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Effects of Soil Moisture Content and Rj Genotype Differences on Soybean Productivity and Soybean-nodulating Bradyrhizobial Occupancy. 土壤含水量和Rj基因型差异对大豆产量和大豆根瘤菌占用的影响
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.ME25075
Soto Ito, Shingo Matsumoto, Masayuki Kadowaki, Hirokazu Sato, Yuichi Saeki, Sokichi Shiro
{"title":"Effects of Soil Moisture Content and Rj Genotype Differences on Soybean Productivity and Soybean-nodulating Bradyrhizobial Occupancy.","authors":"Soto Ito, Shingo Matsumoto, Masayuki Kadowaki, Hirokazu Sato, Yuichi Saeki, Sokichi Shiro","doi":"10.1264/jsme2.ME25075","DOIUrl":"10.1264/jsme2.ME25075","url":null,"abstract":"<p><p>We exami-ned the effects of soil moisture changes on soybean growth, yield, and the structure of soybean-nodulating bradyrhizobial communities in cultivars with different Rj genotypes. The experiment was conducted using cultivation pots with soybean cultivars Bragg (non-Rj), CNS (Rj<sub>2</sub>Rj<sub>3</sub>), D-51 (Rj<sub>3</sub>), and Fukuyutaka (Rj<sub>4</sub>). Test strains included Bradyrhizobium diazoefficiens USDA 110<sup>T</sup>, B. japonicum USDA 6<sup>T</sup> and USDA 123, and B. elkanii USDA 31. Cultivation pots were built with 15-cm ridges, and three soil moisture conditions were generated by varying the presence and placement of drainage holes on the pots. Declining soil moisture significantly reduced shoot length, shoot dry weight, root dry weight, root length, nodule number, pod number, pod dry weight, and seed number. An occupancy anal-ysis showed that USDA 110 dominated Fukuyutaka only; across treatments, it was the most abundant under high soil moisture, but significantly declined with reductions in soil moisture, where USDA 31 became dominant. A non-metric multidimensional scaling anal-ysis revealed shifts in community compositions in response to soil moisture and cultivar. Collectively, these results indicate that soybean growth, yield, and symbiosis with bradyrhizobia are strongly affected by soil moisture and also that these effects vary among cultivars.</p>","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/PMC12999728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147463675","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
Symbiosis Islands of Bradyrhizobium Determine Relationships with Host Legumes Lespedeza cuneata and Glycine max. 慢生根瘤菌共生岛与寄主豆科植物胡枝子和甘氨酸的关系。
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.ME25072
Yuki Konno, Iori Imamura, Tomoyuki Nemoto, Masaya Kajiwara, Yoshiyuki Ohtsubo, Manabu Itakura, Tomoko Sakai, Hisayuki Mitsui, Kiwamu Minamisawa, Masayuki Sugawara
{"title":"Symbiosis Islands of Bradyrhizobium Determine Relationships with Host Legumes Lespedeza cuneata and Glycine max.","authors":"Yuki Konno, Iori Imamura, Tomoyuki Nemoto, Masaya Kajiwara, Yoshiyuki Ohtsubo, Manabu Itakura, Tomoko Sakai, Hisayuki Mitsui, Kiwamu Minamisawa, Masayuki Sugawara","doi":"10.1264/jsme2.ME25072","DOIUrl":"10.1264/jsme2.ME25072","url":null,"abstract":"<p><p>Symbiotic N<sub>2</sub>-fixing bradyrhizobia nodulate various leguminous plants and possess a large symbiosis island (SI) encoding symbiotic functions in their genomes. We obtained 30 rhizobial isolates from root nodules of the tribe Desmodieae of native leguminous plants in northern Japan. Based on their 16S rRNA gene sequences, most isolates (24/30=80%) phylogenetically belonged to Bradyrhizobium. Two isolates (LCT1 and LCT2) from Lespedeza cuneata were placed phylogenetically with Bradyrhizobium diazoefficiens USDA110<sup>T</sup>, a well-studied soybean (Glycine max [L.] Merr.) symbiont. Genomic comparisons revealed different SIs in the Met-tRNA and Val-tRNA genes on the respective genomes. In contrast, core genomic regions outside the SI regions showed strong collinearity between strains LCT2 and USDA110. Phenotypically, LCT2 formed N<sub>2</sub>-fixing root nodules on L. cuneata, an original host plant, but not on soybean, whereas USDA110 formed N<sub>2</sub>-fixing root nodules on soybean, but not on L. cuneata. Therefore, the SI variants were expected to contain the genes responsible for this host specificity. Genes relevant to the type III secretion system (T3SS) showed less homology between LCT2 and USDA110 than nod genes encoding Nod factor biosynthesis. Host plant inoculations with T3SS mutants suggested the involvement of T3SS effectors in differential host specificity. Therefore, the acquisition of distinct SI variants may confer strong host specificity through symbiotic interactions between Bradyrhizobium and host legumes. We discuss the possible pathway of symbiotic bradyrhizobial evolution and its application to the mitigation of greenhouse gas emissions.</p>","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/PMC12999731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326625","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
