Microbes and Environments最新文献

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":"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 (Rj2Rj3), D-51 (Rj3), and Fukuyutaka (Rj4). Test strains included Bradyrhizobium diazoefficiens USDA 110T, B. japonicum USDA 6T 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.","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":"Symbiotic N2-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 USDA110T, 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 N2-fixing root nodules on L. cuneata, an original host plant, but not on soybean, whereas USDA110 formed N2-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.","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

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 N2O-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":"Bradyrhizobium ottawaense has prospects as an environmentally friendly inoculant for soybean farming because of its higher N2O reductase (N2OR) activity than that of B. diazoefficiens. To examine high N2O-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 N2OR 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 N2OR 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 N2O-reducing isolates, with the NopPUSDA122 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 N2O emissions. Therefore, 90 isolates and their observed NopP types are‍ ‍potentially important resources for N2O 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.","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 CO2 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":"A genome anal-ysis is essential for identifying valuable microbial resources for future applications. In the present study, we exami-ned potential CO2-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 CO2 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 CO2-fixing microorganisms. Experimental validation will clarify their roles in the global carbon cycle and their potential for biotechnological applications towards environmental sustainability.","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

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":"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.","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

Oxic Subseafloor Microbial Communities Retain Anabolic Capacity under both Oxic and Oxygen-depleted Conditions. 含氧海底微生物群落在含氧和缺氧条件下都保持合成代谢能力。

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.ME26008

Mako Takada, Motoo Ito, Shu Ying Wee, Jason B Sylvan, Rosalind M Coggon, Emily R Estes, William P Gilhooly Iii, Yi Wang, Masataka Aizawa, Susumu Yoshizawa, Yuki Morono

{"title":"Oxic Subseafloor Microbial Communities Retain Anabolic Capacity under both Oxic and Oxygen-depleted Conditions.","authors":"Mako Takada, Motoo Ito, Shu Ying Wee, Jason B Sylvan, Rosalind M Coggon, Emily R Estes, William P Gilhooly Iii, Yi Wang, Masataka Aizawa, Susumu Yoshizawa, Yuki Morono","doi":"10.1264/jsme2.ME26008","DOIUrl":"https://doi.org/10.1264/jsme2.ME26008","url":null,"abstract":"Marine subseafloor sediments underlying open ocean regions are predominantly low-energy environments; however, they harbor vast microbial populations. How these communities persist and whether they retain anabolic capacity during transient oxygen depletion remain unclear. We herein investigated oxic sediments from the South Atlantic Gyre (SAG; IODP Site U1559D, core 7X-1) using paired incubations under oxic and anoxic (oxygen-depleted) conditions with defined C/N amendments. Sediments were amended with a 13C-amino acid mix+15N-ammonium, 13C-bicarbonate+15N-ammonium, or 15N-ammonium only and then incubated for 10, 30, and 75 d. Single-cell nanoscale secondary ion mass spectrometry (NanoSIMS) confirmed the assimilation of isotope-labeled substrates under oxic and anoxic conditions. Pronounced 13C enrichment occurred primarily in amino acid-amended incubations, whereas 15N incorporation from ammonium was widespread across all treatments, including ammonium-only incubations without added organic carbon, indicating assimilation supported by endogenous sedimentary carbon pools. Biomass-based growth responses varied among amendments and redox regimes, demonstrating that oxic-sourced communities may transition into measurable growth even under oxygen depletion. Amplicon-based community profiles exhibited directional, time-dependent shifts with limited segregation by substrate identity,‍ ‍suggesting that incubation time and shared successional dynamics dominated over amendment identity at the whole-community level. Collectively, these results indicate that SAG subseafloor communities retain a flexible anabolic potential that may be expressed under both oxic and oxygen-depleted conditions when substrates and/or oxidants become available.","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148619960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Performance of Marine Anammox Candidatus Scalindua sp. under High Nitrate Conditions in a Biofilm Reactor. 生物膜反应器中高硝酸盐条件下海洋厌氧氨氧化候选菌Scalindua sp.的性能。

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.ME25094

Jonathan A C Roques, Naoki Fujii, Ebuka Unegbu, Amélie Marqué, Emma Johansson, Kohei Yamamoto, Haruhi Iida, Tomonori Kindaichi

引用次数: 0

Temperature Effects on Symptom Expression of Lettuce Black Root Rot Caused by Berkeleyomyces rouxiae. 温度对生菜黑根腐病症状表达的影响。

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.ME25065

Misaki Edamoto, Toshiyuki Usami

引用次数: 0

Genome-wide Characterization of Non-shared Sequences among Amphora-shaped Giant Viruses. 双耳形巨型病毒非共享序列的全基因组特征。

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.ME25085

Motohiro Akashi, Masaharu Takemura, Seiichi Suzuki

{"title":"Genome-wide Characterization of Non-shared Sequences among Amphora-shaped Giant Viruses.","authors":"Motohiro Akashi, Masaharu Takemura, Seiichi Suzuki","doi":"10.1264/jsme2.ME25085","DOIUrl":"10.1264/jsme2.ME25085","url":null,"abstract":"Giant viruses are distinguished not only by their large particle size, but also by their extensive genomes, often reaching megabase levels. Many sequences within these genomes are considered to have been introduced by hosts, surrounding organisms, or other viruses. Since the natural hosts of many giant viruses remain unidentified, analyzing sequences potentially derived from other organisms may aid in clarifying their hosts. In the present study, we identified eukaryote-homologous sequences by isolating those not shared among viruses, an aspect previously overlooked. Our primary focus was on pandoravirus, which, with a genome size of ~2 Mb, is the largest among giant viruses. We obtained 375 BLAST hits with an average sequence identity of ~90%. Among the 102 detected species, those with higher hits included Mus musculus, Lampetra planeri, Melanogrammus aeglefinus, Lampetra fluviatilis, Scylla paramamosain, Cardiocondyla obscurior, Monodelphis domestica, Vespula pensylvanica, Micromonas pusilla, Physcomitrium patens, and Peromyscus californicus. Similar anal-yses of Cedratvirus and Pithovirus, which share an amphora-shaped particle structure with pandoraviruses, yielded fewer data (48 and 5 hits, respectively), with no common taxa at the order level. Thirteen BLAST hits exceeded 100 bp, including conserved non-coding elements (CNEs) in fish and other taxa, along with sequences of unknown functions. These results indicate the presence of short regions with sequence similarity in non-shared sequences, although direct host identification proved difficult.","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/PMC12999734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147481001","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