Microbes and Environments最新文献

The nitrite oxidizing bacterial genus Ca. Nitrotoga was only recently discovered to be widespread in freshwater systems; however, limited information is currently available on the environmental factors and seasonal effects that influence its distribution in lakes. In a one-year study in a dimictic lake, based on monthly sampling along a vertical profile, the droplet digital PCR quantification of Ca. Nitrotoga showed a strong spatio-temporal patchiness. A correlation ana-lysis with environmental parameters revealed that the abundance of Ca. Nitrotoga correlated with dissolved oxygen and ammonium, suggesting that the upper hypolimnion of the lake is the preferred habitat.

We herein investigated the effects of salt (NaCl) stress on soybean nodulation by rhizobial strains. We specifically exami-ned: (1) the effects of NaCl on nodule maturity and positioning by inoculating three rhizobial strains (Bradyrhizobium diazoefficiens USDA110^T, Bradyrhizobium elkanii USDA31, and Sinorhizobium fredii USDA191) onto soybean variety CNS, (2) the effects of the NaCl treatment on isoflavones (daidzein and genistein) secretion by CNS, (3) the effects of the NaCl treatment on gene expression induced by daidzein and genistein in rhizobia, and (4) the effects of the NaCl treatment on rhizobial growth. The results obtained were as follows: (1) the NaCl treatment delayed nodule development and reduced nodulation on the primary root following the USDA110^T inoculation, minimal sensitivity regarding nodule formation in the USDA 31 inoculation, and significantly increased the mature nodule number and nodules on the primary root following the USDA 191 inoculation. (2) The NaCl treatment significantly reduced the secretion of daidzein from soybean roots, but did not significantly affect that of genistein. (3) NaCl treatment induced a significant decrease in genistein-induced nodC expression in USDA110^T, but not in USDA31, and also caused a significant reduction in daidzein-induced nodC expression, but not genistein-induced expression, in USDA191. (4) NaCl treatment reduced survivability under acidic conditions, but increased survivability under saline-alkaline conditions for USDA191 than bradyrhizobia. These results indicate that saline conditions give S. fredii a competitive advantage over Bradyrhizobium during soybean infection.

Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. A recent metagenomic sequencing ana-lysis showed that Myxococcota are predominant in activated sludge systems; however, their metabolic traits remain unclear. In the present study, we exami-ned the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results obtained showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. The Palsa-1104 and Polyangiales bins contained the glycoside hydrolase GH5 and peptidase M23, which are presumably involved in lysis of the cell wall and cellular cytoplasm, suggesting that some Myxococcota from activated sludge prey on other microorganisms. The cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, but not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, indicating the potential for heterotrophic and autotrophic metabolism by these microbes. In assessments of the social behavior of Myxococcota in activated sludge, the FruA gene and C-signal gene, which are involved in the regulation of fruiting body formation, were lacking in Myxococcota bins, suggesting their inability to form fruiting bodies. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in activated sludge. Our metagenome-based ana-lyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.

The extremely halophilic archaeon Haloarcula japonica accumulates the C₅₀ carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene desaturase candidates were functionally characterized in the present study. Two genes encoding the potential phytoene desaturases, c0507 and d1086, were found from the Ha. japonica genome sequence by a homology search using the Basic Local Align Search Tool. Disruption mutants of c0507 and d1086 and their complemented strains transformed with expression plasmids for c0507 and d1086 were subsequently constructed. High-performance liquid chromatography (HPLC) ana-lyses of carotenoids produced by these strains revealed that C0507 and D1086 were both bifunctional enzymes with the same activities as both phytoene desaturase (CrtI) and 3,4-desaturase (CrtD). C0507 and D1086 complemented each other during BR biosynthesis in Ha. japonica. This is the first study to identify two distinct enzymes with both CrtI and CrtD activities in an extremely halophilic archaeon.

Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.

Extracellular membrane vesicles (MVs) caused by the artificial production of polyhydroxybutyrate (PHB) were previously detected in Escherichia coli. We herein observed MV biogenesis in the mutant strain (-PHB) of the natural PHB producer, Cupriavidus necator H16. This inverse relationship was revealed through comparative electron microscopic ana-lyses of wild-type and mutant strains. Based on these results, we speculate that a physiological relationship exists between MV biogenesis and PHB biosynthesis. Therefore, we propose the potential of MV biogenesis as a fermentative "stress marker" for monitoring the performance of target polymer-producing microbial platforms.

Polyethylene (PE), a widely used recalcitrant synthetic polymer, is a major global pollutant. PE has very low biodegradability due to its rigid C-C backbone and high hydrophobicity. Although microorganisms have been suggested to possess PE-degrading enzymes, our understanding of the PE biodegradation process and its overall applicability is still lacking. In the present study, we used an artificial bacterial consortium for PE biodegradation to compensate for the enzyme availability and metabolic capabilities of individual bacterial strains. Consortium members were selected based on available literature and preliminary screening for PE-degrading enzymes, including laccases, lipases, esterases, and alkane hydroxylases. PE pellets were incubated with the consortium for 200 days. A next-generation sequencing ana-lysis of the consortium community of the culture broth and on the PE pellet identified Rhodococcus as the dominant bacteria. Among the Rhodococcus strains in the consortium, Rhodococcus erythropolis was predominant. Scanning electron microscopy (SEM) revealed multilayered biofilms with bacteria embedded on the PE surface. SEM micrographs of PE pellets after biofilm removal showed bacterial pitting and surface deterioration. Multicellular biofilm structures and surface biodeterioration were observed in an incubation of PE pellets with R. erythropolis alone. The present study demonstrated that PE may be biodegraded by an artificially constructed bacterial consortium, in which R. erythropolis has emerged as an important player. The results showing the robust colonization of hydrophobic PE by R. erythropolis and that it naturally possesses and extracellularly expresses several target enzymes suggest its potential as a host for further improved PE biodeterioration by genetic engineering technology using a well-studied host-vector system.

Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.

Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, which exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies on Parmales have been performed; however, their global distribution has not yet been examined in detail. We herein compiled more than 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the samples analyzed. However, the relative abundance of parmaleans in the eukaryotic community was less than 0.2% on average, and the estimated true richness of parmalean ASVs was approximately 316 ASVs, confirming their low abundance and diversity. A phylogenetic ana-lysis divided these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the poles and decreases towards the tropics, and individual clades/subclades show further distinctions in their distribution. Collectively, the present results suggest clade/subclade-specific adaptation to different ecological niches.