Microbes and Environments最新文献

The anammox process using marine anammox bacteria is a promising nitrogen removal process for recirculating aquaculture system wastewater. Marine anammox bacteria are typically found in oxygen-deficient zones and coastal areas under low phosphate concentrations. The optimal phosphate concentration for marine anammox bacteria remains unknown because most laboratory studies on these bacteria have been conducted under high phosphate concentrations. Therefore, the present study investigated the long-term effects of varying phosphate concentrations on the marine anammox bacteria, Candidatus Scalindua sp., to identify the optimal range of phosphate. Anammox activity and average growth rates were evaluated under seven phosphate concentrations (0, 0.23, 0.46, 0.68, 1.14, 6.15 [control], and 15.48‍ ‍mg P L^-1) over a period of 70 days. After 50 days of reactor operation, reactor performance under phosphate concentrations ranging from 0.23 to 6.15‍ ‍mg P L^-1 stabilized at 70% of total nitrogen removal efficiency, indicating the successful establishment of the anammox process. Conversely, anammox reactor performance under conditions without phosphate addition (0‍ ‍mg P L^-1) and the highest phosphate concentration (15.48‍ ‍mg P L^-1) did not reach 70% of total nitrogen removal efficiency, indicating a suboptimal phosphate concentration for normal anammox activity. Average growth rates calculated from total biomass samples varied from 0.0006 to 0.0012 h^-1. These results indicate that Ca. Scalindua need to be kept at phosphate concentrations between 0.23 and 6.15‍ ‍mg P L^-1 for optimal functioning in wastewater treatment ecosystems.

Recent warming and glacier retreat in the Svalbard Archipelago, part of the Arctic cryosphere, have become increasingly evident. The present study investigated the foreland of Austre Brøggerbreen near Ny-Ålesund to clarify how soil nitrification responds to changing conditions. Two sites, exposed for different periods following glacier retreat, were compared. A manipulation experiment using open-top chambers (OTCs) and homogenized initial soil conditions was conducted to assess the effects of site differences, the OTC treatment, soil depth, and interannual variations on soil and nitrification properties. Although the OTC treatment slightly increased soil temperature and moisture, its overall effect on soil properties, ammonia oxidation potential (AOP), and microbial properties was negligible. In contrast, homogenization markedly increased total nitrogen at both sites and temporarily boosted AOPs for two years before levels returned to baseline. Site 2, exposed for longer, contained more soil nitrogen and showed higher AOP than Site 1. For example, in 2015, AOPs at 10°C were 3.5 and 2.4‍ ‍ng N g^-1 dry soil h^-1 at Sites 2 and 1, respectively. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were both more abundant at Site 2, although AOB clearly dominated at both sites. While AOB-amoA operational taxonomic units (OTUs) were mostly shared between sites, community compositions differed: OTU2 was prevalent at Site 1, but minor at Site 2. OTU2 may act as a pioneer taxon that declines in later stages, or its pattern may reflect site-specific soil conditions. A phylogenetic anal-ysis showed that OTU2 and OTU3 belonged to Cluster ME found near Mount Everest.

In Myanmar, the application of both nitrogen-based chemical fertilizers and biofertilizers is limited and this low input has caused poor agricultural yields. The present study aimed to isolate indigenous endospore-forming nitrogen-fixing bacteria (EFNFB) and examine their potential for co-inoculation with agricultural waste. A total of 387 isolates were obtained from 42 different soil samples in the central dry zone of Myanmar using nitrogen-free Rennie medium. Nitrogen-fixing activity (NFA) assessed with the acetylene reduction assay was positive in 102 isolates. A phylogenetic ana-lysis based on 16S rRNA sequences identified 25 different species, including the genera Paenibacillus, Priestia, Bacillus, Brevibacillus, Sporolactobacillus, Niallia, and Neobacillus. Among these genera, Paenibacillus spp. was the predominant genus, comprising 51 isolates (64%) across 16 different species (64%) that were prevalent in soils rotated with rice and pulses. Paenibacillus spp. showed different NFA levels in Rennie medium. Eleven species belonging to different genera had not been previously documented as nitrogen-fixing bacteria. NFA levels were evaluated in soil inoculated with EFNFB and rice straw or mung bean residue. The results obtained demonstrated that NFA levels were dependent on isolates and the type of agricultural waste. NFA in soil was significantly increased by inoculations with some isolates, suggesting their potential as biofertilizers. The inoculation of Priestia aryabhattai S10 with rice straw or mung bean resulted in significantly higher NFA levels in soil. These results indicate the potential of EFNFB as biofertilizer inoculants in Myanmar.

