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Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems. 粘球菌在活性污泥系统中潜在代谢功能的综合见解。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24068
Hazuki Kurashita, Masashi Hatamoto, Shun Tomita, Takashi Yamaguchi, Takashi Narihiro, Kyohei Kuroda
{"title":"Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems.","authors":"Hazuki Kurashita, Masashi Hatamoto, Shun Tomita, Takashi Yamaguchi, Takashi Narihiro, Kyohei Kuroda","doi":"10.1264/jsme2.ME24068","DOIUrl":"10.1264/jsme2.ME24068","url":null,"abstract":"<p><p>Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. A recent metagenomic sequencing ana-lysis showed that Myxococcota are predominant in activated sludge systems; however, their metabolic traits remain unclear. In the present study, we exami-ned the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results obtained showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. The Palsa-1104 and Polyangiales bins contained the glycoside hydrolase GH5 and peptidase M23, which are presumably involved in lysis of the cell wall and cellular cytoplasm, suggesting that some Myxococcota from activated sludge prey on other microorganisms. The cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, but not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, indicating the potential for heterotrophic and autotrophic metabolism by these microbes. In assessments of the social behavior of Myxococcota in activated sludge, the FruA gene and C-signal gene, which are involved in the regulation of fruiting body formation, were lacking in Myxococcota bins, suggesting their inability to form fruiting bodies. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in activated sludge. Our metagenome-based ana-lyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932115","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
Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method. 通过浮萍-微生物共培养法成功分离出多种疣状微生物菌株
IF 2.2 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.me24019
Yasuhiro Tanaka,Erina Tozawa,Tomoki Iwashita,Yosuke Morishita,Hideyuki Tamaki,Tadashi Toyama,Masaaki Morikawa,Yoichi Kamagata,Kazuhiro Mori
{"title":"Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method.","authors":"Yasuhiro Tanaka,Erina Tozawa,Tomoki Iwashita,Yosuke Morishita,Hideyuki Tamaki,Tadashi Toyama,Masaaki Morikawa,Yoichi Kamagata,Kazuhiro Mori","doi":"10.1264/jsme2.me24019","DOIUrl":"https://doi.org/10.1264/jsme2.me24019","url":null,"abstract":"The \"duckweed-microbes co-cultivation method\" is a microbial isolation technique that effectively recovers diverse microbes, including rarely cultivated bacterial phyla, from environmental samples. In this method, aseptic duckweed and microbes collected from an environmental sample are co-cultivated for several days, and duckweed-associated microbes are then isolated from its roots using a conventional agar plate-based cultivation method. We herein propose several improvements to the method in order to specifically obtain members of the rarely cultivated bacterial phylum, Verrucomicrobiota. In systems using river water as the inoculum, the marked enrichment of Verrucomicrobiota was observed after 10 days of co-cultivation, particularly in the roots and co-cultivated media. We also successfully isolated 44 strains belonging to subdivisions 1, 3, and 4 of the phylum Verrucomicrobiota from these systems. This was achieved by changing the concentration of nitrogen in the co-cultivation medium, which is known to affect duckweed growth and/or metabolism, and by subjecting the fronds and co-cultivated media as well as the roots after co-cultivation to microbial isolation.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"13 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209416","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
Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits. 元基因组学对深海大型硫化物矿床浅层区 Zetaproteobacteria 和 Gammaproteobacteria 生态生理学的启示。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23104
Nao Masuda, Shingo Kato, Moriya Ohkuma, Kazuyoshi Endo
{"title":"Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.","authors":"Nao Masuda, Shingo Kato, Moriya Ohkuma, Kazuyoshi Endo","doi":"10.1264/jsme2.ME23104","DOIUrl":"https://doi.org/10.1264/jsme2.ME23104","url":null,"abstract":"<p><p>Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349767","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
