Microbes and Environments最新文献_第3页

Isolation and Genomic Characterization of a Novel Japanese Strain of Pseudomonas protegens and an Evaluation of Its Biocontrol Potential. 一株日本假单胞菌蛋白的分离、基因组鉴定及其生物防治潜力评价。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25086

Rohyanti Yuliana, Saki Ikeda, Yuichiro Ikagawa, Kosei Yamauchi, Kotaro Kuwahara, Nur Adliza Baharom, Haruhisa Suga, Masafumi Shimizu

{"title":"Isolation and Genomic Characterization of a Novel Japanese Strain of Pseudomonas protegens and an Evaluation of Its Biocontrol Potential.","authors":"Rohyanti Yuliana, Saki Ikeda, Yuichiro Ikagawa, Kosei Yamauchi, Kotaro Kuwahara, Nur Adliza Baharom, Haruhisa Suga, Masafumi Shimizu","doi":"10.1264/jsme2.ME25086","DOIUrl":"10.1264/jsme2.ME25086","url":null,"abstract":"Pseudomonas protegens, a member of the P. fluorescens complex, is a key biocontrol bacterium with well-documented potential to protect plants against diverse pathogens. Although P. protegens strains have been widely exami-ned globally, those originating from Japan have not been well described. In this study, we isolated and characterized a new P. protegens strain, GSF-73, from the rhizosphere of Allium fistulosum in Gifu, Japan, and assessed its performance against several major plant diseases. Draft genome sequencing produced a 7.13-Mbp assembly, and average nucleotide identity values of 97.81-98.26% with reference strains (Cab75, CHA0, and Pf-5) confirmed its species identity. A comparative genomic anal-ysis showed that GSF-73 possessed a larger genome than the reference strains, containing eight conserved biosynthetic gene clusters for antimicrobial compounds and an expanded set of strain-specific genes related to metabolism, regulation, mobilome functions, and secretion. GSF-73 exhibited broad-spectrum antagonistic activity in vitro against fungal, oomycete, and bacterial pathogens. In biocontrol assays, GSF-73 significantly suppressed spinach Fusarium wilt, cucumber anthracnose on detached cotyledons, tomato bacterial wilt, and cucumber downy mildew. In contrast, root and/or seed treatments enhanced Pythium root rot in spinach and anthracnose in pot-grown cucumbers, indicating pathosystem-dependent efficacy. Despite these contrasting outcomes, GSF-73 shows strong biocontrol potential and merits further study to elucidate the mechanisms underlying both beneficial and adverse effects for its optimized use as a locally adapted biocontrol agent for Japanese agriculture.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom. 自然赤石异sigma病毒种群在宿主开花期间的快速多样化。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME26018

Jun Xia, Lingjie Meng, Yue Fang, Hiroki Ban, Yusuke Okazaki, Takashi Yoshida, Hisashi Endo, Keizo Nagasaki, Hiroyuki Ogata

{"title":"Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom.","authors":"Jun Xia, Lingjie Meng, Yue Fang, Hiroki Ban, Yusuke Okazaki, Takashi Yoshida, Hisashi Endo, Keizo Nagasaki, Hiroyuki Ogata","doi":"10.1264/jsme2.ME26018","DOIUrl":"10.1264/jsme2.ME26018","url":null,"abstract":"Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Knowledge on their population genetic dynamics is mostly derived from a small number of laboratory-based experiments, while patterns in nature are rarely observed. To overcome this limitation, we traced the genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan by integrating cell counting, metabarcoding, and metagenomic and metatranscriptomic sequencing. The results obtained revealed that HaV dominated the giant virus community in most samples, with relative abundance up to 56%. Despite its high abundance, the HaV population exhibited a low level of microdiversity, but had a higher pN/pS ratio than other giant viruses in the study site. Microdiversity increased during the early sampling period, peaked mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, which may be driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Collectively, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variations.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 3","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148430640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Biodegradation Mechanism of Thiophene by Candida tropicalis through Electric Field-assisted Technology. 热带假丝酵母电场辅助降解噻吩的机理

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25081

Lin Huang, Jiaji Li, Bohan Zhai, Jiahui Liu, Fuli Li, Runyan Zhu, Ran You, Chaozheng Zhang

引用次数: 0

Genome Plasticity Depends on Positions both Inside and Outside of the Symbiosis Island of Bradyrhizobium diazoefficiens. 基因组可塑性取决于重氮效率慢生根瘤菌共生岛内外的位置。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25074

