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Microbes and Environments

Léa Girard, Elodie Blanchet, Didier Stien, Julia Baudart, Marcelino Suzuki, Raphaël Lami
Vibrio fischeri possesses a complex AHL-mediated Quorum-sensing (QS) system including two pathways, LuxI/R (3-oxo-C6-HSL and C6-HSL) and AinS/R (C8-HSL), which are important for the regulation of physiological traits. Diverse QS-dependent functional phenotypes have been described in V. fischeri; however, AHL diversity is still underestimated. In the present study, we investigated AHL diversity in five symbiotic V. fischeri strains with distinct phenotypic properties using UHPLC-HRMS/MS. The results obtained (1) revealed an unexpectedly high diversity of signaling molecules, (2) emphasized the complexity of QS in V...
February 13, 2019: Microbes and Environments
Kazuki Suzuki, Manami Takemura, Takaaki Miki, Masanori Nonaka, Naoki Harada
Soil bacterial community compositions and temporal changes in organic paddy fields were elucidated using a 16S rRNA gene amplicon sequencing analysis with a high-throughput next generation sequencer. At transplanting, bacterial community compositions in organic and conventional paddy fields were mostly similar despite differences in field management. The bacterial community composition in organic fields differed from that under conventional management during the rice growth period, possibly as a result of the decomposition process of organic fertilizers...
February 13, 2019: Microbes and Environments
Sayed Ziauddin Hashami, Hiroyuki Nakamura, Naoko Ohkama-Ohtsu, Katsuhiro Kojima, Salem Djedidi, Izumi Fukuhara, Mohammad Daud Haidari, Hitoshi Sekimoto, Tadashi Yokoyama
Legumes form root nodules and fix atmospheric nitrogen by establishing symbiosis with rhizobia. However, excessive root nodules are harmful to plants because of the resulting overconsumption of energy from photosynthates. The delay of an inoculation of the soybean super-nodulation mutant NOD1-3 with Bradyrhizobium diazoefficiens USDA110T by 5 d after an inoculation with several soil bacteria confirmed that one bacterial group significantly decreased root nodules throughout the study period. Moreover, no significant changes were observed in nitrogen fixation by root nodules between an inoculation with USDA 110T only and co-inoculation treatments...
February 5, 2019: Microbes and Environments
Yu-Hung Yeh, Roland Kirschner
Vitex rotundifolia L. f. (Lamiaceae), which commonly grows at sand coasts, is important for coast protection and the prevention of erosion. However, the diversity and roles of fungi associated with this plant remain unclear. A total of 1,052 endophytic isolates from 1,782 plants tissues from two sand beaches in northern Taiwan were classified into 76 morphospecies based on culture morphology and ITS or LSU rRNA gene sequence comparisons. Critical species were further identified using protein gene sequences and microscopy...
February 5, 2019: Microbes and Environments
Toshihiro Suzuki, Tomoki Yazawa, Naonori Morishita, Akihiko Maruyama, Hiroyuki Fuse
The Gram-negative marine propylene-assimilating bacterium, strain PE-TB08W, was isolated from surface seawater. A structural gene analysis using the 16S rRNA gene showed 96, 94, and 95% similarities to Halioglobus species, Haliea sp. ETY-M, and Haliea sp. ETY-NAG, respectively. A phylogenetic tree analysis showed that strain PE-TB08W belonged to the EG19 (Chromatocurvus)-Congregibacter-Haliea cluster within the Halieaceae (formerly Alteromonadaceae) family. Thus, strain PE-TB08W was characterized as a newly isolated Halieaceae bacterium; we suggest that this strain belongs to a new genus...
January 16, 2019: Microbes and Environments
Turgut Yigit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saito, Tatsuhiro Ezawa, Shusei Sato
Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields...