The Discovery of Membrane Vesicle Biogenesis in the Polyhydroxybutyrate-non-producing Mutant Strain of Cupriavidus necator H16. 在不产生多羟基丁酸的突变株中发现膜囊泡的生物生成过程。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24007
Sangho Koh, Michio Sato, Hiromi Matsusaki, Seiichi Taguchi
{"title":"The Discovery of Membrane Vesicle Biogenesis in the Polyhydroxybutyrate-non-producing Mutant Strain of Cupriavidus necator H16.","authors":"Sangho Koh, Michio Sato, Hiromi Matsusaki, Seiichi Taguchi","doi":"10.1264/jsme2.ME24007","DOIUrl":"https://doi.org/10.1264/jsme2.ME24007","url":null,"abstract":"<p><p>Extracellular membrane vesicles (MVs) caused by the artificial production of polyhydroxybutyrate (PHB) were previously detected in Escherichia coli. We herein observed MV biogenesis in the mutant strain (-PHB) of the natural PHB producer, Cupriavidus necator H16. This inverse relationship was revealed through comparative electron microscopic ana-lyses of wild-type and mutant strains. Based on these results, we speculate that a physiological relationship exists between MV biogenesis and PHB biosynthesis. Therefore, we propose the potential of MV biogenesis as a fermentative \"stress marker\" for monitoring the performance of target polymer-producing microbial platforms.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349768","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
Polyethylene Biodegradation by an Artificial Bacterial Consortium: Rhodococcus as a Competitive Plastisphere Species. 人工细菌联盟对聚乙烯的生物降解:罗氏球菌是一种具有竞争力的塑球菌种。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24031
Jyothi Priya Putcha, Wataru Kitagawa
{"title":"Polyethylene Biodegradation by an Artificial Bacterial Consortium: Rhodococcus as a Competitive Plastisphere Species.","authors":"Jyothi Priya Putcha, Wataru Kitagawa","doi":"10.1264/jsme2.ME24031","DOIUrl":"10.1264/jsme2.ME24031","url":null,"abstract":"<p><p>Polyethylene (PE), a widely used recalcitrant synthetic polymer, is a major global pollutant. PE has very low biodegradability due to its rigid C-C backbone and high hydrophobicity. Although microorganisms have been suggested to possess PE-degrading enzymes, our understanding of the PE biodegradation process and its overall applicability is still lacking. In the present study, we used an artificial bacterial consortium for PE biodegradation to compensate for the enzyme availability and metabolic capabilities of individual bacterial strains. Consortium members were selected based on available literature and preliminary screening for PE-degrading enzymes, including laccases, lipases, esterases, and alkane hydroxylases. PE pellets were incubated with the consortium for 200 days. A next-generation sequencing ana-lysis of the consortium community of the culture broth and on the PE pellet identified Rhodococcus as the dominant bacteria. Among the Rhodococcus strains in the consortium, Rhodococcus erythropolis was predominant. Scanning electron microscopy (SEM) revealed multilayered biofilms with bacteria embedded on the PE surface. SEM micrographs of PE pellets after biofilm removal showed bacterial pitting and surface deterioration. Multicellular biofilm structures and surface biodeterioration were observed in an incubation of PE pellets with R. erythropolis alone. The present study demonstrated that PE may be biodegraded by an artificially constructed bacterial consortium, in which R. erythropolis has emerged as an important player. The results showing the robust colonization of hydrophobic PE by R. erythropolis and that it naturally possesses and extracellularly expresses several target enzymes suggest its potential as a host for further improved PE biodeterioration by genetic engineering technology using a well-studied host-vector system.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860202","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
Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta. 越南湄公河三角洲使用猪-牲畜沼气消化废水和合成肥料施肥的稻田中的甲烷营养群落和甲烷滋养菌的培养。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24021
Huynh Van Thao, Mitsunori Tarao, Hideshige Takada, Tomoyasu Nishizawa, Tran Sy Nam, Nguyen Van Cong, Do Thi Xuan
{"title":"Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta.","authors":"Huynh Van Thao, Mitsunori Tarao, Hideshige Takada, Tomoyasu Nishizawa, Tran Sy Nam, Nguyen Van Cong, Do Thi Xuan","doi":"10.1264/jsme2.ME24021","DOIUrl":"10.1264/jsme2.ME24021","url":null,"abstract":"<p><p>Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365801","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
Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica. 两种不同的酶同时具有植物烯去饱和酶和 3,4-去饱和酶的活性,它们参与了极嗜卤古菌 Haloarcula japonica 的类胡萝卜素生物合成。
