Comparative Analysis of Microbial Communities in Fronds and Roots of Three Duckweed Species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis

Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction

The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.

Heavy metals/-metalloids (As) phytoremediation with Landoltia punctata and Lemna sp. (duckweeds): coupling with biorefinery prospects for sustainable phytotechnologies

Heavy metals/-metalloids can result in serious human health hazards. Phytoremediation is green bioresource technology for the remediation of heavy metals and arsenic (As). However, there exists a knowledge gap and systematic information on duckweed-based metal phytoremediation in an eco-sustainable way. Therefore, the present review offers a critical discussion on the effective use of duckweeds (genera Landoltia and Lemna)-based phytoremediation to decontaminate metallic contaminants from wastewater. Phytoextraction and rhizofiltration were the major mechanism in 'duckweed bioreactors' that can be dependent on physico-chemical factors and plant-microbe interactions. The biotechnological advances such as gene manipulations can accelerate the duckweed-based phytoremediation process. High starch and protein contents of the metal-loaded duckweed biomass facilitate their use as feedstock in biorefinery. Biorefinery prospects such as bioenergy production, value-added products, and biofertilizers can augment the circular economy approach. Coupling duckweed-based phytoremediation with biorefinery can help achieve Sustainable Development Goals (SDGs) and human well-being.

Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method

The "duckweed-microbes co-cultivation method" is a microbial isolation technique that effectively recovers diverse microbes, including rarely cultivated bacterial phyla, from environmental samples. In this method, aseptic duckweed and microbes collected from an environmental sample are co-cultivated for several days, and duckweed-associated microbes are then isolated from its roots using a conventional agar plate-based cultivation method. We herein propose several improvements to the method in order to specifically obtain members of the rarely cultivated bacterial phylum, Verrucomicrobiota. In systems using river water as the inoculum, the marked enrichment of Verrucomicrobiota was observed after 10 days of co-cultivation, particularly in the roots and co-cultivated media. We also successfully isolated 44 strains belonging to subdivisions 1, 3, and 4 of the phylum Verrucomicrobiota from these systems. This was achieved by changing the concentration of nitrogen in the co-cultivation medium, which is known to affect duckweed growth and/or metabolism, and by subjecting the fronds and co-cultivated media as well as the roots after co-cultivation to microbial isolation.

Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources

Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.

Presence of microbiome decreases fitness and modifies phenotype in the aquatic plant Lemna minor

Plants live in close association with microbial organisms that inhabit the environment in which they grow. Much recent work has aimed to characterize these plant-microbiome interactions, identifying those associations that increase growth. Although most work has focused on terrestrial plants, Lemna minor, a floating aquatic angiosperm, is increasingly used as a model in host-microbe interactions and many bacterial associations have been shown to play an important role in supporting plant fitness. However, the ubiquity and stability of these interactions as well as their dependence on specific abiotic environmental conditions remain unclear. Here, we assess the impact of a full L. minor microbiome on plant fitness and phenotype by assaying plants from eight natural sites, with and without their microbiomes, over a range of abiotic environmental conditions. We find that the microbiome systematically suppressed plant fitness, although the magnitude of this effect varied among plant genotypes and depended on the abiotic environment. Presence of the microbiome also resulted in phenotypic changes, with plants forming smaller colonies and producing smaller fronds and shorter roots. Differences in phenotype among plant genotypes were reduced when the microbiome was removed, as were genotype by environment interactions, suggesting that the microbiome plays a role in mediating the plant phenotypic response to the environment.

