Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses

BACKGROUND

Zoysiagrass (Zoysia spp.) is a warm-season turfgrass. It is widely used as turfgrasses throughout the world, offers good turf qualities, including salt tolerance, resistance to drought and heat. However, the underlying genetic mechanism of zoysiagrass responsive to salt stress remains largely unexplored.

RESULTS

In present study, we performed a whole-genome comparative analysis for ten plant genomes. Evolutionary analysis revealed that Chloridoideae diverged from Panicoideae approximately 33.7 million years ago (Mya), and the phylogenetic relationship among three zoysiagrasses species suggested that Zoysia matrella may represent an interspecific hybrid between Zoysia japonica and Zoysia pacifica. Genomic synteny indicated that Zoysia underwent a genus-specific whole-genome duplication (WGD) event approximately 20.8 Mya. The expression bais of homologous genes between the two subgenomes suggested that the B subgenome of Z. japonica contributes to salt tolerance. In additon, comparative genomic analyses revealed that the salt adaptation of Zoysia is likely attributable to the expanded cytochrome P450 and ABA biosynthetic gene families. Furthermore, we further found that many duplicated genes from the extra WGD event exhibited distinct functional divergence in response to salt stress using transcriptomic analysis, suggesting that this WGD event contributed to strong resistance to salt stress.

CONCLUSIONS

Here, our results revealed that expanded cytochrome P450 and ABA biosynthetic gene families, and many of those duplicated genes from recent zoysia-specific WGD event contributed to salt adaptation of zoysiagrass, which provided insight into the genetic underpinning of salt adaptation and valuable information for further studies on salt stress-related traits in Zoysia.

Adaptation and evolution of freshwater Anammox communities treating saline/brackish wastewater

The most common way to apply Anammox for saline wastewater treatment is via salt adaptation of freshwater Anammox bacteria (FAB). To better apply this process in practice, it's essential to understand the salt adaptation process of FBA, as well as the underlying mechanisms. This study investigated the long-term salt adaptation process of a fixed-film FAB culture in three reactors (namely R1-R3), under salinities of 2, 8, and 12 NaCl g/L, correspondingly. All three reactors were under stable operation and achieved 80-90% total inorganic nitrogen removal efficiency throughout the 425-day operation period. R1 servers as a blank control, based on the clear microbial community shifts in R2 and R3, the operation period was divided into 2 phases. During Phase 1, all FAB in the three reactors belonged to Ca. Brocadia sp.. The Anammox activity (AA) and the ratio of nitrite/ammonium (NO₂^--N/NH₄⁺-N) consumption in R2 and R3 decreased with the increase of salinity and did not recover to the initial levels. During Phase 2, the relative abundance of Ca. Kuenenia sp. in R2 and R3 increased from nearly 0 to about 60 and 77%, respectively. With the growth of Ca. Kuenenia sp., the AA and stoichiometry of R2 and R3 gradually recovered. AA of R2 and R3 both reached 1.0 g NH₄⁺-N/L/day at the end of this phase, which was about 80% of that in R1. These results indicated that the salt adaptation of FAB culture was achieved by species shift from a low salt-tolerance one to a high salt-tolerance one.

Nanoparticles potentially mediate salt stress tolerance in plants

In the era of climate change, salt stress is a promising threat to agriculture, limiting crop production via imposing primary effects such as osmotic and ionic, as well as secondary effects such as oxidative stress, perturbance in hormonal homeostasis, and nutrient imbalance. On the other hand, production areas are expanding into the salt affected regions due to excessive pressure for fulfilling food security targets to meet the needs of continuously increasing human population. Accumulating evidences demonstrate that supplementation of nanoparticles to plants can significantly alleviate the injurious effects caused by various harsh conditions including salt stress, and hence, regulate adaptive mechanisms in plants. Various types of NPs and nanofertilizers have shown a promising evidence so far regarding salt stress management. In this review, we recapitulate recent pioneering progress made towards acquiring salt stress tolerance in crop plants utilizing NPs. Finally, future research directions in this domain to explicate the comprehensive roles of nanoparticles in improving salt tolerance in plants are underscored. To ensure social acceptance and safe use of NPs, some conclusive directions have been elaborated in order to achieve sustainable progress in crop production under saline environments.

