Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil

Response of bacterial community structure in saline soils to the application of kitchen waste-derived fermented organic fertilizer

Saline soils, which inhibit plant growth and diminish soil functions such as carbon storage, present a significant challenge to agricultural productivity. Consequently, soil improvement is crucial for achieving sustainable agricultural development. Organic fertilizers, particularly those derived from kitchen waste, have shown potential in enhancing soil fertility and structure. However, the interaction between kitchen waste - derived fermented organic fertilizers and their impact on microbial diversity, community structure, and nutrient dynamics in saline soils remains an underexplored area within environmental research. In this study, microcosm experiments were conducted with saline soil samples. We examined the temporal changes in soil nutrient levels and microbial diversity after the application of inorganic and organic fertilizer for a 15-day period. The results demonstrated that short-term application of kitchen waste fermented organic fertilizer significantly increased the levels of organic matter (OM), total nitrogen (TN), hydrolyzed nitrogen (HN), total phosphorus (TP), available phosphorus (AP), and available potassium (AK); however, it also led to a reduction in microbial diversity within saline soils while simultaneously promoting the presence of beneficial microorganisms such as Photobacterium, Pseudoalteromonas, and Planococcus. The relative abundance of Bacillus increased from 0.34 to 35.22% in the COS (treatment with 30% organic fertilizer) treatment. The redundancy analysis demonstrated that, except for TK (total potassium), the physicochemical properties of the saline soils were positively correlated with the dominant bacterial community abundance under the BOS (treatment with 10% organic fertilizer) and COS treatments but negatively correlated with the salt-tolerant bacterial abundance under the CK (treatment with saline soil) and AIS (treatment with saline soil and inorganic fertilizer) treatments. In conclusion, the application of kitchen waste fermented organic fertilizer is a beneficial strategy for enhancing saline soil fertility, promoting the proliferation of beneficial microorganisms, and rehabilitating saline soils.

Unveiling metabolic integration in psyllids and their nutritional endosymbionts through comparative transcriptomics analysis

Psyllids, a group of insects that feed on plant sap, have a symbiotic relationship with an endosymbiont called Carsonella. Carsonella synthesizes essential amino acids and vitamins for its psyllid host, but lacks certain genes required for this process, suggesting a compensatory role of psyllid host genes. To investigate this, gene expression was compared between two psyllid species, Bactericera cockerelli and Diaphorina citri, in specialized cells where Carsonella resides (bacteriomes). Collaborative psyllid genes, including horizontally transferred genes, showed patterns of conserved gene expression; however, species-specific patterns were also observed, suggesting differences in the nutritional metabolism between psyllid species. Also, the recycling of nitrogen in bacteriomes may primarily rely on glutamate dehydrogenase (GDH). Additionally, lineage-specific gene clusters were differentially expressed in B. cockerelli and D. citri bacteriomes and are highlighted here. These findings shed light on potential host adaptations for the regulation of this symbiosis due to host, microbiome, and environmental differences.

Antioxidant properties of water-soluble polysaccharides prepared by co-culture fermentation of straw and shrimp shell

Herein, we present a method for producing water-soluble polysaccharides (WSPs) by co-culture fermentation of straw and shrimp shells. The chitin-degrading strain was isolated and genotypically identified as the non-pathogen Photobacterium sp. LYM-1 in this study. Photobacterium sp. LYM-1 and Aureobasidium pullulans 2012 could coexist without antagonism. WSPs concentrations were higher in co-culture fermentations of Photobacterium sp. LYM-1 and A. pullulans 2012 (PsL/AP-WSPs) compared to monocultures (PsL-WSPs and AP-WSPs). FTIR was used to examine the polysaccharide properties of three WSP fractions. The monosaccharide compositions of three WSPs fractions were primarily composed of mannose, ribose, glucosamine, glucose, galactose, and arabinose with varying molecular weights and molar ratios according to HPLC analysis. PsL/AP-WSPs showed better scavenging effects on DPPH, ABTS, and OH free radicals, demonstrating the application potential of PsL/AP-WSPs from straw and shrimp shells. The maximum yield obtained under optimum conditions (fermentation time of 6 days, temperature of 31°C, inoculum concentration of 10% (w/v), and inoculum composition of 2:1) was 5.88 ± 0.40 mg/mL, based on the PsL/AP-WSPs production optimization by orthogonal design. The results suggest that an environmentally friendly approach for WSPs production from agro-food wastes straw and shrimp shells was developed.

Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism

The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.

Photobacterium arenosum WH24, Isolated from the Gill of Pacific Oyster Crassostrea gigas from the North Sea of Germany: Co-cultivation and Prediction of Virulence

Cream colored bacteria from marine agar, strain WH24, WH77, and WH80 were isolated from the gill of the Crassostrea gigas a Pacific oyster with a filter-feeding habit that compels accompanying bacteria to demonstrate a high metabolic capacity, has proven able to colonize locations with changing circumstances. Based on the 16S rRNA gene sequence, all strains had high similarity to Photobacterium arenosum CAU 1568^T (99.72%). This study involved phenotypic traits, phylogenetic analysis, antimicrobial activity evaluation, genome mining, Co-cultivation experiments, and chemical studies of crude extracts using HPLC and LC-HRESIMS. Photobacterium arenosum WH24 and Zooshikella harenae WH53^Twere co-cultivated for 3 days in a rotary shaker at 160 rpm at 30 °C, and LC-MS monitored the chemical profiles of the co-cultures on the third day. The UV chromatograms of the extracts of the co-cultivation experiments show that Zooshikella harenae WH53^T could be inhibited by strain WH24. The high virulence of Photobacterium arenosum WH24 was confirmed by genome analysis. Gene groups with high virulence potential were detected: tssA (ImpA), tssB (ImpB/vipA), tssC (ImpC/vipB), tssE, tssF (ImpG/vasA), tssG (ImpH/vasB), tssM (IcmF/vasK), tssJ (vasD), tssK (ImpJ/vasE), tssL (ImpK/vasF), clpV (tssH), vasH, hcp, lapP, plpD, and tpsB family.

Pseudomarimonas arenosa gen. nov., sp. nov. isolated from marine sand

A novel Gram-negative, aerobic, non-motile, rod-shaped, bacterial strain (CAU 1598^T) was isolated from marine sand. Strain CAU 1598^T grew well at 30 °C, pH 6.5-7.0 and with 3 % NaCl (w/v). Phylogeny results based on 16S rRNA gene sequencing indicated that the identified strain had the highest similarity (94.3%) to Pseudoxanthomonas putridarboris, indicating that strain CAU 1598^T belongs to the family Xanthomonadaceae. Further, the fatty acid profile of the strain was primarily composed of C_16:0, iso-C_15 : 0, iso-C_16 : 0, summed feature 3 (consisting of C_16 : 1  ω7c/iso-C_15 : 0 2-OH) and summed feature 9 (consisting of iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl), with ubiquinone-8 as the major isoprenoid quinone. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, an unidentified aminolipid and an unidentified lipid. The G+C content of the bacterial genome was 62.6 mol% and its 5.4 Mb length encompassed 144 contigs and 4236 protein-coding genes. These phenotypic, chemotaxonomic and phylogenetic data indicate that CAU 1598^T belongs to a new genus and species, for which the name Pseudomarimonas arenosa gen. nov., sp. nov. is proposed. The type strain is CAU 1598^T (=KCTC 82406^T=MCCC 1K05673^T).

Roseibium limicola sp. nov., isolated from tidal mudflat

A novel bacterium, designated strain CAU 1637^T, was isolated from a tidal mudflat. Cells of strain CAU 1637^T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637^T was closely related to the genus Roseibium, with the highest similarity to Roseibium aestuarii NRBC 112946^T (97.4 %), followed by Roseibium hamelinense NRBC 16783^T (96.8 %), Roseibium aquae JCM 19310^T (96.4 %), Roseibium sediminis KCTC 52373^T (95.8 %) and Roseibium denhamense JCM 10543^T (95.3 %). The predominant cellular fatty acids were C_18 : 1  ω7c 11-methyl and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA-DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637^T represents a novel species of the genus Roseibium, for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637^T (=KCTC 82429^T=MCCC 1K06080^T).

Photobacterium arenosum sp. nov., isolated from marine sediment sand

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568^T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25-30 °C, at pH 6.5-8.5 and with 0-4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568^T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852^T (97.7 %), Photobacterium halotolerans KACC 17089^T (97.3 %) and Photobacterium galatheae LMG F28894^T (97.3 %). The predominant cellular fatty acids were C_16 : 0, summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568^T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568^T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568^T (=KCTC 82404^T=MCCC 1K05668^T).