Microbes and Environments最新文献

We herein exami-ned the inoculation effects of indigenous Bradyrhizobium diazoefficiens isolates on the growth and yield of adzuki beans and their competition with other bradyrhizobia using pot and field experiments. In the pot experiment, shoot nitrogen content was significantly higher following inoculations with AMP1 and Bd (a mixture of AN9 and AN20) than with the control. Furthermore, a correlation was observed between shoot nitrogen content and shoot dry weight. In the field experiment, the inoculating isolates did not significantly affect growth or yield. However, an interaction effect was observed in pod numbers and yield, suggesting that the effects of inoculation varied depending on the cultivar and inoculating isolate. In the correlation ana-lysis, pod number correlated with node number and nodule number. Similarly, yield correlated with shoot length, node number, nodule number, and pod number. Regarding competition between inoculated isolates and other strains, B. elkanii was dominant in pot and field experiments. To enhance the yield of adzuki bean through inoculations, it is necessary to overcome competition from indigenous B. elkanii and increase the occupancy rate of B. diazoefficiens isolates.

We recently proposed a novel microbial isolation technique, the "duckweed-microbe co-cultivation method", for isolating a wide variety of microbes, including rarely cultivated microbes. This method involves the inoculation of aseptic duckweed with environmental microbes followed by co-cultivation for a set period. Plants and their surrounding medium are then used as microbial sources for isolation in the conventional agar plate method. In the present study, we improved the method by using microfilter membranes (pore sizes of 0.8-1.2‍ ‍μm) to pretreat microbial inocula, which increased the isolation efficiency of rarely cultivated microbes representing the phylum Verrucomicrobiota.

Since nitrogenase is intrinsically sensitive to oxygen (O₂), diverse aerobic diazotrophs need strategies to cope with nitrogenase damage by O₂. In the present study, we investigated the mechanisms by which aerobic methane-oxidizing bacteria (methanotrophs) enable the concurrent activities of methane monooxygenase, which uses O₂, and nitrogenase in the cytoplasm of the same cell. By using ¹⁵N labeling, we confirmed the capacity of alphaproteobacterial methanotroph Methylosinus sp. 3S-1 for nitrogen fixation and diazotrophic growth across a wide range of O₂ concentrations <20%. When the initial O₂ concentration was increased from 2 to 20% in a diazotrophic culture, similar decreases were observed in fixed nitrogen and NifH protein levels. In contrast, the mRNA levels of nitrogen fixation genes (nif genes) markedly increased and remained elevated for the duration of slow growth at high O₂ concentrations. This pattern of nif expression in response to O₂ may be attributed to the properties of the nif-specific transcriptional regulator NifA. The present results suggest that the increase in nif transcription is one of the strategies by which this methanotroph maintains nitrogen fixation on the background of aerobic methane oxidation.

Agricultural soils are an important source of nitrous oxide (N₂O), which has greenhouse and ozone-depleting effects. Bradyrhizobium ottawaense SG09 is a nitrogen-fixing rhizobium with high N₂O-reducing activity. Rhizobia form symbiotic nodules in leguminous plants. The initial physical attachment of bacteria to plant roots is a critical step in the establishment of symbiotic interactions. In the present study, we performed a microscopic anal-ysis using DsRed-expressing B. ottawaense SG09. We revealed that B. ottawaense SG09 attached to both the root surface and root hairs via single cellular poles. This polar attachment was observed not only to the symbiotic host soybean, but also to non-leguminous plants, such as Arabidopsis, rice, corn, and wheat. We identified and analyzed the unipolar polysaccharide (upp) gene cluster, which is proposed to be involved in the polar attachment of rhizobia, in the genome of B. ottawaense SG09. We established an Arabidopsis-based interaction assay and demonstrated that uppC and uppE play a critical role in attachment to both the root surface and root hairs.

Cooling towers are a major source of Legionella, which causes Legionnaires' disease. These bacteria grow in predatory organisms; however, the impact of non-predatory organisms in cooling towers on Legionella survival and growth remains unclear. Therefore, we investigated the effects of photosynthetic algae, the primary component of biofilms in open cooling water systems, on Legionella. We cultivated Legionella with algae collected from the towers or with pure algal strain under alkaline conditions and revealed that the Legionella 16S rRNA copy number was higher than that of Legionella alone. We also exami-ned Legionella using an in situ hybridization chain reaction and found that some were elongated and exhibited a filamentous morphology on algal cells. Furthermore, Legionella was more active when co-cultured with pure algal strain plus Serratia spp. than when co-cultured with pure alga alone. 18S rRNA gene sequencing revealed that the algae collected had not previously been reported to coexist with Legionella. This result suggests that diverse algae in the environment support the growth of Legionella. This is the first study to experimentally demonstrate that algae promote Legionella elongation, and also that the coexistence of bacteria furthers this phenomenon. These results provide a new perspective on the ecology of Legionella and the role of non-predatory organisms.