Metatranscriptome Data Support the Existence of Two Distinct Morphotypes in a Single Parmalean Species in Natural Environments. 元转录组数据支持自然环境中单个帕玛龙物种存在两种不同的形态型。
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.ME26037
Hiroto Sasaki, Hisashi Endo, Eric Pelletier, Shinya Yoshikawa, Akira Kuwata, Hiroyuki Ogata
{"title":"Metatranscriptome Data Support the Existence of Two Distinct Morphotypes in a Single Parmalean Species in Natural Environments.","authors":"Hiroto Sasaki, Hisashi Endo, Eric Pelletier, Shinya Yoshikawa, Akira Kuwata, Hiroyuki Ogata","doi":"10.1264/jsme2.ME26037","DOIUrl":"10.1264/jsme2.ME26037","url":null,"abstract":"<p><p>Parmales, the sister clade of diatoms, includes isolates exhibiting one of two morphotypes: a silicified non-flagellated form (S-type) and a naked flagellated form (F-type). Although the alternation of these forms for a single isolate has not been formally established, these morphotypes have been hypothesized to represent alternating stages of a single parmalean population. We herein investigated the global expression patterns of S- and F-type markers by integrating parmalean environmental genomes and metatranscriptomic data from Tara Oceans. We detected the expression of both S- and F-type marker genes from individual environmental genomes, providing the first metatranscriptomic evidence supporting the hypothesis of a life cycle involving two morphotypes. Furthermore, the expression of F-type markers showed a broad distribution across various environmental conditions, whereas that of S-type markers was more restricted and associated with specific environmental conditions. Based on these patterns, we propose a threshold-based model in which F-type-dominated populations persist under a wide range of conditions, from oligotrophic to eutrophic environments, and a morphological switch to the S-type is triggered in a minor subset of F-type populations once environmental conditions exceed a critical threshold for growth. This study provides insights into the evolutionary acquisition of a cell type specialized for photoautotrophy in the common ancestor of parmaleans and diatoms.</p>","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/PMC13659343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149030781","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 Bradyrhizobium ottawaense with High N2O-reducing Activity from Soybean Nodules in Japan. 日本大豆根瘤中高还原n2o活性缓生根瘤菌的筛选
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.ME25062
Manabu Itakura, Kaori Kakizaki, Atsuo Suzuki, Satoshi Okubo, Hiromi Kato, Masayuki Sugawara, Yuichi Saeki, Kiwamu Minamisawa
{"title":"Screening of Bradyrhizobium ottawaense with High N<sub>2</sub>O-reducing Activity from Soybean Nodules in Japan.","authors":"Manabu Itakura, Kaori Kakizaki, Atsuo Suzuki, Satoshi Okubo, Hiromi Kato, Masayuki Sugawara, Yuichi Saeki, Kiwamu Minamisawa","doi":"10.1264/jsme2.ME25062","DOIUrl":"10.1264/jsme2.ME25062","url":null,"abstract":"<p><p>Bradyrhizobium ottawaense has prospects as an environmentally friendly inoculant for soybean farming because of its higher N<sub>2</sub>O reductase (N<sub>2</sub>OR) activity than that of B. diazoefficiens. To examine high N<sub>2</sub>O-reducing B. ottawaense, we performed a PCR anal-ysis of nosZ genes in 8,640 soybean nodules from 68 fields in Japan. Of 384 PCR-positive nodules, we obtained 90 isolates of bradyrhizobia with B. ottawaense-type nosZ, derived exclusively from 18 fields in Gunma and Osaka prefectures. Of 77 monophyletic isolates, 73 had significantly higher N<sub>2</sub>OR activity than B. diazoefficiens USDA110. Another 13 isolates‍ ‍from Osaka were phylogenetically placed outside of the B. ottawaense clade with B. liaoningense or B. betae, 8 of which also exhibited significantly higher N<sub>2</sub>OR activity than B. diazoefficiens USDA110. An anal-ysis of nopP gene sequences revealed amino acid sequence variations in the NopP effector protein among these high N<sub>2</sub>O-reducing isolates, with