Microbes and Environments最新文献

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.

Nitrogen-fixing sulfate-reducing bacteria have not yet been exami-ned in thermal environments. In this study, strain TK110, belonging to the genus Thermodesulfovibrio, was successfully isolated from a geothermal spring using an NH₃-free inorganic medium. Strain TK110 harbored genes associated with the Calvin-Benson-Bassham cycle and nitrogen fixation-related genes, nifHDKENXIIB. Nitrogenase activity was assessed using an acetylene reduction assay and detected in strain TK110 under autotrophic conditions, as well as in Thermodesulfovibrio yellowstonii DSM 11347^T under heterotrophic conditions at 65°C. To the best of our knowledge, this is the first study to demonstrate nitrogen fixation by thermophilic sulfate-reducing bacteria.

Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.

There is a growing demand for the reuse of sediment basin soil in cabbage fields; however, reusing soil poses a potential challenge of spreading Verticillium wilt to the fields via pathogen-infested sediments. We evaluated the density of the Verticillium wilt pathogen in sediment basin soil using a quantitative nested real-time polymerase chain reaction assay and its incidence using pot cultivation tests. We detected low pathogenic DNA levels in the sediment, coupled with a low Verticillium wilt incidence and severity in the pot experiment, indicating a low risk of spreading Verticillium wilt with the reuse of sediment basin soil.

Azorhizobium caulinodans is a nitrogen-fixing bacterium that forms stem and root nodules on Sesbania rostrata. All tested A. caulinodans strains exhibited degradation activity against the quorum-sensing signaling compounds, N-acyl-l-homoserine lactones (AHL). The AHL-degrading gene homolog, attM, was identified in the genome sequences of A. caulinodans MAFF 210031^T and other A. caulinodans strains. Recombinant AttM functions as an AHL lactonase that hydrolyzes the lactone bond of AHL and retains its stable activity at environmental temperatures. The AHL-degrading activity of the attM-deletion mutant was completely diminished, which revealed that AHL degradation by MAFF 210031 was dependent on attM.

Digital PCR is a technique that quantifies target genes based on the absence or presence of the targets in PCR amplicons. The present study exami-ned group-specific probes for the quantification of mcrA genes in six methanogenic archaeal groups and "Candidatus Methanoperedens" by digital PCR with the universal primers ML-f and ML-r. A digital PCR ana-lysis of paddy field soil detected all the targets, with the dominant and minor groups being Methanomicrobiales and Methanobrevibacter spp., respectively (10⁷ and 10⁴ copies [g dry soil]^-1). This method has the potential to reveal the dynamics of specific methanogenic archaeal groups in the environment.

Chemotaxis is essential for infection by plant pathogenic bacteria. The causal agent of tobacco wildfire disease, Pseudomonas syringae pv. tabaci 6605 (Pta6605), is known to cause severe leaf disease and is highly motile. The requirement of chemotaxis for infection has been demonstrated through the inoculation of mutant strains lacking chemotaxis sensory component proteins. Pta6605 possesses 54 genes that encode chemoreceptors (known as methyl-accepting chemotaxis proteins, MCPs). Chemoreceptors are classified into several groups based on the type and localization of ligand-binding domains (LBD). Cache LBD-type chemoreceptors have been reported to recognize formate in several bacterial species. In the present study, we identified Cache_3 Cache_2 LBD-type Mcp26 encoded by Pta6605_RS00335 as a chemoreceptor for formate using a quantitative capillary assay, and named it McpF. Although the deletion mutant of mcpF (ΔmcpF) retained attraction to 1% yeast extract, its chemotactic response to formate was markedly reduced. Swimming and swarming motilities were also impaired in the mutant. To investigate the effects of McpF on bacterial virulence, we conducted inoculations on tobacco plants using several methods. The ΔmcpF mutant exhibited weaker virulence in flood and spray assays than wild-type and complemented strains, highlighting not only the involvement of McpF in formate recognition, but also its critical role in leaf entry during the early stages of infection.