This study investigated the effects of elevated hydrostatic pressure on methane production and gene expression in a hydrogenotrophic methanogen isolated from subseafloor sediments at biogenic gas hydrate sites, with a focus on the implications of CO₂ availability. Using high-pressure cultivation, the methane production rate decreased by 15% at 25 MPa, while a transcriptomic anal-ysis revealed the marked up-regulation of methyl-coenzyme M reductase and ATP synthase. These results suggest that methanogens compensate for pressure-driven constraints on CO₂ utilization by increasing the expression of key methanogenic enzymes, underscoring the overlooked role of CO₂ in deep biosphere microbial processes.

Nitrite is a key intermediate in global nitrogen cycles. It has been widely recognized that the accumulation of nitrite is often not appreciable in environments, and nitrite concentrations in canonical media for the cultivation of nitrite-oxidizing bacteria (NOB) in laboratories may not be low enough to recover oligotrophic NOB. We herein report the isolation, physiology, and genomics of oligotrophic NOB from a Japanese forest soil. NOB in soil samples were enumerated using the most probable number method with a medium containing urea for enriching oligotrophic NOB. Urea was completely converted into nitrate, and nitrite was not detected in any nitrifier-positive tubes cultivated after 9‍ ‍weeks of incubation. After subculturing NOB several times in a medium supplemented with 1‍ ‍mM nitrite and performing the extinction-dilution procedure, a novel strain oxidizing nitrite to nitrate was obtained and designated as strain CN101, which was affiliated with the genus Nitrobacter at the 16S rRNA gene level. The half-saturation constant of strain CN101 was lower than other known Nitrobacter strains, suggesting that Nitrobacter strains do not always exhibit low affinity for nitrite. The complete genome of strain CN101 included a larger number of nitrite/nitrate transporters than other Nitrobacter strains, which may serve as tools for flexibly adapting to varying nitrite concentrations in soils. Therefore, the physiological and genomic characteristics of strain CN101 will expand knowledge of the ecologically important but understudied genus Nitrobacter.

Legionella survive in the natural environment by remaining within protist host cells. Many protist species, including Paramecium spp., are potential hosts for Legionella. However, the factors and mechanisms involved in the establishment of this relationship are unknown. The advantages gained by Paramecium spp. when they maintain Legionella are also unclear, and the existence of these relationships has not been confirmed. In the present study, feeding with Legionella increased the number of Paramecium cells over time. However, the growth-promoting effect of Legionella was weaker than that of Klebsiella pneumoniae, which is considered the optimal bacterial feed for Paramecium. Phagocytosis was strongly inhibited in Paramecium cells fed Legionella, indicating that this relationship prevents the uptake of harmful organisms. The inhibition of phagocytosis was also observed when Paramecium cells were treated with the Legionella culture supernatant. Despite the inhibition of phagocytosis, the presence of live Legionella within host cells allowed Paramecium spp. to survive and even increase in number, as observed earlier. This result suggests that Legionella support the survival of Paramecium hosts from a nutritional aspect. Although it is difficult to definitively state whether the relationship between Legionella and Paramecium hosts is completely mutualistic, the present results provide one rationale for defining their relationship.