Stability of microbial functionality in anammox sludge adaptation to various salt concentrations and different salt-adding steps

The stability of community functioning in anaerobic ammonia oxidation (anammox) sludge adaptation to various salinity changes are concerned but not fully explored. In this study, two anammox reactors were designed in response to different salt levels and salt-adding methods. The reactor PI, run with small stepwise salt increments (0.5%-1.0%), removed >90% of nitrite and ammonium in the influent over the range of 0%-4% salt. By contrast, the reactor SI, run with a sharp salt increment (>2.5%), exhibited a reduced performance (by up to 44%) over the same salt range with a new steady state. The observed resilience times after salt perturbations indicated that the PI reactor recovered substantially and rapidly at all imposed salt levels. Principal coordinates analysis of 16S rRNA gene amplicon sequences revealed that bacterial community structures of the anammox sludge altered conspicuously in response to the salinity changes. However, quantitative PCR analysis showed that the shift in copy number of studied nitrogen-converting genes encoding hydrazine synthase (hzsA), bacterial and archaeal ammonia monooxygenases (amoA), nitrite oxidoreductase (nxrB), nitrite reductase (nirK), and nitrous oxide reductase (nosZ) was not significant (p > 0.05) in anammox sludge across the salt levels of 0.5%-4%, which suggests the stability of microbial community functioning in the osmoadaptation processes. The freshwater anammox Ca. Kuenenia showed high osmoadaptation by potentially adopting both high-salt-in and low-salt-in strategies to dominate in both reactors. The quantitative transcript analysis showed that the active anammox bacteria represented by hzsA transcripts in the SI reactor were approximately two orders of magnitude lower than those in the PI reactor during the long-term exposure to 4% salinity, manifesting the influence by the salt-increasing methods. These results provided new insight into osmo-adaptation of the anammox microbiome and will be useful for managing salinity effects on nitrogen removal processes.

Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba

BACKGROUND

Mangroves have adapted to intertidal zones - the interface between terrestrial and marine ecosystems. Various studies have shown adaptive evolution in mangroves at physiological, ecological, and genomic levels. However, these studies paid little attention to gene regulation of salt adaptation by transcriptome profiles.

RESULTS

We sequenced the transcriptomes of Sonneratia alba under low (fresh water), medium (half the seawater salinity), and high salt (seawater salinity) conditions and investigated the underlying transcriptional regulation of salt adaptation. In leaf tissue, 64% potential salinity-related genes were not differentially expressed when salinity increased from freshwater to medium levels, but became up- or down-regulated when salt concentrations further increased to levels found in sea water, indicating that these genes are well adapted to the medium saline condition. We inferred that both maintenance and regulation of cellular environmental homeostasis are important adaptive processes in S. alba. i) The sulfur metabolism as well as flavone and flavonol biosynthesis KEGG pathways were significantly enriched among up-regulated genes in leaves. They are both involved in scavenging ROS or synthesis and accumulation of osmosis-related metabolites in plants. ii) There was a significantly increased percentage of transcription factor-encoding genes among up-regulated transcripts. High expressions of salt tolerance-related TF families were found under high salt conditions. iii) Some genes up-regulated in response to salt treatment showed signs of adaptive evolution at the amino acid level and might contribute to adaptation to fluctuating intertidal environments.

CONCLUSIONS

This study first elucidates the mechanism of high-salt adaptation in mangroves at the whole-transcriptome level by salt gradient experimental treatments. It reveals that several candidate genes (including salt-related genes, TF-encoding genes, and PSGs) and major pathways are involved in adaptation to high-salt environments. Our study also provides a valuable resource for future investigation of adaptive evolution in extreme environments.

Metabolic Adjustment of Arabidopsis Root Suspension Cells During Adaptation to Salt Stress and Mitotic Stress Memory