IF 2.1 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24004
Rie Yatsunami, Ai Ando, Nobuhiro Miyoko, Ying Yang, Shinichi Takaichi, Satoshi Nakamura
{"title":"Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica.","authors":"Rie Yatsunami, Ai Ando, Nobuhiro Miyoko, Ying Yang, Shinichi Takaichi, Satoshi Nakamura","doi":"10.1264/jsme2.ME24004","DOIUrl":"10.1264/jsme2.ME24004","url":null,"abstract":"<p><p>The extremely halophilic archaeon Haloarcula japonica accumulates the C<sub>50</sub> carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene desaturase candidates were functionally characterized in the present study. Two genes encoding the potential phytoene desaturases, c0507 and d1086, were found from the Ha. japonica genome sequence by a homology search using the Basic Local Align Search Tool. Disruption mutants of c0507 and d1086 and their complemented strains transformed with expression plasmids for c0507 and d1086 were subsequently constructed. High-performance liquid chromatography (HPLC) ana-lyses of carotenoids produced by these strains revealed that C0507 and D1086 were both bifunctional enzymes with the same activities as both phytoene desaturase (CrtI) and 3,4-desaturase (CrtD). C0507 and D1086 complemented each other during BR biosynthesis in Ha. japonica. This is the first study to identify two distinct enzymes with both CrtI and CrtD activities in an extremely halophilic archaeon.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11946383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175540","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
Global Distribution and Diversity of Marine Parmales. 海洋豚鼠的全球分布和多样性。
IF 2.2 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23093
Hiroki Ban, Hisashi Endo, Akira Kuwata, Hiroyuki Ogata
{"title":"Global Distribution and Diversity of Marine Parmales.","authors":"Hiroki Ban, Hisashi Endo, Akira Kuwata, Hiroyuki Ogata","doi":"10.1264/jsme2.ME23093","DOIUrl":"10.1264/jsme2.ME23093","url":null,"abstract":"<p><p>Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, which exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies on Parmales have been performed; however, their global distribution has not yet been examined in detail. We herein compiled more than 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the samples analyzed. However, the relative abundance of parmaleans in the eukaryotic community was less than 0.2% on average, and the estimated true richness of parmalean ASVs was approximately 316 ASVs, confirming their low abundance and diversity. A phylogenetic ana-lysis divided these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the poles and decreases towards the tropics, and individual clades/subclades show further distinctions in their distribution. Collectively, the present results suggest clade/subclade-specific adaptation to different ecological niches.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140207264","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
Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity. 微生物群落的稳定状态是由动态代谢网络形成的,其成员的功能是实现稳健性和可塑性。
IF 2.2 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23091
Masahiro Honjo, Kenshi Suzuki, Junya Katai, Yosuke Tashiro, Tomo Aoyagi, Tomoyuki Hori, Takashi Okada, Yasuhisa Saito, Hiroyuki Futamata
{"title":"Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity.","authors":"Masahiro Honjo, Kenshi Suzuki, Junya Katai, Yosuke Tashiro, Tomo Aoyagi, Tomoyuki Hori, Takashi Okada, Yasuhisa Saito, Hiroyuki Futamata","doi":"10.1264/jsme2.ME23091","DOIUrl":"10.1264/jsme2.ME23091","url":null,"abstract":"<p><p>A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3<sup>rd</sup> transferred cultures and stable states from the 5<sup>th</sup> to 10<sup>th</sup> transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140306121","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
Does Rhizobial Inoculation Change the Microbial Community in Field Soils? A‍ ‍Comparison with Agricultural Land-use Changes. 根瘤菌接种会改变田间土壤中的微生物群落吗?与农业用地变化的比较。
IF 2.2 4区 环境科学与生态学
Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.me24006
Shintaro Hara,Kaori Kakizaki,Masaru Bamba,Manabu Itakura,Masayuki Sugawara,Atsuo Suzuki,Yuma Sasaki,Masanori Takeda,Kanako Tago,Tsubasa Ohbayashi,Toshihiro Aono,Luciano Nobuhiro Aoyagi,Hiroaki Shimada,Ryo Shingubara,Sachiko Masuda,Arisa Shibata,Ken Shirasu,Rota Wagai,Hiroko Akiyama,Shusei Sato,Kiwamu Minamisawa
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