Leguminous plants establish root nodule symbiosis, which is initiated by the recognition of rhizobial nodulation factors by plant receptor kinases. However, other factors, such as Type III effector proteins, also affect host specificity. We herein investigated the role of nodulation outer protein M (NopM), a Type III effector of Bradyrhizobium elkanii USDA61, in symbiosis with Lotus japonicus MG-20 and Lotus burttii. NopM, annotated as an E3 ubiquitin ligase, triggers an early senescence-like response, inducing brown nodules that hinder effective symbiosis. NopM shares structural features with E3 ubiquitin ligases derived from both pathogenic and symbiotic bacteria, including a leucine-rich-repeat and E3 ubiquitin ligase domain. The deletion of these domains or substitution of the cysteine residue, predicted to be the active site of the ubiquitin ligase domain, suppressed the formation of brown nodules. These results suggest that NopM interacts with target proteins through its leucine-rich-repeat domain and mediates ubiquitination via its ligase domain, thereby contributing to the induction of brown nodules. A transcriptome ana-lysis further suggested that the early senescence-like response closely resembled the plant hypersensitive response, with the up-regulation of defense-related genes. Therefore, L. japonicus may recognize NopM in infected nodule cells, leading to an immune response that disrupts symbiosis. The present study provides insights into the mole-cular mechanisms by which rhizobial effectors modulate symbiotic interactions in infected nodule cells, highlighting the ability of L. japonicus to activate immune responses even in nodule cells where rhizobia have been accepted.

Several enzymes have subunits that require the addition of cofactors or maturation of the active center, which is facilitated by other genes. Information on these functionally-related genes not only aids in the functional anal-ysis of target genes, but is also useful for heterologous expression. In the present study, we analyzed the homologs of a target gene and their relationships with adjacent genes within the genome by constructing clusters of neighboring genes, quantifying the number of clustered genes, and examining their conservation in a taxonomic clade of target gene homologs. [NiFe]-hydrogenase was selected as the target because of the availability of a concrete database for subsequent evaluations in our anal-ysis. The present results indicate that genes associated with target gene function were conserved according to the molecular phylogeny of the target gene. We subsequently introduced automated clustering of the phylogenetic tree clade of clustered genes and applied this method to large datasets not yet analyzed and our previous data. The results obtained suggest that this approach provides insights into a comprehensive set of genes involved in cellular functions, particularly when the genes being analyzed are complex and require maturation. The procedure developed herein also provided similar and reproducible results on previously analyzed succinate dehydrogenase, which was not arbitrary.

Most phytophagous species of stinkbugs have mutualistic relationships with bacterial symbionts, which are often located within specialized midgut regions called M4. Heterogastridae, previously classified within the family Lygaeidae, are now classified as a family proper; however, the symbiotic organ's morphology and symbiont identity remain unclear. We herein investigated symbiotic systems from two heterogastrid species. The results obtained show that they possess two rows of midgut crypts akin to those of Coreoidea and consistently associate with Caballeronia symbionts of the SBE-α and Coreoidea clades. The present study clearly demonstrates that Caballeronia bacteria are symbionts of Heterogastridae and is the first to report a Coreoidea clade symbiont from the superfamily Lygaeoidea.

The whitefly, Bemisia tabaci, is a notorious insect pest that transmits plant pathogenic viruses to a wide range of economically important crops. An invasive genetic group of B. tabaci, Mediterranean Q2 (MED Q2), has recently spread to Europe, USA, and Asia. In the present study, we investigated the prevalence of MED Q2 in Japanese agricultural sites and found that its distribution has expanded since it was initially detected in 2013. A polymerase chain reaction ana-lysis revealed that all MED Q2 individuals were infected with Rickettsia. Rickettsia titers increased during nymphal development, presumably in response to the nutritional needs of the host. A fluorescence in situ hybridization ana-lysis revealed that Rickettsia was densely located near Portiera-containing bacteriocytes at all growth stages. Therefore, Rickettsia may play an important role, such as supplying nutrients to the host, in cooperation with Portiera. Transfer experiments indicated that MED Q2 was as effective a vector for Tomato yellow leaf curl virus as MED Q1 and, thus, is a high-risk agricultural pest. These results provide important insights into the biology and ecology of invasive MED Q2 to effectively control its spread and minimize its impact on crops.