Publications

4359

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

An anaerobic isolate, designated me31T, was isolated from pit mud in Yibin, Sichuan Province, PR China. Phylogenetic results based on 16S rRNA gene sequence showed that strain me31T belongs to the family Dysgonomonadaceae, and the most closely related isolated relatives were Seramator thermalis SYSU GA16112T (93.65%) and Proteiniphilum propionicum JNU-WLY501T (93.22%). The DNA G+C content was 44.26 mol%. The ANI and AAI values between strain me31T and the closely related strains were 69.25–71.18% and 69.59–71.15%, respectively. Cells of strain me31T were Gram-stain-negative, rod-shaped and non-motile. Growth of strain me31T was observed at 25–37 °C, pH 6.0–8.0 and a salt tolerance range of 0–1.0% (w/v). The predominant respiratory quinone was MK-9. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C17 : 0 2OH. The polar lipids of strain me31T were found to consist of phosphatidylethanolamine, three unidentified phospholipids, three unidentified phosphoglycolipids, one unidentified phosphoglycolipid, one unidentified lipid, two unidentified glycolipids and one aminophosphoglycolipid. According to the results of morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic analysis, strain me31T represents a novel species of a novel genus of the family Dysgonomonadaceae, for which the name Limibacterium fermenti gen. nov., sp. nov. is proposed. The type strain is me31T (=GDMCC 1.4237T=KCTC 25756T=WMCC 10035T).

A taxonomic study was conducted on four bacterial strains isolated from the soil of a coking plant. Phylogenetic analysis showed that the four strains belonged to three families: Comamonadaceae, Micrococcaceae and Roseiarcaceae. Identification of the 16S rRNA gene exhibited that their sequence similarities were between 94.96 and 98.98% when compared to known and validly nominated species. Their genomes ranged from 3.4 to 7.2 Mb, with DNA G+C molar contents varying from 62.3 to 67.2%. The average nucleotide identities ranged from 71.4 to 92.3%, and digital DNA–DNA hybridization values were 19.7–47.0% when comparing them with closely related type species, supporting the classification of these four strains. Functional analysis demonstrated that strain H3Y2-7T was robustly resistant to chromate (VI) and arsenite (III) and was able to grow on aromatic compounds including naphthalene as carbon sources even in the presence of chromate (VI). These features reflect its ability to treat combined pollutants and adapt to a polluted environment. Based on the analysis of polyphasic taxonomy, we propose the four bacterial strains representing novel species, namely Curvibacter soli sp. nov. (type strain H39-3-26T=JCM 36178T=CGMCC 1.61344T), Extensimonas soli sp. nov. (type strain H3M7-6T=JCM 36176T=CGMCC 1.61336T), Pseudarthrobacter naphthalenicus sp. nov. (type strain H3Y2-7T=JCM 36482T=CGMCC 1.61323T) and Terripilifer ovatus gen. nov., sp. nov. (type strain H3SJ34-1T=JCM 36465T=CGMCC 1.61333T).

A motile, rod-shaped and anaerobic strain WK13T was isolated from a secondary root canal infection of a human tooth. WK13T cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C16 : 0, C18 : 0, C16 : 1  ω7c, C18 : 1  ω9c and C18 : 2  ω6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13T belongs to the class Betaproteobacteria. WK13T showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, Propionivibrio pelophilus strain DSM 12018T and Propionivibrio dicarboxylicus strain DSM 5885T, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Betaproteobacteria, for which we propose the name Dentiradicibacter hellwigii gen. nov., sp. nov. The type strain is WK13T (=DSM 112713T=NCTC 14938T).

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071T was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus Niallia, with its closest relative being Niallia circulans ATCC 4513T. The genome of JL1B1071T is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between JL1B1071T and N. circulans ATCC 4513T are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071T demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071T revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus Niallia. Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071T was considered a novel species within the genus Niallia and is proposed to be named Niallia tiangongensis sp. nov. The type strain is JL1B1071T (=GDMCC 1.4642=KCTC 43715).

Abstract Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.

AbstractBACKGROUNDThe brown marmorated stink bug Halyomorpha halys has become an invasive insect pest of many crops. A promising control strategy to manage the proliferation of H. halys is based on the suppression of its obligate and vertically transmitted uncultivated symbiotic bacterium Candidatus Pantoea carbekii through surface‐sterilization of H. halys eggs. Indeed, the application of antimicrobial formulations on the eggs of H. halys could cause mortality of endosymbiont and consequently of newly emerged nymphs.In this study, a microbial live/dead assay was applied directly on H. halys eggs to evaluate Ca. P. carbekii loss of viability after treatments with seven commercial formulations including fungicides (copper hydroxide, sulphur, sweet orange essential oil) and plant biostimulants (flavonoids and chestnut tannin extract) compared with two disinfectants for civil and industrial use (sodium hypochlorite/hydrated sodium/tetraborate decahydrate and peracetic acid/hydrogen peroxide). Impact of mode of application was also evaluated, as surface treatment of egg masses was performed through spraying and dipping in laboratory conditions. Antimicrobial activity data were finally complemented with observations of egg hatching and vitality of the nymphs.RESULTSThe optimization of live/dead staining is useful for evaluating Ca. P. carbekii mortality directly on eggs, providing a rapid and reliable culture‐independent approach. Sodium hypochlorite, copper, sulphur, tannins and sweet orange essential oil showed an antimicrobial effect against Ca. P. carbekii and a H. halys egg hatching reduction and nymph's vitality.CONCLUSIONSThe antimicrobial and insecticidal effects of these commercial products should be further studied to assess their in‐field efficiency as well as the impact of these substances on non‐target organisms. The approach followed in this study could be considered a robust pipeline of analyses to evaluate the effectiveness of antimicrobial eco‐friendly compounds in symbiotic control of H. halys. © 2024 Society of Chemical Industry.