Microbes and Environments最新文献

The present study proposes a categorization of bacteria that leak from activated sludge processes to secondary treated water (STW). Bacterial populations in primary treated water (PTW), activated sludge (AS), STW, and the 0.2‍ ‍μm-filtrate of STW (FSTW) in a full-scale wastewater treatment plant with two treatment trains were observed for a period of one year using a 16S rRNA ana-lysis approach. The taxonomic groups detected were categorized as different "leak types" based on the read occupancies in PTW, AS, STW, and FSTW, where a leak type indicates the likelihood of a taxonomic group to leak to STW. Five leak types were introduced: "LTE", "LTE-I", "LTEF", "LTF", and "NLT", with "LT" for leak type, "E" for high read occupancy in STW or the effluent of secondary settling tanks, "I" for high read occupancy in PTW or influent to the AS process, "F" for high read occupancy in FSTW, and "NLT" for a smaller likelihood to leak. Representative taxonomic groups for each leak type were Neisseria and ABY1 for "LTE" Parcubacteria for "LTEF", Campylobacterota for "LTE-I", and Saccharimonadia, Bdellovibrionota, and some lineages in Comamonadaceae for "LTF". Although some taxonomic groups, such as Comamonadaceae, included different leak types, the categorization assigned to each taxonomic group was mostly consistent between the two treatment trains. The categorization scheme proposed herein may become a useful key for understanding the characteristics of bacteria that appear in AS and STW.

Naturally occurring caves are sites of significant cultural value, while also displaying the unique biodiversity of associated microbiomes that may provide an untapped source of potentially beneficial organisms. However, the touristic exploitation of show caves may ultimately result in the biodeterioration of speleothems, primarily through the introduction and establishment of alien microbiota or the uncontrolled growth of indigenous species, exacerbated by the use of artificial lighting. These habitat characteristics are present in the Dictean cave, also known as "Diktaion Andron", a highly visited cave in eastern Crete, Greece, which was regarded in ancient Greek mythology as one of the putative sites of the birth of Zeus. Therefore, an efficient approach to controlling these ecological niches without irreversibly disturbing microbial diversity is needed, and essential oils are currently being investigated as a mild cleaning method. The present study exami-ned the microbial diversity of the Dictean cave using 16S and 18S rRNA gene amplicon sequencing and methods for quantitative metabolic activity estimations and also investigated the application of a formulation containing specific essential oils as a mild cleaning method. Amplicon sequencing ana-lyses revealed distinct profiles among the different sample sites, with species of the genera Pseudomonas, Sporosarcina, Butiauxella, Glutamicibacter, Paenibacillus, Mortierella, and Jenufa being the most abundant, while uncharacterized microorganisms were also detected. The single simultaneous application of a formulation of 0.2% (v/v) oregano and 0.4% (v/v) cinnamon essential oils was effective at significantly reducing microbial metabolic activity by up to 89.2% within 24 h, without adversely affecting the coloration of speleothems.

Despite its ecological importance, the gut microbiota of whale sharks (Rhincodon typus) remains poorly understood. Therefore, the present study exami-ned how environmental differences affect the fecal microbiota by comparing long-term captive and newly captured individuals. Fecal samples were collected over time from four long-term captive and two newly captured whale sharks, with seawater also being sampled from their respective tanks. Using 16S rRNA sequencing, 12,497 amplicon sequence variants (ASVs) were identified, including 6,976 classified as major ASVs. There were no significant differences in alpha diversity indexes between long-term captive and newly captured sharks; however, the latter showed slightly larger variance in four indexes. The ASV count per individual was slightly lower in long-term captive sharks than in their newly captured counterparts. In long-term captive individuals, Photobacterium was highly abundant. Conversely, Ureaplasma was dominant in newly captured individuals, but was barely detected in long-term captive sharks. Although alpha diversity did not differ significantly between the groups, a beta diversity ana-lysis showed clear distinctions. The high abundance of Ureaplasma in newly captured sharks suggests its involvement in nitrogen metabolism, possibly through urea recycling. Although further research is needed to clarify the taxonomic position and ecological functions of these Ureaplasma populations, the present study provides key insights for the conservation of wild whale sharks and improving health management for captive individuals.

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.

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.

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.

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.