Microbes and Environments最新文献

A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3^rd transferred cultures and stable states from the 5^th to 10^th transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.

The Loess Plateau is one of the key areas for soil and water erosion control in China. Planting vegetation, such as Robinia pseudoacacia, is one of the mainstream methods to prevent soil and water erosion. However, the combination of abundant calcium ions and phosphate in the soil of the Loess Plateau limits the phosphorus nutrition of plants. In the present study, soil samples were collected under the R. pseudoacacia forest, from which two PSB strains with efficient phosphate solubilization capacities, named PSB2 and PSB7, were isolated and screened. The dissolved phosphate concentrations of their culture media were 9.68-fold and 11.61-fold higher, respectively, than that of the control group. After identification, PSB2 was classified as Pseudomonas and PSB7 as Inquilinus. This is the first time that Inquilinus has been isolated as a PSB from calcareous soil in the Loess Plateau. We then investigated the effects of different growth conditions on their phosphate solubilization capacities. Both strains effectively utilized glucose and ammonium nitrogen while maintaining high phosphate solubilization efficiency. In addition, PSB2 preferred to survive under neutral conditions and PSB7 under acidic conditions. Pot experiments indicated that the inoculation with PSB7 significantly increased the phosphorus content in the roots of R. pseudoacacia. These results imply the potential of this PSB as a phosphorus biofertilizer for R. pseudoacacia, which may be beneficial for soil and water management on the Loess Plateau.

Nitrite-oxidizing bacteria (NOB), which perform the second step of aerobic nitrification, play an important role in soil. In the present study, we report a novel isolate from agricultural soil affiliated with the genus Nitrobacter and its physiological characteristics. We sampled the surface soil of a vegetable field and obtained mixed culture A31 using the most probable number (MPN) method with inorganic medium containing 0.75‍ ‍mM urea (pH 5.5). The dilution-extinction procedure on culture A31 led to the isolation of a strain that was designated as Nitrobacter sp. A67. The nxrB1 gene sequence of Nitrobacter sp. A67 (302 bp) was classified into Cluster 5, and the highest sequence identity was 96.10% with Nitrobacter sp. BS5/19. The NO₂^- oxidation activity of Nitrobacter sp. A67 was investigated at various pH. The optimum pH for NO₂^- oxidation was 5.8-6.4. This result indicates that Nitrobacter sp. A67 is a moderately acidophilic nitrite-oxidizing bacterium.

Microcystins (MCs) produced by Microcystis aeruginosa are harmful to animal and human health, and there is currently no effective method for their removal. Therefore, the development of biological approaches that inhibit cyanobacteria and remove MCs is needed. We identified strain MB1, confirmed as Morchella, using morphological and mole-cular evolution methods. To assess the impact of strain MB1 on M. aeruginosa, we conducted an experiment in which we inoculated M. aeruginosa with Morchella strain MB1. After their co-cultivation for 4‍ ‍d, the inoculation with 0.9696‍ ‍g MB1 completely inhibited and removed M. aeruginosa while concurrently removing up to 95% of the MC content. Moreover, within 3‍ ‍d of their co-cultivation, MB1 removed more than 50% of nitrogen and phosphorus from the M. aeruginosa solution. Therefore, the development of effective biological techniques for MC removal is paramount in safeguarding both the environment and human well-being. We herein successfully isolated MB1 from its natural habitat. This strain effectively inhibited and removed M. aeruginosa and also reduced the content of nitrogen and phosphorus in the M. aeruginosa solution. Most importantly, it exhibited a robust capability to eliminate MCs. The present results offer a new method and technical reference for mitigating harmful algal blooms.

Gut microbes have many beneficial functions for host animals, such as food digestion and development of the immune system. An increasing number of studies report that gut bacteria also affect host neural function and behavior. The sucrose responsiveness of the western honey bee Apis mellifera, which harbors a characteristic gut microbiota, was recently reported to be increased by the presence of gut microbes. However, this responsiveness may vary depending on the experimental design, as animal behavior may be modulated by physiological states and environmental conditions. To evaluate the robustness of the effects of the gut microbiota on host gustatory responsiveness, we herein examined the sucrose responsiveness of honey bees colonized with a defined bacterial community or a conventional gut microbiota extracted from a field-collected bee. Although colonization was experimentally verified, sucrose responsiveness did not significantly differ among treatments after the 2- or 5-h starvation period. We concluded that the sucrose responsiveness of A. mellifera is not always affected by its gut microbiota. Therefore, host physiological conditions and environmental factors need to be considered when evaluating the impact of the gut microbiota on host neural function and behavior.