Soil nutrient loss from intensive farming is a critical issue in sub-Saharan Africa that affects food security. While soil microbial nitrification supplies available nitrogen, excessive nitrification leads to nitrogen loss. However, the species driving nitrification and their functions in this region remain largely unknown. Therefore, we investigated the responses of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to land-use changes in Zambia and their relationship with nitrification potential. Soil samples were collected from three sites in Zambia that all had neighboring natural and farmed (maize) lands. We measured nitrification potential, quantified AOB and AOA, and analyzed these communities by targeting the ammonia monooxygenase subunit A (amoA) gene, which encodes a key enzyme in nitrification. Nitrification potential was 1.51-fold higher in farmlands than in natural lands. AOB abundance tended to be greater in farmlands, whereas AOA abundance was smaller. Farming changed the AOB community structure, increasing Nitrosospira cluster 3a.2 at the three sites, while minor site-specific responses were also observed. In contrast, the AOA community structure was not significantly different between land uses, but varied among sites, with cluster NS-ζ being more prominent in one site with neutral soil (pH 7.64) than in the other sites (pH 5.70 and 5.71). These results suggest that AOA species were generally vulnerable to farming, decreasing in abundance without structural changes, while some AOB species increased, driving changes in their community structure. These insights are fundamental for understanding soil nitrogen depletion due to microbial changes under farming and are crucial for developing sustainable land-use practices in sub-Saharan Africa.

A sulfate-reducing bacterium was isolated from the anode surface of a microbial fuel cell (MFC) producing a high current density. 16S rRNA gene ana-lyses showed that the isolate was affiliated with the genus Nitratidesulfovibrio, and the strain was named HK-II. When Nitratidesulfovibrio sp. strain HK-II was incubated anaerobically under sulfate-reducing conditions with Fe(III) citrate, a black precipitate formed. The resulting black precipitate was investigated using multidisciplinary methods. An X-ray diffraction (XRD) ana-lysis revealed that the black precipitate was mainly composed of mackinawite. A cyclic voltammetry ana-lysis showed clear redox peaks, and biogenic mackinawite possessed rechargeable properties. The XRD ana-lysis also showed that the form of the rechargeable biogenic mineral induced by strain HK-II (RBM-II) was changed by discharge and recharge treatments. Field-emission transmission electron microscopy revealed that lepidocrocite and amorphous iron oxide formed from mackinawite under discharged conditions, and the three mineral types were intermingled via charge and discharge cycles. Physicochemical parameters regularly changed under the treatments, suggesting that discharge occurred via iron oxidation followed by sulfur reduction and vice versa. These results indicate that sulfur dynamics are important key processes in charge and discharge mechanisms. MFCs equipped with lactate, strain HK-II, and an anode containing RBM-II consumed lactate under open-circuit conditions, after which MFCs generated a higher current density under reclosed-circuit conditions. These results demonstrate that RBM-II is a rechargeable material that enables the capture of electrons produced by bacterial cells and is useful for enhancing the performance of MFCs.

The standardization of strain identification methods is essential for effectively managing the genetic resources of arbuscular mycorrhizal (AM) fungi. Due to their highly polymorphic rRNA sequence and multinucleate nature, conventional strain identification using a single sequence of the rRNA region is often inadequate for these fungi. Therefore, the present study exami-ned the use of genetic diversity information obtained through high-throughput sequencing to improve the strain identification of AM fungal isolates. Five previously reported primer pairs were used to amplify a portion of the rRNA region from DNA extracted from AM fungal spores, which was then sequenced using the Illumina MiSeq platform. The majority of amplicon sequence variants (ASVs) matched the same strain as the source isolate. A cluster anal-ysis indicated that strains of the same species generally grouped together, demonstrating the method's effectiveness for species-level identification. Furthermore, a phylogenetic anal-ysis revealed some strain-specific ASVs that may be valuable for differentiating between different strains within the same species. Based on these results, it is feasible to develop a reliable identification protocol for AM fungal isolates using MiSeq sequencing.