Sessile plants reprogram their metabolic and developmental processes during adaptation to prolonged environmental stresses. To understand the molecular mechanisms underlying adaptation of plant cells to saline stress, we established callus suspension cell cultures from Arabidopsis roots adapted to high salt for an extended period of time. Adapted cells exhibit enhanced salt tolerance compared with control cells. Moreover, acquired salt tolerance is maintained even after the stress is relieved, indicating the existence of a memory of acquired salt tolerance during mitotic cell divisions, known as mitotic stress memory. Metabolite profiling using 1H-nuclear magnetic resonance (NMR) spectroscopy revealed metabolic discrimination between control, salt-adapted and stress-memory cells. Compared with control cells, salt-adapted cells accumulated higher levels of sugars, amino acids and intermediary metabolites in the shikimate pathway, such as coniferin. Moreover, adapted cells acquired thicker cell walls with higher lignin contents, suggesting the importance of adjustments of physical properties during adaptation to elevated saline conditions. When stress-memory cells were reverted to normal growth conditions, the levels of metabolites again readjusted. Whereas most of the metabolic changes reverted to levels intermediate between salt-adapted and control cells, the amounts of sugars, alanine, γ-aminobutyric acid and acetate further increased in stress-memory cells, supporting a view of their roles in mitotic stress memory. Our results provide insights into the metabolic adjustment of plant root cells during adaptation to saline conditions as well as pointing to the function of mitotic memory in acquired salt tolerance.

Characterization and mutation analysis of a halotolerant serine protease from a new isolate of Bacillus subtilis

OBJECTIVES

A bacterial halotolerant enzyme was characterized to understand the molecular mechanism of salt adaptation and to explore its protein engineering potential.

RESULTS

Halotolerant serine protease (Apr_No16) from a newly isolated Bacillus subtilis strain no. 16 was characterized. Multiple alignments with previously reported non-halotolerant proteases, including subtilisin Carlsberg, indicated that Apr_No16 has eight acidic or polar amino acid residues that are replaced by nonpolar amino acids in non-halotolerant proteases. Those residues were hypothesized to be one of the primary contributors to salt adaptation. An eightfold mutant substituted with Ala residues exhibited 1.2- and 1.8-fold greater halotolerance at 12.5% (w/v) NaCl than Apr_No16 and Carlsberg, respectively. Amino acid substitution notably shifted the theoretical pI of the eightfold mutant, from 6.33 to 9.23, compared with Apr_No16. The resulting protein better tolerated high salt conditions.

CONCLUSIONS

Changing the pI of a bacterial serine protease may be an effective strategy to improve the enzyme's halotolerance.

Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

Nitrification and microalgae cultivation for two-stage biological nutrient valorization from source separated urine

Urine contains the majority of nutrients in urban wastewaters and is an ideal nutrient recovery target. In this study, stabilization of real undiluted urine through nitrification and subsequent microalgae cultivation were explored as strategy for biological nutrient recovery. A nitrifying inoculum screening revealed a commercial aquaculture inoculum to have the highest halotolerance. This inoculum was compared with municipal activated sludge for the start-up of two nitrification membrane bioreactors. Complete nitrification of undiluted urine was achieved in both systems at a conductivity of 75mScm(-1) and loading rate above 450mgNL(-1)d(-1). The halotolerant inoculum shortened the start-up time with 54%. Nitrite oxidizers showed faster salt adaptation and Nitrobacter spp. became the dominant nitrite oxidizers. Nitrified urine as growth medium for Arthrospira platensis demonstrated superior growth compared to untreated urine and resulted in a high protein content of 62%. This two-stage strategy is therefore a promising approach for biological nutrient recovery.

Comparative proteome analysis reveals proteins involved in salt adaptation in Photobacterium damselae subsp. piscicida

Proteomic approaches were applied to investigate whether Photobacterium damselae subsp. piscicida (Phdp) can directly sense and respond to growth conditions under different salinities, 0.85% and 3.5% NaCl concentrations, mimicking the osmotic conditions in host and marine water bodies, respectively. Proteins significantly altered were analyzed by two-dimensional gel electrophoresis (2-DE), liquid chromatography-electrospray ionization-quadrupole-time-of-flight tandem mass spectrometry (LC-ESI-Q-TOF MS/MS) and bioinformatics analysis, thus resulting in 16 outer membrane proteins (OMPs), 12 inner membrane proteins (IMPs), and 20 cytoplasmic proteins (CPs). Quantitative real-time PCR was also applied to monitor the mRNA expression level of these target proteins. Cluster of orthologous groups of protein (COG) analysis revealed that when shifting from 3.5% to 0.85% salinity, the majority of the up-regulated proteins were involved in posttranslational modification, protein turnover, and chaperones, while the down-regulated proteins were mainly related to energy production and conversion, compatible solutes (carbohydrates, amino acids and their derivatives) biogenesis and transport. Differentially expressed proteins identified in the current study could be used to elucidate the salt adaptation mechanisms of Phdp during their transition between host cells and the marine habitats.