Haruka Arashida, Hiroko Maita, Shusei Sato, Kiwamu Minamisawa

{"title":"Genome Plasticity Depends on Positions both Inside and Outside of the Symbiosis Island of Bradyrhizobium diazoefficiens.","authors":"Haruka Arashida, Hiroko Maita, Shusei Sato, Kiwamu Minamisawa","doi":"10.1264/jsme2.ME25074","DOIUrl":"10.1264/jsme2.ME25074","url":null,"abstract":"Insertion sequences (ISs) are major drivers of genomic plasticity in rhizobia, frequently promoting local recombination events. To quantitatively compare the stability of genomic regions inside and outside of the symbiosis island, we engineered Bradyrhizobium diazoefficiens USDA122 mutants carrying a sacB/aadA counter-selectable cassette at four distinct loci-three on symbiosis island A (SymA) and one in the core genome. During 5 days of saprophytic growth, cassette deletion occurred at frequencies of up to 1.77×10-3 within SymA, whereas the deletion rate in core genomic regions was markedly lower (3.29×10-6). Within SymA, cassettes inserted adjacent to the nif and rhc clusters, where IS copies with the same orientation were enriched, were lost more frequently than those placed in other SymA regions, indicating marked intra-island variability in genomic stability. Similar yet overall lower deletion frequencies were observed in B. diazoefficiens USDA110. These results demonstrate that SymA contains genomic loci with greater susceptibility to IS-mediated rearrangements and also that such recombination events may contribute to the diversification of Bradyrhizobium symbiosis islands. Based on our comparative IS mapping in B. japonicum and B. ottawaense, we discuss the potential for the IS-mediated deletion of genome regions harboring nod genes.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12999730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Distinct and Intermediate Bacterial Community Structure of the Wasabi Rhizome Based on Compartment-resolved 16S rRNA Gene Profiling. 基于区室分辨16S rRNA基因图谱的山葵根茎不同和中间细菌群落结构

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME26005

Masayoshi Hashimoto, Kana Ohata, Ryohei Thomas Nakano, Hisae Hirata, Yusuke Katai

引用次数: 0

Restoration of Nitrate Respiration in Pseudomonas aeruginosa under Growth Limitations. 生长限制下铜绿假单胞菌硝酸盐呼吸作用的恢复。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25064

Ayaka Uehara, Chunqi Jiang, Susumu Yoshizawa, Kazuhiro Kogure, Nobuhiko Nomura, Toshiki Nagakubo, Masanori Toyofuku

{"title":"Restoration of Nitrate Respiration in Pseudomonas aeruginosa under Growth Limitations.","authors":"Ayaka Uehara, Chunqi Jiang, Susumu Yoshizawa, Kazuhiro Kogure, Nobuhiko Nomura, Toshiki Nagakubo, Masanori Toyofuku","doi":"10.1264/jsme2.ME25064","DOIUrl":"10.1264/jsme2.ME25064","url":null,"abstract":"Gene mutations are a fundamental survival strategy in bacteria and often accompany cell growth. We herein demonstrate that Pseudomonas aeruginosa recovered growth under anoxic conditions through a mutation in an essential regulatory gene required for nitrate respiration, overcoming initial growth limitations. Although the open-ocean isolate P. aeruginosa Ocean-1187 possesses denitrification-related genes, it was initially unable to grow under nitrate-respiring conditions due to a defect in the transcriptional regulator NarL, part of the NarX-NarL two-component system that controls the expression of denitrification genes. The growth of this strain was limited by the defective NarL; however, a prolonged incubation under anoxic conditions led to the emergence of spontaneous mutants that regained the ability to grow. Whole-genome sequencing and functional complementation assays revealed that a single amino acid substitution in NarL was sufficient to restore nitrate respiration. Additional variants independently isolated from separate cultures also carried substitutions at the same residue, underscoring its functional importance. The present study shows that a single amino acid substitution in an essential regulatory protein restored metabolic function. These results offer novel insights into the adaptive strategies of bacteria, highlighting the emergence of critical mutations even under restricted growth conditions.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12999733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Screening of Nonpathogenic Fusarium Species Suppressing Fusarium Crown and Root Rot in Asparagus Using Wheat Bran as an Inoculum Carrier. 以麦麸为接种载体筛选抑制芦笋枯萎病冠腐病和根腐病的非致病性镰刀菌。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25063

Yosuke Maeda, Seishi Akino, Norio Kondo

{"title":"Screening of Nonpathogenic Fusarium Species Suppressing Fusarium Crown and Root Rot in Asparagus Using Wheat Bran as an Inoculum Carrier.","authors":"Yosuke Maeda, Seishi Akino, Norio Kondo","doi":"10.1264/jsme2.ME25063","DOIUrl":"10.1264/jsme2.ME25063","url":null,"abstract":"Fusarium crown and root rot (FCRR), caused by the fungus Fusarium oxysporum f. sp. asparagi, is one of the most destructive diseases affecting asparagus worldwide. Despite evidence of the suppression of FCRR by several nonpathogenic F. oxysporum sensu lato strains in laboratory experiments, biological control trials in FCRR-infested fields have not consistently demonstrated the effectiveness of these strains. Therefore, we screened nonpathogenic Fusarium spp. strains for the biological control of FCRR with the modified inoculation method considering the colonization to soil of biocontrol agents (BCAs). Two strains from different lineages (SM007 and FAoc5), inoculated by irrigating a bud-cell suspension and applying cultured wheat bran medium around the root of the transplants, effectively suppressed FCRR on young asparagus seedlings. These strains also suppressed FCRR on mature second-year plants to some extent by the application of cultured wheat bran medium as an inoculation carrier. Both strains exhibited the capacity to impede chlamydospore germination of the pathogen when glucose was incorporated into soil. Although SM007 sometimes failed to show biocontrol effects, differences in efficiency appeared to be related to the fungal density colonizing wheat bran medium. These results suggest that the screened strains interact with the pathogen and also that the amount of BCAs introduced into soil is closely related to their biocontrol efficacy.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147982337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Directional Colony Growth of Cupriavidus toward Sphingomonads. 铜蛉对鞘单胞虫的定向菌落生长。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25087

