antifibrotic effect of Kasugamycin is mediated through regulation of TGFBRAP1, at least in part. ConclusionsThese studies demonstrate that Kasugamycin is a novel CHIT1 inhibitor with strong antifibrotic effect that can be further developed as an effective and safe therapeutic drug for pulmonary fibrosis.

immunology↗

bioRxiv2021

Succinate Dehydrogenase (SDH)-subunit C regulates muscle oxygen consumption and fatigability in an animal model of pulmonary emphysema.

Patients with pulmonary emphysema often develop locomotor muscle dysfunction, which is independently associated with disability and higher mortality in that population. Muscle dysfunction entails reduced force-generation capacity which partially depends on fibers oxidative potential, yet very little mechanistic research has focused on muscle respiration in pulmonary emphysema. Using a recently established animal model of pulmonary emphysema-driven skeletal muscle dysfunction, we found downregulation of succinate dehydrogenase (SDH) subunit C in association with lower oxygen consumption and fatigue-tolerance in locomotor muscles. Reduced SDH activity has been previously observed in muscles from patients with pulmonary emphysema and we found that SDHC is required to support respiration in cultured muscle cells. Moreover, in-vivo gain of SDH function in emphysema animals muscles resulted in better oxygen consumption rate (OCR) and fatigue tolerance. These changes correlated with a larger number of relatively more oxidative type 2-A and 2X fibers, and a reduced amount of 2B fibers. Our data suggests that SDHC is a key regulator of respiration and fatigability in pulmonary emphysema-driven skeletal muscles, which could be impactful to develop strategies aimed at attenuating this comorbidity.

physiology↗

bioRxiv2021

Chitinase 3-like-1 Stimulates PD-L1 and Other Immune Checkpoint Inhibitors

PD-1 and its ligand PD-L1 are major mediators of tumor-induced immunosuppression. Chitinase 3-like-1 (Chi3l1) is induced in many cancers where it portends a poor prognosis and contributes to tumor metastasis. Here we demonstrate that Chi3l1 regulates the expression of PD-L1, PD-L2, PD-1 and LAG3 in melanoma lung metastasis. Chi3l1 stimulates macrophage PD-L1 expression and mediates optimal IFN-{gamma}-stimulated PD-L1 expression via IL-13R2. We also demonstrate that RIG-like helicase innate immune activation suppresses Chi3l1, PD-L1, LAG3 and pulmonary metastasis. At least additive antitumor responses were seen in metastasis models treated simultaneously with individual antibodies against PD-1 and Chi3l1. At least additive cytotoxic T cell-induced tumor cell death was also seen in co-cultures of T and tumor cells treated with antibodies that target Chi3l1 and PD-1. Thus, Chi3l1 contributes to pulmonary metastasis by stimulating the PD1-PD-L1 axis and other checkpoint molecules. The simultaneous targeting of Chi3l1 and the PD-1-PD-L1 axis, represents a promising therapeutic strategy for pulmonary metastasis.

cancer biology↗

bioRxiv2021

Mutational impact and signature of ionizing radiation

Whole-genome sequencing (WGS) of human tumors and normal cells exposed to various carcinogens has revealed distinct mutational patterns that provide deep insights into the DNA damage and repair processes. Although ionizing radiation (IR) is conventionally known as a strong carcinogen, its genome-wide mutational impacts have not been comprehensively investigated at the single-nucleotide level. Here, we explored the mutational landscape of normal single-cells after exposure to the various levels of IR. On average, 1 Gy of IR exposure generated [~]16 mutational events with a spectrum consisting of predominantly small nucleotide deletions and a few characteristic structural variations. In [~]30% of the post-irradiated cells, complex genomic rearrangements, such as chromoplexy, chromothripsis, and breakage-fusion-bridge cycles, were resulted, indicating the stochastic and chaotic nature of DNA repair in the presence of the massive number of concurrent DNA double-strand breaks. These mutational signatures were confirmed in the genomes of 22 IR-induced secondary malignancies. With high-resolution genomic snapshots of irradiated cells, our findings provide deep insights into how IR-induced DNA damage and subsequent repair processes operate in mammalian cells.