the NopP<sub>USDA122</sub> type being one of the variations identified. The NopP-mediated symbiotic incompatibility of soybean host plants may eliminate nodulation by indigenous bradyrhizobia and facilitate inoculant nodulation to reduce N<sub>2</sub>O emissions. Therefore, 90 isolates and their observed NopP types are‍ ‍potentially important resources for N<sub>2</sub>O mitigation. Furthermore, the dense geographical map of Bradyrhizobium species based on Internal Transcribed Spacer-Restriction Fragment Length Polymorphisms (ITS-RFLP) of the 16S-23S rRNA gene from 8,640 nodules revealed the recent northward expansion of B. elkanii to central Japan potentially due to global warming. This change in indigenous soybean bradyrhizobia is important for application strategies of bradyrhizobial inoculants under field conditions.</p>","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/PMC12999735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147463644","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
Exploring the Diversity and Metabolic Potential of CO2 fixation Mediated by RubisCO in Prokaryotes in the Japan Collection of Microorganisms. 日本微生物群中RubisCO介导的原核生物二氧化碳固定的多样性及其代谢潜力的探索。
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.ME25035
Arisa Nishihara, Shingo Kato, Moriya Ohkuma
{"title":"Exploring the Diversity and Metabolic Potential of CO<sub>2</sub> fixation Mediated by RubisCO in Prokaryotes in the Japan Collection of Microorganisms.","authors":"Arisa Nishihara, Shingo Kato, Moriya Ohkuma","doi":"10.1264/jsme2.ME25035","DOIUrl":"10.1264/jsme2.ME25035","url":null,"abstract":"<p><p>A genome anal-ysis is essential for identifying valuable microbial resources for future applications. In the present study, we exami-ned potential CO<sub>2</sub>-fixing microorganisms based on the presence of the Calvin-Benson-Bassham (CBB) cycle using 6,262 bacterial and 487 archaeal genomes from available cultures in the Japan Collection of Microorganisms (JCM), a well-established culture collection, in October 2023. A total of 306 strains (147 genera, eight phyla) carried CBB cycle genes, and a literature survey showed that 74 genera had experimental evidence of autotrophic growth while 73 lacked supporting information. A phylogenetic anal-ysis of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcL) identified diverse forms (IA, IB, IC, IE, I+α, II, and III) with distinct metabolic associations; IA was associated with sulfur species oxidation and formed IC with hydrogen oxidation. Genome-based metabolic predictions identified the potential for CO<sub>2</sub> fixation in numerous species lacking experimental evidence. Our anal-yses indicate that members of Actinomycetota harboring IE RbcL were generally associated with hydrogen oxidation, possibly by using oxygen or nitrate as an electron acceptor. Additionally, 12 species in Pseudomonadota contained photosystem II reaction center proteins (PufL and PufM), suggesting phototrophic capabilities. However, the prediction of electron donors failed in some of these species. They may use the CBB cycle to regulate the intracellular redox balance under photoheterotrophic growth. The present results reveal unrecognized autotrophic potential in JCM strains and broaden our knowledge of the diversity of CO<sub>2</sub>-fixing microorganisms. Experimental validation will clarify their roles in the global carbon cycle and their potential for biotechnological applications towards environmental sustainability.</p>","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/PMC12999727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018992","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
Kinetics of Nitrous Oxide (N2O)-reducing Activity of Bradyrhizobium ottawaense by an Automated Analysis. 慢生根瘤菌氧化亚氮还原活性的自动分析动力学。
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.ME25070
Manabu Itakura, Kiwamu Minamisawa