December 22, 2018: Microbes and Environments
Takashi Narihiro, Masaru Konishi Nobu, Tomoyuki Hori, Tomo Aoyagi, Yuya Sato, Tomohiro Inaba, Hidenobu Aizawa, Hideyuki Tamaki, Hiroshi Habe
The present study characterized the interactions of microbial populations in activated sludge systems during the operational period after an increase in the wastewater flow rate and consequential ammonia accumulation using a 16S rRNA gene sequencing-based network analysis. Two hundred microbial populations accounting for 81.8% of the total microbiome were identified. Based on a co-occurrence analysis, Nitrosomonas-type ammonia oxidizers had one of the largest number of interactions with diverse bacteria, including a bulking-associated Thiothrix organism...
December 22, 2018: Microbes and Environments
Kazuki Shinoda, Midori Yano, Muneoki Yoh, Makoto Yoshida, Akiko Makabe, Yohei Yamagata, Benjamin Z Houlton, Keisuke Koba
Changes in 15 N/14 N in the soil microbial biomass during nitrogen (N) mineralization have been hypothesized to influence 15 N/14 N in soil organic matter among ecosystem sites. However, a direct experimental test of this mechanism has not yet been performed. To evaluate the potential control of microbial N mineralization on the natural N isotope composition, we cultured fungi (Aspergillus oryzae) in five types of media of varying C:N ratios of 5, 10, 30, 50, and 100 for 4 d, and tracked changes in δ15 N in the microbial biomass, NH4 + , and dissolved organic N (DON: glycine) over the course of the experiment...
December 15, 2018: Microbes and Environments
Yusuke Takashima, Kensuke Seto, Yousuke Degawa, Yong Guo, Tomoyasu Nishizawa, Hiroyuki Ohta, Kazuhiko Narisawa
Endofungal bacteria are widespread within the phylum Mucoromycota, and these include Burkholderiaceae-related endobacteria (BRE). However, the prevalence of BRE in Mortierellomycotinan fungi and their phylogenetic divergence remain unclear. Therefore, we examined the prevalence of BRE in diverse species of Mortierella. We surveyed 238 isolates of Mortierella spp. mainly obtained in Japan that were phylogenetically classified into 59 species. BRE were found in 53 isolates consisting of 22 species of Mortierella...
December 8, 2018: Microbes and Environments
Yasuhiro Nakanishi, Tatsuya Yamamoto, Nozomu Obana, Masanori Toyofuku, Nobuhiko Nomura, Akihiro Kaneko
Bacterial interspecies interactions in the oral cavity influence the structural development of cariogenic biofilms and dental caries. Visualization of the biofilm architecture and bacterial localization within biofilms is essential for understanding bacterial interactions. We herein demonstrated that the spatial localization of Streptococcus mutans within dual-species biofilms was altered in a manner that depended on the partner. Furthermore, we found that these biofilms influenced the survival of S. mutans against disinfectants...
December 8, 2018: Microbes and Environments
Mina Ootsuka, Tomoyasu Nishizawa, Morifumi Hasegawa, Yasurou Kurusu, Hiroyuki Ohta
Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289T were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae JCM 10874T . An opdA homolog (opdADSM16289 ) encoding BNP degradation activity was identified in DSM 16289T , in contrast with JCM 10874T , possessing both the opdA homolog and nmoA. The degradation profile of different BNP isomers was examined by Escherichia coli transformants harboring opdADSM16289 , opdAJCM10874 , and nmoAJCM10874 to characterize and compare the expression activities of these genes...
December 5, 2018: Microbes and Environments
Tatsunori Nakagawa, Yuki Tsuchiya, Shingo Ueda, Manabu Fukui, Reiji Takahashi
Nitrous oxide (N2 O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2 O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2 O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2 O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan...
