Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals

Serratia spp. as plant growth-promoting bacteria alleviating salinity, drought, and nutrient imbalance stresses

In agricultural environments, plants are often exposed to abiotic stresses including temperature extremes, salt stress, drought, and heavy metal soil contamination, which leads to significant economic losses worldwide. Especially salt stress and drought pose serious challenges since they induce ionic toxicity, osmotic stress, and oxidative stress in plants. A potential solution can be the application of bacteria of the Serratia spp. known to promote plant growth under normal conditions Thus the mini-review aims to summarize the current knowledge on plant growth promotion by Serratia spp. (under the conditions of salinity stress, drought, and nutrient deficit) and highlight areas for development in the field. So far, it has been proven that Serratia spp. strains exhibit a variety of traits contributing to enhanced plant growth and stress tolerance, such as phytohormone production, ACC deaminase activity, nitrogen fixation, P and Zn solubilization, antioxidant properties improvement, and modulation of gene expression. Nevertheless, further research on Serratia spp. is needed, especially on two subjects: elucidating its mechanisms of action on plants at the molecular level and the effects of Serratia spp. on the indigenous soil and plant microbiota and, particularly, the rhizosphere. In both cases, it is advisable to use omics techniques to gain in-depth insights into the issues. Additionally, some strains of Serratia spp. may be phytopathogens, therefore studies to rule out this possibility are recommended prior to field trials. It is believed that by improving said knowledge the potential of Serratia spp. to stimulate plant growth will increase and strains from the genus will serve as an eco-friendly biofertilizer in sustainable agriculture more often.

Molecular insights and omics-based understanding of plant-microbe interactions under drought stress

The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize (Zea mays)

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790)

BACKGROUND

A wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR).

RESULTS

In this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain.

CONCLUSIONS

This study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.

Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.

Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks

Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants' health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion.

Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review

Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil–plant–microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.

Effect of copper stress on Phaseolus coccineus in the presence of exogenous methyl jasmonate and/or Serratia plymuthica from the Spitsbergen soil

Copper stress in the presence of exogenous methyl jasmonate and Serratia plymuthica in a complete trifactorial design with copper (0, 50 µM), methyl jasmonate (0, 1, 10 µM) and Serratia plymuthica (without and with inoculation) was studied on the physiological parameters of Phaseolus coccineus. Copper application reduced biomass and allantoin content, but increased chlorophyll and carotenoids contents as well as catalase and peroxidases activities. Jasmonate did not modify biomass and organic acids levels under copper treatment, but additional inoculation elevated biomass and content of tartrate, malate and succinate. Jasmonate used alone or in combination with bacteria increased superoxide dismutase activity in copper application. With copper, allantoin content elevated at lower jasmonate concentration, but with additional inoculation - at higher jasmonate concentration. Under copper stress, inoculation resulted in higher accumulation of tartrate, malate and citrate contents in roots, which corresponded with lower allantoin concentration in roots. Combined with copper, inoculation reduced catalase and guaiacol peroxidase activities, whereas organic acids content was higher. Under metal stress, with bacteria, jasmonate reduced phenolics content, elevated superoxide dismutase and guaiacol peroxidase activities. The data indicate that jasmonate and S. plymuthica affected most physiological parameters of P. coccineus grown with copper and revealed some effect on biomass.

Serratia plymuthica MBSA-MJ1 Increases Shoot Growth and Tissue Nutrient Concentration in Containerized Ornamentals Grown Under Low-Nutrient Conditions

High fertilizer rates are often applied to horticulture crop production systems to produce high quality crops with minimal time in production. Much of the nutrients applied in fertilizers are not taken up by the plant and are leached out of the containers during regular irrigation. The application of plant growth promoting rhizobacteria (PGPR) can increase the availability and uptake of essential nutrients by plants, thereby reducing nutrient leaching and environmental contamination. Identification of PGPR can contribute to the formulation of biostimulant products for use in commercial greenhouse production. Here, we have identified Serratia plymuthica MBSA-MJ1 as a PGPR that can promote the growth of containerized horticulture crops grown with low fertilizer inputs. MBSA-MJ1 was applied weekly as a media drench to Petunia×hybrida (petunia), Impatiens walleriana (impatiens), and Viola×wittrockiana (pansy). Plant growth, quality, and tissue nutrient concentration were evaluated 8weeks after transplant. Application of MBSA-MJ1 increased the shoot biomass of all three species and increased the flower number of impatiens. Bacteria application also increased the concentration of certain essential nutrients in the shoots of different plant species. In vitro and genomic characterization identified multiple putative mechanisms that are likely contributing to the strain’s ability to increase the availability and uptake of these nutrients by plants. This work provides insight into the interconnectedness of beneficial PGPR mechanisms and how these bacteria can be utilized as potential biostimulants for sustainable crop production with reduced chemical fertilizer inputs.

Potential of Serratia plymuthica IV-11-34 strain for biodegradation of polylactide and poly(ethylene terephthalate)

Serratia plymuthica strain IV-11-34 belongs to the plant growth promoting bacteria (PGPR). In the sequenced genome of S. plymuthica IV-11-34, we have identified the genes involved in biodegradation and metabolisms of xenobiotics. The potential of S. plymuthica IV-11-34 for the degradation of biodegradable aliphatic polyester polylactide (PLA) and resistant to biodegradation - poly(ethylene terephthalate) (PET) was assessed by biochemical oxygen consumption (BOD) and carbon dioxide methods. After seven days of growth, the bacteria strain showed more than 80% and 60% increase in respiratory activity in the presence of PLA and PET, respectively. We assume that during biodegradation, S. plymuthica IV-11-34 colonise the surface of PLA and PET, since the formation of a biofilm on the surface of polymers was shown by the LIVE/DEAD method. We have demonstrated for the relA gene, which is an alarmone synthetase, a 1.2-fold increase in expression in the presence of PLA, and a 4-fold decrease in expression in the presence of PET for the spoT gene, which is a hydrolase of alarmones. Research has shown that the bacterium has the ability to biodegrade PLA and PET, and the first stage of this process involves bacterial stringent response genes responsible for survival under extreme conditions.