Antibiotic resistance genes (ARGs) have been emerging as a concerning threat to both environment and public health. The continuous input of manure, irrigation water, and fertilizers increases the abundance of ARGs in agricultural environments. However, current risk assessments have focused on clinical settings, which are not applicable to environmental settings. Therefore, we herein aimed to identify and assess indicator genes to reduce the time and effort required for ARG surveillance. A nationwide ana-lysis of 322 ARGs and 58 mobile genetic elements (MGEs) was performed on 42 greenhouse and 19 control soil samples. The chemical properties and pH of soil were also investigated to characterize differences between greenhouse and control soil samples. The results obtained showed that the abundance of ARGS was significantly higher and ion concentrations were higher in greenhouse samples than in control samples. These results indicate that agricultural activities increased the abundance of ARGs. Furthermore, the abundance of core genes was significantly higher in greenhouse samples than in control samples, and the chemical characteristics of soil significantly differed between these samples. Among the discriminatory genes selected, tetM was identified as an ARG surveillance indicator gene based on its clinical relevance, prevalence in the soil resistome, and relationship with mobile genetic elements. The present results will contribute to the continuous and rapid surveillance of antibiotic resistance dissemination and proliferation in greenhouses in South Korea.

N₂O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N₂O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N₂O reducers in an anammox reactor. We hypothesized that N₂O is limiting for N₂O-reducing bacteria‍ ‍and an‍ ‍exogeneous N₂O supply enriches as-yet-uncultured N₂O-reducing bacteria. We conducted a 1200-day incubation of N₂O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N₂O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A ¹⁵N tracer test indicated that the supply of N₂O resulted in an enriched biomass with a higher N₂O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N₂O-reducing bacteria as protagonists of N₂O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N₂O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N₂O reducers. We identified Dehalococcoidia and Clostridia as predominant N₂O sinks in an anammox consortium fed exogenous N₂O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

The genomes of obligately host-restricted bacteria suffer from accumulating mildly deleterious mutations, resulting in marked size reductions. Psyllids (Hemiptera) are phloem sap-sucking insects with a specialized organ called the bacteriome, which typically harbors two vertically transmitted bacterial symbionts: the primary symbiont "Candidatus Carsonella ruddii" (Gammaproteobacteria) and a secondary symbiont that is phylogenetically diverse among psyllid lineages. The genomes of several Carsonella lineages were revealed to be markedly reduced (158-174‍ ‍kb), AT-rich (14.0-17.9% GC), and structurally conserved with similar gene inventories devoted to synthesizing essential amino acids that are scarce in the phloem sap. However, limited genomic information is currently available on secondary symbionts. Therefore, the present study investigated the genomes of the bacteriome-associated dual symbionts, Secondary_AM (Gammaproteobacteria) and Carsonella_AM, in the mulberry psyllid Anomoneura mori (Psyllidae). The results obtained revealed that the Secondary_AM genome is as small and AT-rich (229,822 bp, 17.3% GC) as those of Carsonella lineages, including Carsonella_AM (169,120 bp, 16.2% GC), implying that Secondary_AM is an evolutionarily ancient obligate mutualist, as is Carsonella. Phylogenomic ana-lyses showed that Secondary_AM is sister to "Candidatus Psyllophila symbiotica" of Cacopsylla spp. (Psyllidae), the genomes of which were recently reported (221-237‍ ‍kb, 17.3-18.6% GC). The Secondary_AM and Psyllophila genomes showed highly conserved synteny, sharing all genes for complementing the incomplete tryptophan biosynthetic pathway of Carsonella and those for synthesizing B vitamins. However, sulfur assimilation and carotenoid-synthesizing genes were only retained in Secondary_AM and Psyllophila, respectively, indicating ongoing gene silencing. Average nucleotide identity, gene ortholog similarity, genome-wide synteny, and substitution rates suggest that the Secondary_AM/Psyllophila genomes are more labile than Carsonella genomes.

To investigate mycobacterial cases of farmed yellowtail fish in coastal areas of western Japan (Kagoshima, Kyushu), where aquaculture fisheries are active, Mycobacterium pseudoshottsii, the causative agent, was isolated from six neighboring fishing ports in 2012 and 2013. A phylogenetic ana-lysis revealed that the strains isolated from one fishing port were closely related to those isolated from other regions of Japan, suggesting the nationwide spread of a single strain. However, strains from Japan were phylogenetically distinct from those from the Mediterranean and the United States; therefore, worldwide transmission was not observed based on the limited data obtained on the strains exami-ned in this study. The present results demonstrate that a bacterial genomic ana-lysis of infected cases, a mole-cular epidemiology strategy for public health, provides useful data for estimating the prevalence and transmission pathways of M. pseudoshottsii in farmed fish. A bacterial genome ana-lysis of strains, such as that performed herein, may play an important role in monitoring the prevalence of this pathogen in fish farms and possible epidemics in the future as a result of international traffic, logistics, and trade in fisheries.