December 1, 2018: Microbes and Environments
James S Evans, Susanna López-Legentil, Patrick M Erwin
Various DNA extraction methods are often used interchangeably for the characterization of microbial communities despite indications that different techniques produce disparate results. The microbiomes of two ascidian species were herein characterized using two common DNA extraction kits, the DNeasy Blood and Tissue Kit (Qiagen) and the PowerSoil DNA Isolation Kit (Mo Bio Laboratories), followed by next-generation (Illumina) sequencing of partial 16S rRNA genes. Significant differences were detected in microbial community diversity and structure between ascidian species, but not between kits, suggesting similar recovery of biological variation and low technical variation between the two extraction methods for ascidian microbiome characterization...
November 27, 2018: Microbes and Environments
Lee Hudek, Aydin Enez, Lambert Bräu
Plant growth-promoting bacteria (PGPB) inhabit the rhizosphere of plants and are capable of enhancing plant growth through a number of mechanisms. A strain of Pseudomonas fluorescens DUS1-27 was identified as a potential PGPB candidate based on its ability to increase the growth of Brassica napus L. (canola) over that of uninoculated control plants in a soil-based system. The same P. fluorescens isolate was found to reduce plant growth in a hydroponic growth system, with plants showing the symptoms of a microbe-associated molecular pattern (MAMP) response to the bacteria...
November 23, 2018: Microbes and Environments
Arisa Nishihara, Katsumi Matsuura, Marcus Tank, Shawn E McGlynn, Vera Thiel, Shin Haruta
The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae...
November 23, 2018: Microbes and Environments
Fumiaki Mori, Yu Umezawa, Ryuji Kondo, Minoru Wada
We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0-5 mm) and subsurface (5-10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers...
November 17, 2018: Microbes and Environments
Emma J Gagen, Alan Levett, Jeremiah Shuster, Danielle Fortin, Paulo M Vasconcelos, Gordon Southam
The surface crust that caps highly weathered banded iron formations (BIFs) supports a unique ecosystem that is a post-mining restoration priority in iron ore areas. Geochemical evidence indicates that biological processes drive the dissolution of iron oxide minerals and contribute to the ongoing evolution of this duricrust. However, limited information is available on present-day biogeochemical processes in these systems, particularly those that contribute to the precipitation of iron oxides and, thus, the cementation and stabilization of duricrusts...
November 16, 2018: Microbes and Environments
Yasuhiro Tanaka, Hideyuki Tamaki, Kazuya Tanaka, Erina Tozawa, Hiroaki Matsuzawa, Tadashi Toyama, Yoichi Kamagata, Kazuhiro Mori
We herein described a new microbial isolation method using the interaction between the floating aquatic plant, duckweed, and microbes. We harvested microbial cells from Japanese loosestrife roots and co-cultivated these cells with aseptic duckweed using artificial inorganic medium for the plant for four weeks. During the co-cultivation, some duckweeds were collected every week, and the roots were used for microbial isolation using a low-nutrient plate medium. As a result, diverse microbial isolates, the compositions of which differed from those of the original source (Japanese loosestrife root), were obtained when the roots of duckweed were collected after 2 weeks of cultivation...
November 7, 2018: Microbes and Environments
Mariana Grillo-Puertas, Paola Delaporte-Quintana, Raúl Osvaldo Pedraza, Viviana Andrea Rapisarda
Gluconacetobacter diazotrophicus is a plant growth-promoting bacterium that is used as a bioinoculant. Phosphate (Pi) modulates intracellular polyphosphate (polyP) levels in Escherichia coli, affecting cellular fitness and biofilm formation capacity. It currently remains unclear whether environmental Pi modulates polyP levels in G. diazotrophicus to enhance fitness in view of its technological applications. In high Pi media, cells accumulated polyP and degraded it, thereby improving survival, tolerance to environmental stressors, biofilm formation capacity on abiotic and biotic surfaces, and competence as a growth promoter of strawberry plants...
November 7, 2018: Microbes and Environments
Arisa Nishihara, Vera Thiel, Katsumi Matsuura, Shawn E McGlynn, Shin Haruta
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70-86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae...
November 7, 2018: Microbes and Environments
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