Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome’s bidirectional relationship exhibits their capability to influence each other’s physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.

Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11^T and HCMS5-2 ^T, were isolated from soil in South Korea. The growth of strain SJ11^T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0–7.0) and with NaCl 0–1% (w/v) (optimum, 0%) and that of strain HCMS5-2 ^T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0–5% (w/v) (optimum, 0–1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11^T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3^T (98.5%) and strain HCMS5-2 ^T had the highest similarities with Pedobacter nototheniae 36B243^T (98.7%). The digital DNA-DNA hybridization value of strain SJ11^T with Pedobacter jejuensis THG-DR3^T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 ^T with Pedobacter nototheniae 36B243^T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11^T and HCMS5-2 ^T were iso-C_15:0, summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c) and iso-C_17:0 3-OH. The genome size of strain SJ11^T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 ^T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11^T and HCMS5-2 ^T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11^T and HCMS5-2 ^T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11^T (= KACC 22884 ^T = TBRC 16597 ^T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 ^T (= KACC 22863 ^T = TBRC 16598 ^T) were respectively proposed.

The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62^T (= DSM 115720 ^T = NBRC 115938 ^T), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146 ^T (95.6% identity) and J. formosa 12N15^T (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62^T clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62^T (= DSM 115720 ^T = NBRC 115938 ^T).

A novel bacterial symbiont, strain A19^T, was previously isolated from a root-nodule of Aeschynomene indica and assigned to a new lineage in the photosynthetic clade of the genus Bradyrhizobium. Here data are presented for the detailed genomic and taxonomic analyses of novel strain A19^T. Emphasis is placed on the analysis of genes of practical or ecological significance (photosynthesis, nitrous oxide reductase and nitrogen fixation genes). Phylogenomic analysis of whole genome sequences as well as 50 single-copy core gene sequences placed A19^T in a highly supported lineage distinct from described Bradyrhizobium species with B. oligotrophicum as the closest relative. The digital DNA-DNA hybridization and average nucleotide identity values for A19^T in pair-wise comparisons with close relatives were far lower than the respective threshold values of 70% and ~ 96% for definition of species boundaries. The complete genome of A19^T consists of a single 8.44 Mbp chromosome and contains a photosynthesis gene cluster, nitrogen-fixation genes and genes encoding a complete denitrifying enzyme system including nitrous oxide reductase implicated in the reduction of N₂O, a potent greenhouse gas, to inert dinitrogen. Nodulation and type III secretion system genes, needed for nodulation by most rhizobia, were not detected. Data for multiple phenotypic tests complemented the sequence-based analyses. Strain A19^T elicits nitrogen-fixing nodules on stems and roots of A. indica plants but not on soybeans or Macroptilium atropurpureum. Based on the data presented, a new species named Bradyrhizobium ontarionense sp. nov. is proposed with strain A19^T (= LMG 32638^T = HAMBI 3761^T) as the type strain.

In this research, two novel Fe(III)-reducing bacteria, SG10^T and SG198^T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10^T and SG198^T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10^T and SG198^T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189^T (99.0–99.5%) and Geothrix paludis SG195^T (99.0–99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10^T and SG198^T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1–94.3% and 30.7–59.5%, respectively. The major fatty acids were iso-C_15:0, anteiso-C_15:0, C_16:0 and iso-C_13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10^T (= GDMCC 1.3406 ^T = JCM 39331 ^T) and SG198^T (= GDMCC 62910 ^T = KCTC 25635 ^T), respectively.

The pink-colored and strictly aerobic bacterium strain, designated as TK19036^T, was isolated from mesopelagic layer of the Southwest Indian Ocean. This novel isolate can grow at 10–45 °C (optimum, 30 °C), pH 6.0–8.0 (optimum, pH 7.0), and 2–14% NaCl concentrations (w/v) (optimum, 6%). The predominant respiratory quinone was Menaquinone-7. Major polar lipid profiles contained two aminolipids, aminophospholipid, two glycolipids, phosphatidylethanolamine, and three unknown polar lipids. The preponderant cellular fatty acids were iso-C_15:0, C_16:1 ω5c and iso-C_17:0 3-OH. Phylogenetic analyses based on 16S rRNA gene sequence uncovered that the strain TK19036^T pertained to the family Catalinimonadaceae under phylum Bacteroidota, and formed a distinct lineage with the closed species Tunicatimonas pelagia NBRC 107804^T. The up-to-bacteria-core gene phylogenetic trees also demonstrated a deep and novel branch formed by the strain TK19036^T within the family Catalinimonadaceae. Based on chemotaxonomic, phylogenetic and genomic features presented above, strain TK19036^T represents a novel species from a novel genus of the family Catalinimonadaceae, for which the name Roseihalotalea indica gen. nov. sp. nov. is proposed. The type strain is TK19036^T (= CGMCC 1.18940^T = NBRC 116371^T).

A bacterial strain PJ23^T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4–29℃ (optimal at 24℃), pH 6.0–8.6 (optimal at 8.0) and in the presence of 0–5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23^T were Summed feature 8 (C_{18:1 ω6c} and/or C_{18:1 ω7c}) (39.42%) and C_16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6^T and Flaviflagellibacter deserti SYSU D60017^T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23^T and Terrihabitans soli IZ6^T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23^T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23^T (= KCTC 92977 ^T = CGMCC 1.61577 ^T).

Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.