{"title":"Kinetics of Nitrous Oxide (N<sub>2</sub>O)-reducing Activity of Bradyrhizobium ottawaense by an Automated Analysis.","authors":"Manabu Itakura, Kiwamu Minamisawa","doi":"10.1264/jsme2.ME25070","DOIUrl":"10.1264/jsme2.ME25070","url":null,"abstract":"<p><p>The biological reduction of N<sub>2</sub>O, a potent greenhouse gas, is crucial for environmental sustainability. We developed an automated system for continuous N<sub>2</sub>O monitoring in the gas phase of a flask containing an anaerobic bradyrhizobial culture, and then exami-ned the kinetic parameters of bacterial N<sub>2</sub>O reduction. The maximum reaction rate (V<sub>max</sub>) was approximately 61-fold higher for Bradyrhizobium ottawaense SG09 (1,471‍ ‍nmol h<sup>-1</sup> 10<sup>9</sup> cells<sup>-1</sup>) than for B. diazoefficiens USDA110 (24‍ ‍nmol h<sup>-1</sup> 10<sup>9</sup> cells<sup>-1</sup>). Our kinetics anal-ysis confirmed that SG09 maintained higher N<sub>2</sub>O-reducing activity than USDA110 even at the atmospheric concentration of N<sub>2</sub>O (0.34 ppm).</p>","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/PMC12999729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147491239","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
Root-associated Bacterial Communities of Sugarcane Cultivated for Traditional Wasanbon Sugar differ among Cultivation Sites in Kagawa, Japan. 日本香川地区种植传统Wasanbon糖的甘蔗根部相关细菌群落在不同种植地点的差异。
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.ME26030
Yasunobu Yamada, Md Shahidul Islam, Kaoru Matsumoto, Masahiro Morokuma, Mika Nomura
{"title":"Root-associated Bacterial Communities of Sugarcane Cultivated for Traditional Wasanbon Sugar differ among Cultivation Sites in Kagawa, Japan.","authors":"Yasunobu Yamada, Md Shahidul Islam, Kaoru Matsumoto, Masahiro Morokuma, Mika Nomura","doi":"10.1264/jsme2.ME26030","DOIUrl":"10.1264/jsme2.ME26030","url":null,"abstract":"<p><p>Sugarcane for traditional Wasanbon sugar has long been cultivated in Higashi-Kagawa. Three sugarcane cultivars were cultivated at three sites in Kagawa Prefecture, and root-associated bacterial communities were analyzed using 16S rRNA gene amplicon sequencing. Bacterial community compositions varied primarily according to the cultivation site rather than the cultivar, and soil bacterial communities showed similar site-dependent clustering patterns. These results indicate that the cultivation site affects the root-associated bacterial community structure.</p>","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/PMC13659341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148900527","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
A Novel Epiphytic Clonostachys chloroleuca Strain that Effectively Controls Cucumber Anthracnose. 一株能有效控制黄瓜炭疽病的附生菌绿绿梭菌。
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.ME26058
Alchemi Putri Juliantika Kusdiana, Yuta Hayakawa, Stephany Angelia Tumewu, Haruhisa Suga, Masafumi Shimizu
{"title":"A Novel Epiphytic Clonostachys chloroleuca Strain that Effectively Controls Cucumber Anthracnose.","authors":"Alchemi Putri Juliantika Kusdiana, Yuta Hayakawa, Stephany Angelia Tumewu, Haruhisa Suga, Masafumi Shimizu","doi":"10.1264/jsme2.ME26058","DOIUrl":"10.1264/jsme2.ME26058","url":null,"abstract":"<p><p>Cucumber anthracnose is a destructive disease caused by Colletotrichum orbiculare that affects global cucumber production. Although plant-associated fungi are promising sources of biological control agents, their efficacy against cucumber anthracnose has not been established. In the present study, 108 spore-forming endophytic and epiphytic fungal strains were isolated from the leaves of seven plant species and screened for biocontrol activity against C. orbiculare using detached cucumber cotyledon assays and pot experiments. Three highly suppressive strains (GUSF-44, GUSF-66, and GUSF-153) identified in detached cotyledon assays were further evaluated in pot experiments, in which GUSF-66 exhibited the most consistent and pronounced disease suppression, reducing the lesion area by approximately 75%. A multilocus phylogenetic anal-ysis based on the internal transcribed spacer region, RNA polymerase II second largest subunit gene, and translation elongation factor 1-alpha gene sequences identified GUSF-66 as Clonostachys chloroleuca. Microscopic observations showed that this strain successfully colonized the cucumber cotyledon epiphytically. In vitro assays revealed that GUSF-66 produced lytic enzymes, including chitinase, β-1,3-glucanase, and protease, and inhibited the conidial germination and hyphal growth of C. orbiculare. Although some C. chloroleuca strains have been implicated in soybean root rot, GUSF-66 caused no visible symptoms in soybean plants. To the best of our knowledge, this is the first study to demonstrate the biocontrol potential of C. chloroleuca against cucumber anthracnose.</p>","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/PMC13659348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111781","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
