Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus

Exploring Halophiles for Reclamation of Saline Soils: Biotechnological Interventions for Sustainable Agriculture

Soil salinization is a major constraint on agricultural productivity, particularly in arid and semi-arid regions where limited rainfall cannot wash salts from plant root zones. This leads to disruptions in water uptake, ion balance, photosynthesis, respiration, nutrient absorption, hormone regulation and rhizosphere microbiome disturbances in plants. Chemical and biological methods can help mitigate soil salinity, but biological approaches, like using halophytes and salt-tolerant microorganisms, are preferred for environmental sustainability. Halophytes, however, represent only about 1% of flora and are habitat specific, so halophilic plant growth-promoting (PGP) microbes have emerged as a key eco-friendly solution. Halophilic PGP bacteria have shown promise in remediating saline soils, enhancing fertility and boosting crop resilience by inducing salinity tolerance (IST) and promoting plant growth traits. In the era of modern agriculture where chemical inputs are at their peak of application rendering the soil infertile, halophilic PGP bacteria represent a promising, sustainable approach to support food security, aligning with Sustainable Development Goals for zero hunger.

Characterization of halotolerant Kushneria isolates that stimulate growth of alfalfa in saline conditions

A key barrier to crop production is soil salinity, which is a serious and growing problem world-wide due to inadequate water drainage, saline ground water, or inadequate rainfall to wash away soil salts. There is substantial promise for plant-associated microbes isolated from halophytes (salt-tolerant plants) to enhance growth of salt-sensitive crop plants in salty soils. The objective of this study was to identify salt-tolerant bacteria from native halophytes and characterize their ability to stimulate the growth of alfalfa in salty soil conditions. Several halotolerant bacteria, including Kushneria, Halomonas, and Bacillus, were identified from the rhizosphere or roots of three halophyte species (Salicornia rubra, Sarcocornia utahensis, and Allenrolfea occidentalis) in a saline area south of Utah Lake, Utah, USA. Biochemical properties, including indole acetic acid production, biofilm formation, phosphate solubilization and siderophore production activities, which have been associated with plant growth promoting (PGP) activity, were characterized for several isolates. Selected strains were screened for the ability to stimulate growth of alfalfa in controlled laboratory experiments. Among these strains, two independent isolates of the genus Kushneria were found to have significant growth-promoting activity for inoculated alfalfa plants grown under saline conditions (0.205 M or 1.2% NaCl) that mimic common salinity levels of affected soils. Plants inoculated with a combination of two Kushneria strains that have salt-tolerant PGP (ST-PGP) properties exhibited a statistically significant increase in plant growth over uninoculated plants. A GFP marker confirmed presence of Kushneria in the roots of inoculated plants. Bacteria with ST-PGP activity will be a key resource to facilitate increased crop yield from land affected by salinity, and the data presented here for two Kushneria isolates are promising.

Halophilic Plant-Associated Bacteria with Plant-Growth-Promoting Potential

The salinization of soils is a growing agricultural concern worldwide. Irrigation practices, drought, and climate change are leading to elevated salinity levels in many regions, resulting in reduced crop yields. However, there is potential for a solution in the microbiome of halophytes, which are naturally salt-tolerant plants. These plants harbor a salt-tolerant microbiome in their rhizosphere (around roots) and endosphere (within plant tissue). These bacteria may play a significant role in conferring salt tolerance to the host plants. This leads to the possibility of transferring these beneficial bacteria, known as salt-tolerant plant-growth-promoting bacteria (ST-PGPB), to salt-sensitive plants, enabling them to grow in salt-affected areas to improve crop productivity. In this review, the background of salt-tolerant microbiomes is discussed and their potential use as ST-PGPB inocula is explored. We focus on two Gram-negative bacterial genera, Halomonas and Kushneria, which are commonly found in highly saline environments. These genera have been found to be associated with some halophytes, suggesting their potential for facilitating ST-PGPB activity. The study of salt-tolerant microbiomes and their use as PGPB holds promise for addressing the challenges posed by soil salinity in the context of efforts to improve crop growth in salt-affected areas.

Combined application of high-throughput sequencing and UHPLC-Q/TOF-MS-based metabolomics in the evaluation of microorganisms and metabolites of dry-cured ham of different origins

Ham fermentation relies on environmental and indigenous microorganisms forming a rich microbiome, which is pivotal to taste and flavor formation. Previous studies have focused on the appearance of differences of microorganisms and metabolites, this study aims to establish the relationship between microorganisms and metabolites over a period of two years in the fermentation of hams from Jinghua (JH2), Xuanwei (XW2), Rugao (RG2), Iberian (IB2) and Parma (PA2). We profiled bacterial communities by sequencing the V3-V4 region of the 16S rRNA genes and metabolites were analyzed using LC-Q-TOF-MS. LefSe analysis showed that different biomarkers in five ham groups. OPLS analysis showed that most differential metabolites are amino acids and were associated with four metabolic pathways. Correlation analysis implies a firm positive relationship between microorganisms and metabolites. This study provides novel insights into the taste and flavor quality of dry-cured hams of different origins due to fermentation.

Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca

BACKGROUND

Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca.

RESULTS

A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities).

CONCLUSION

The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.

Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta

Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

Panxian ham, a traditional Chinese dry-cured ham, is protected by national geographical indication. Similar to other fermented foods, the microbial population of dry-cured ham is pivotal to taste and flavor formation. This study aimed to establish the relationship between microorganisms and metabolites during the spontaneous fermentation of Panxian ham. Multivariate analysis based on metabolomics data revealed that continuous metabolic changes occurred during the entire fermentation process, with the most significant changes occurring in the initial stage of ripening. Thirty-one significantly different metabolites (SDMs) were identified as discriminant factor, and pathway analysis suggested that these metabolites were involved in 30 pathways, including alanine, aspartate, and glutamate metabolism; glycine, serine, and threonine metabolism; and arginine and proline metabolism. Microbial community analysis using the Illumina MiSeq platform indicated that the bacterial community was more complex than the fungal community, and their succession regulation differed during processing. At the genus level, 11 bacteria and five fungi were identified as core microbes, of which Staphylococcus was the dominant bacteria and Debaryomyces and Aspergillus were the dominant fungi. Further, statistical redundancy analysis (RDA) indicated that Staphylococcus, Debaryomyces, and Chromohalobacter promoted the production of amino and fatty acids; Cobetia and Aspergillus were associated with sugar metabolism, and Kushneria, Penicillium, and Yamadazyma were closely related with organic acids. These findings provide fundamental knowledge regarding the metabolically active microorganisms in Panxian ham, helping industrial processors to develop effective strategies for standardizing quality parameters.