genomics↗

bioRxiv2021

Chitinase 3-like-1 is a Therapeutic Target That Mediates the Effects of Aging in COVID-19

COVID-19 is caused by the SARS-CoV-2 (SC2) virus and is more prevalent and severe in the elderly and patients with comorbid diseases (CM). Because chitinase 3-like-1 (CHI3L1) is induced during aging and CM, the relationships between CHI3L1 and SC2 were investigated. Here we demonstrate that CHI3L1 is a potent stimulator of the SC2 receptor ACE2 and viral spike protein priming proteases (SPP), that ACE2 and SPP are induced during aging and that anti-CHI3L1, kasugamycin and inhibitors of phosphorylation, abrogate these ACE2- and SPP-inductive events. Human studies also demonstrated that the levels of circulating CHI3L1 are increased in the elderly and patients with CM where they correlate with COVID-19 severity. These studies demonstrate that CHI3L1 is a potent stimulator of ACE2 and SPP; that this induction is a major mechanism contributing to the effects of aging during SC2 infection and that CHI3L1 coopts the CHI3L1 axis to augment SC2 infection. CHI3L1 plays a critical role in the pathogenesis of and is an attractive therapeutic target in COVID-19.

immunology↗

bioRxiv2019

Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation

Anaerobic soil disinfestation (ASD) is a chemical-independent method that can reduce pathogens. Although soil microbes play essential roles in ASD, the relationship between the microbial community structure and disinfestation efficiency remains unclear. To this end, we investigated changes in the microbial community and pathogen density during a period of ASD under field conditions for 14 days in a greenhouse using three different substrates. Soil samples were collected at 0, 3, 7, and 14 days after ASD treatment. The pathogen densities were analyzed by real-time polymerase chain reactions, prokaryotic community analysis was conducted using unidirectional pyrosequencing, and the factors related to pathogen density were statistically analyzed. The pathogen density rapidly decreased by >90% at 3 days after treatment and then slowly decreased until day 14, but the rate of decrease differed among the substrates. The microbial communities became altered after 3 days and recovered to their original state on day 14. The dipyridyl reaction, microbial diversity, richness, and community structure were not correlated with pathogen density. The most negatively correlated operational taxonomic units with pathogen density were Clostridia and Bacilli, both belonging to Firmicutes. These results suggested that the growth of specific microbes, but not the changes in microbial community structure, might be important for ASD disinfestation efficiency.

microbiology↗

bioRxiv2019

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation

Anaerobic soil disinfestation (ASD) is a chemical-independent fumigation method used for reducing the abundance of pathogens at soil depths of <40 cm. However, its disinfestation efficiency is unstable under field conditions. The microbial community reflects the soil environment and is a good indicator of soil health. Therefore, soil with a good disinfestation efficiency may have a unique microbial community. The aim of the present study was to compare the prokaryotic communities among soils obtained from 17 geographically different greenhouses that experienced tomato bacterial wilt but exhibited different disinfestation efficiencies after ASD treatment with the same substrate. In the present study, soil prokaryotic communities in the field, which indicate difference in disinfestation effects after ASD treatment among several fields, were compared using next-generation sequencing. The prokaryotic communities in the fields showing different disinfestation effects were roughly separated into sampling fields. The relative abundances of Betaproteobacteria and Clostridia were significantly increased in well-disinfested fields. Overall, 25 operational taxonomic units (OTUs) were specifically increased in various well-disinfested soils and 18 OTUs belonged to phylogenetically diversified Clostridia. Other OTUs belonged to aerobic bacteria and were not previously detected in sample collected from ASD-treated fields. The results showed that the changes to the prokaryotic communities did not affect ASD efficiency, whereas changes in the abundance of specific microbes in the community were related to disinfestation.

microbiology↗