Single-cell Genomic Analysis of Fiber-adhering Rumen Bacteria during an in situ Incubation of Timothy Hay. 海草原位培养过程中纤维粘附瘤胃细菌的单细胞基因组分析。
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.ME26040
Shuhei Takizawa, Miho Fujimori, Takumi Shinkai
{"title":"Single-cell Genomic Analysis of Fiber-adhering Rumen Bacteria during an in situ Incubation of Timothy Hay.","authors":"Shuhei Takizawa, Miho Fujimori, Takumi Shinkai","doi":"10.1264/jsme2.ME26040","DOIUrl":"10.1264/jsme2.ME26040","url":null,"abstract":"<p><p>Rumen microorganisms adhere to the surface of ingested feed and degrade fibrous compounds into short-chain fatty acids, which are the primary source of energy for milk and meat production. A more detailed understanding of uncultured ruminal bacteria involved in polysaccharide degradation may help improve the feed digestion efficiency of ruminants. The aim of the present study was to identify the ability of uncultured ruminal bacteria to degrade polysaccharides by constructing bacterial genomes and linking their 16S rRNA genes with functional genes using single-cell genome sequencing. The ruminal fibrolytic community was enriched on the surface of Timothy hay via a time-limited in situ incubation. A single-cell genomic anal-ysis was used to construct 83 single-cell-assembled genomes from the ruminal fibrolytic community, and 16S rRNA genes were recovered from 80 genomes. The uncultured Ruminococcus, Ruminococcus_D, and Fibrobacter groups had a high percentage of carbohydrate-binding module genes involved in attachment to fibrous compounds. Uncultured Prevotella showed different profiles of genes encoding major carbohydrate-active enzymes from those of known P. ruminicola spp., and the amino acid sequence of glycoside hydrolase family 43 had various deletions and substitutions. The single-cell genomic anal-ysis enabled the construction of genomes with 16S rRNA genes from fiber-adherent rumen bacteria and linked their 16S rRNA genes with the DNA and amino acid sequences of functional genes involved in carbohydrate utilization. Several uncultured rumen bacteria possess functional genes that contribute to feed digestion and biofilm formation.</p>","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/PMC13659345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149111805","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
Host Genetic Constraints on the Horizontal Transmission of Daphnia-associated Microbiota. 水蚤相关菌群水平传播的宿主遗传制约。
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.ME26003
Ryotaro Ichige, Jotaro Urabe
{"title":"Host Genetic Constraints on the Horizontal Transmission of Daphnia-associated Microbiota.","authors":"Ryotaro Ichige, Jotaro Urabe","doi":"10.1264/jsme2.ME26003","DOIUrl":"10.1264/jsme2.ME26003","url":null,"abstract":"<p><p>The taxonomic composition of Daphnia microbiota is affected not only by external environmental conditions, but also by the host's internal physiological state, which is partly governed by genetic factors. However, the extent to which host genetics constrain the composition of associated bacterial communities remains unclear. In the present study, we conducted mixed-culture experiments using obligately parthenogenetic Daphnia cf. pulex individuals from genetically distinct lineages. The results obtained showed that the taxonomic composition of host-associated microbiota significantly differed between genotypes, both within and across lineages, with certain bacterial taxa being exclusive to specific genotypes. When genetically distinct hosts were co-cultured, some bacterial taxa initially exclusive to one genotype appeared in the microbiota of another, indicating the horizontal transmission of microbiota between hosts. Nevertheless, the overall taxonomic composition of microbiota was largely unaffected by the presence of genetically different hosts. These results suggest that although the horizontal transfer of microbiota occurs between different Daphnia genotypes, it is not extensive enough to override genotype-specific microbiota compositions. Therefore, in D. cf. pulex, host genetics play a major role in shaping the composition of the associated microbiota.</p>","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/PMC13293707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148042744","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
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