The present study aimed to isolate and characterize a marine bacterium capable of passing through a 0.1-μm pore-sized filter (0.1-μm filter). Sediment suspension samples were filtered through 0.1-μm filters, inoculated into sterile media, and incubated. Isolated SspURN76 belonged to Saccharospirillum, according to 16S rRNA gene sequencing, and showed a very slender shape. The minimum cell size of SspURN76 was 0.09×3.2‍ ‍μm. These morphological features of SspURN76 were likely responsible for its passage through 0.1-μm filters. Based on the results obtained herein, marine bacteria may be present in 0.1-μm filtered fractions.

Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using ¹⁴C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L^-1 of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.

Chironomids (Diptera; Chironomidae), non-biting midges, are a highly diverse family of holometabolous insects, many of which are known for their tolerance to extreme environmental conditions, such as desiccation, pollution, and high acidity. The contribution of microbial symbionts to these adaptations was recently suggested. Therefore, we herein exami-ned the microbiome associated with the larvae of the undescribed acid-tolerant chironomid species, Polypedilum sp., which inhabits the Yukawa River (Gunma, Japan), an environment that is characterized by an extremely low pH (≤2) and high concentrations of heavy metal ions (including arsenic). Amplicon sequencing of the 16S rRNA gene revealed a distinct larval microbiome with a lower alpha diversity value and more enriched and specific bacterial taxa than the surrounding river water and detritus. Full-length 16S rRNA gene sequencing using nanopore long-read technology identified several previously undescribed operational taxonomic units (OTUs), among which OTU_Bacillaceae_Yukawa was consistently present in larvae reared in the laboratory for more than 4 months, suggesting persistent, possibly vertically transmitted, symbiosis. An inferred pathway ana-lysis suggested the contribution of the larval microbiome to host nutritional physiology. The possibly acid-sensitive OTU_Bacillaceae_Yukawa localized to midgut segments, indicating internal pH-buffered niches for microbial survival. These results provide novel insights into the ecology of acid-tolerant chironomids and lay the groundwork for further examinations of holobiont-based stress tolerance.

In traditional indigo dyeing, water-insoluble indigo is anaerobically converted into soluble leuco-indigo via microbial reduction in alkaline dye suspensions, allowing its use as a fabric dye. Although various indigo-reducing bacteria have been isolated to date, culture-independent microbial community ana-lyses have suggested that bacteria belonging to uncultured clades also contribute to indigo reduction. Therefore, we aimed to isolate previously overlooked indigo-reducing bacteria using an unconventional culture method. We conducted enrichment cultures and single-colony isolation using a medium supplemented with sukumo, an indigo dye source derived from the composted leaves of indigo-containing plants, as the sole energy, carbon, and nitrogen sources. We isolated a previously uncultured bacterium belonging to the family Tissierellaceae, which had been predicted as a major indigo reducer in various indigo dyeing processes solely based on microbial community ana-lyses. The insoluble indigo-reducing activity of the Tissierellaceae isolate, strain TU-1 was significantly higher than that of known indigo-reducing bacteria. The addition of the culture supernatant of strain TU-1 enhanced the reduction of indigo powder by other indigo-reducing bacteria, with similar stimulatory effects to those of the insoluble electron mediator, anthraquinone. These results indicate that strain TU-1 possesses a high capacity for secreting electron mediators, conferring a significant reduction capacity for insoluble indigo. Further investigations, including the discovery of additional unknown indigo-reducing bacteria and the identification of the mediators they produce, will provide a more detailed understanding of the mechanisms underlying indigo reduction in practical dyeing processes.

Sweet potato foot rot disease caused by Diaporthe destruens (formerly Plenodomus destruens) severely affects the yield and quality of sweet potatoes. To gain basic knowledge on regulating the pathogen using indigenous soil bacteria, the following organic materials were applied to potted soils collected from a sweet potato field contaminated with D. destruens: Kuroihitomi (compost made from shochu waste and chicken manure), Soil-fine (material made by adsorbing shochu waste on rice bran), and rice bran. Soil samples were periodically collected during an incubation for bacterial colony counts and a community ana-lysis using a meta 16S amplicon ana-lysis. The number of bacterial colonies was significantly higher with the Soil-fine and rice bran treatments and slightly higher with the Kuroihitomi treatment than with a chemical fertilizer as the control, and then gradually decreased over time. An amplicon ana-lysis showed that the Soil-fine and rice bran treatments increased the relative abundance of Streptomycetaceae and Micrococcaceae belonging to Actinobacteria and Burkholderiaceae belonging to Beta-proteobacteria. The Kuroihitomi treatment also increased the relative abundance of Streptomycetaceae. The dominant amplicon sequencing variant (ASV) sequences among these families were affiliated with the genera Kitasatospora, Arthrobacter, and Paraburkholderia. Bacteria with sequences identical to these ASVs were isolated from the incubated soils using selective media for dual culture assays. Bacterial isolates in a cluster of Kitasatospora exhibited antagonistic activity against D. destruens. The present results suggest that combining organic materials with antagonistic bacteria may be an effective approach to regulating the growth of D. destruens.