Hiromi Kato, Shoko Hirano, Chiaki Haga, Sayaka Sakogawa, Yoshiyuki Ohtsubo, Yuji Nagata

{"title":"Directional Colony Growth of Cupriavidus toward Sphingomonads.","authors":"Hiromi Kato, Shoko Hirano, Chiaki Haga, Sayaka Sakogawa, Yoshiyuki Ohtsubo, Yuji Nagata","doi":"10.1264/jsme2.ME25087","DOIUrl":"10.1264/jsme2.ME25087","url":null,"abstract":"Bacterial communities often originate from physical encounters between distinct species on solid surfaces; however, the mechanisms underlying these initial interactions remain unclear. The γ-hexachlorocyclohexane (γ-HCH; a toxic recalcitrant insecticide)-degrading consortium includes the surface-motile bacterium Cupriavidus sp. strain TKC and the γ-HCH-degrading Sphingobium sp. strain TKS. During a co-culture on R2A agar, TKC colonies exhibited directional colony growth (DCG), characterized by asymmetric expansion toward neighboring TKS colonies. When TKC colonies eventually overgrew TKS colonies, non-motile TKS cells were passively carried along the expanding TKC front, indicating that DCG facilitates the physical association and surface dispersal of Sphingobium cells. DCG activity was also observed against various strains of Sphingobium, Sphingomonas, and Novosphingobium, whereas extremely weak or no DCG activity was observed toward other bacterial groups, including representatives of α-, β-, and γ-proteobacteria as well as actinobacteria. These results indicate that TKC exhibits DCG selectively toward sphingomonads, recognizing taxon-specific cues rather than responding indiscriminately to neighboring colonies. Among the components tested, sphingosine reproducibly triggered DCG in a dose-dependent manner, and the inhibition of sphingolipid biosynthesis in Sphingobium with myriocin markedly suppressed the inducing effect. These results highlight the sphingosine-mediated induction of DCG as a molecular mechanism underlying the initial step in the spatial organization of bacterial communities on solid surfaces.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 2","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Symbiont- and Bacterial Cell Size-dependent Backpacking and Grazing of Acanthamoeba. 共生和细菌细胞大小依赖性棘阿米巴的背包和放牧。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25024

Nana Tanaka, Kotoka Kuriki, Torahiko Okubo, Yoshiaki Enoeda, Ayano Konno, Shinji Nakamura, Toyotaka Sato, Shin-Ichi Yokota, Hiroyuki Yamaguchi

{"title":"Symbiont- and Bacterial Cell Size-dependent Backpacking and Grazing of Acanthamoeba.","authors":"Nana Tanaka, Kotoka Kuriki, Torahiko Okubo, Yoshiaki Enoeda, Ayano Konno, Shinji Nakamura, Toyotaka Sato, Shin-Ichi Yokota, Hiroyuki Yamaguchi","doi":"10.1264/jsme2.ME25024","DOIUrl":"10.1264/jsme2.ME25024","url":null,"abstract":"On solid media, Acanthamoeba harboring the endosymbiotic bacterium (Neochlamydia) carries live Escherichia coli on its cell surface without phagocytosing this bacterium, and defends against infection by Legionella pneumophila of a small size in an endosymbiotic bacterium-dependent manner. This implies the presence of an unknown protective mechanism. Therefore, we exami-ned the physical properties of the carried bacteria using transposon insertion mutants that had lost the \"backpack\" on solid media. A mutant was selected from a library in which the nhaA gene, encoding a Na+/H+ antiporter, was disrupted. The knockout mutant was longer than the parental strain and was gradually consumed by symbiotic amoebae. Similarly, the NhaA-knockout mutant strain was longer and lacked the backpack. The complementation of nhaA restored bacterial cells to their normal size, and the backpack phenomenon reappeared. Using E. coli elongated by a treatment with mitomycin C, the backpack was not evident, and enlarged bacteria were consumed by symbiotic amoebae. Therefore, symbiotic amoebae protected themselves from intruders by not engulfing small bacteria in an endosymbiosis-dependent manner. The present results propose a novel countermeasure by phagocytic cells against intruders that involves the recognition of bacterial sizes and is dependent on endosymbiosis.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"41 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12999725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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}

引用次数: 0

Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota. 小叶藻门的分类与生态学研究进展。

IF 2.6 4区环境科学与生态学

Microbes and Environments Pub Date : 2026-01-01 DOI: 10.1264/jsme2.ME25084

Naoki Fujii, Meri Nakajima, Takashi Narihiro, Kyohei Kuroda, Tomonori Kindaichi

引用次数: 0