Subcellular distribution, chemical forms of cadmium and rhizosphere microbial community in the process of cadmium hyperaccumulation in duckweed

Duckweed is a newly reported Cd hyperaccumulator that grow rapidly; however, little is known about its tolerance and detoxification mechanisms. In this study, we investigated the tissue, subcellular, and chemical form distribution of the Cd in duckweed and studied the influences of Cd on duckweed growth, ultrastructure, and rhizosphere microbial community. The results showed that Cd could negatively affect the growth of duckweed and shorten the root length. More Cd accumulated in the roots than in the leaves, and Cd was transferred from the roots to the leaves with time. During 12-24 h, Cd mainly existed in the cell wall fraction (2.05 %-95.52 %) and the organelle fraction (5.03 %-97.80 %), followed the soluble fraction (0.14 %-16.98 %). Over time, the proportion of Cd in the organelles increased (46.64 %-92.83 %), exceeding that in the cell wall (6.79 %-66.23 %), which indicated that duckweed detoxification mechanism may be related to the retention of cell wall and vacuole. The main chemical form of Cd was the NaCl-extracted state (30.15 %-88.66 %), which was integrated with pectate and protein. With increasing stress concentration and time, the proportion of the HCl-extracted state and HAc-extracted state increased, and they were low-toxic Cd oxalate and Cd phosphate, respectively. Cd damaged the ultrastructure of cells such as chloroplasts and mitochondria and inhibited the diversity of microbial communities in the duckweed rhizosphere; however, the dominant populations that could tolerate heavy metals increased. It was speculated that duckweed distributed Cd in a less toxic chemical form in a less active location, mainly through retention in the root cell wall and sequestration in the leaf vacuoles, and is dynamically adjusted. The rhizosphere microbial communities tolerate heavy metals may also be one of the mechanisms by which duckweed can tolerate Cd. This study revealed the mechanism of duckweed tolerance and detoxification of Cd at the molecular level and provides a theoretical basis for further development of duckweed.

Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3

Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome.

Microplastics and co-pollutant with ciprofloxacin affect interactions between free-floating macrophytes

Microplastic and antibiotic contamination are considered an increasing environmental problem in aquatic systems, while little is known about the impact of microplastics and co-pollutant with antibiotics on freshwater vascular plants, particularly the effects of interactions between macrophytes. Here, we performed a mesocosm experiment to evaluate the impact of polyethylene-microplastics and their co-pollutants with ciprofloxacin on the growth and physiological characteristics of Spirodela polyrhiza and Lemna minor and the interactions between these two macrophytes. Our results showed that microplastics alone cannot significantly influence fresh weight and specific leaf area of the two test free-floating macrophytes, but the effects on photosynthetic pigments, malondialdehyde, catalase and soluble sugar contents were species-specific. Ciprofloxacin can significant adverse effects on the growth and physiological traits of the two test macrophytes and microplastic mitigated the toxicity of ciprofloxacin on the two free-floating plants to a certain extent. In addition, our studies showed that microplastics and co-pollutants can influence relative yield and competitiveness of S. polyrhiza and L. minor by directly or indirectly influencing their physiology and growth. Therefore our findings suggest that species-specific sensibility to microplastic and its co-pollutant among free-floating macrophytes may influence macrophyte population dynamics and thereby community structure and ecosystem functioning. And microplastics altered other contaminant behaviours and toxicity, and may directly or indirectly influence macrophytes interactions and community structure. The present study is the first experimental study exploring the effects of microplastics alone and with their co-pollutants on interactions between free-floating macrophytes, which can provide basic theoretical guidance for improving the stability of freshwater ecosystems.

Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition

Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.

Degradation of Three Microcystin Variants in the Presence of the Macrophyte Spirodela polyrhiza and the Associated Microbial Communities

Cyanobacteria, which form water blooms all over the world, can produce a wide range of cyanotoxins such as hepatotoxic microcystins (MCs) and other biologically active metabolites harmful to living organisms, including humans. Microcystin biodegradation, particularly caused by bacteria, has been broadly documented; however, studies in this field focus mainly on strains isolated from natural aquatic environments. In this paper, the biodegradation of microcystin-RR (MC-RR), microcystin-LR (MC-LR), and microcystin-LF (MC-LF) after incubation with Spirodela polyrhiza and the associated microorganisms (which were cultured under laboratory conditions) is shown. The strongest MC biodegradation rate after nine days of incubation was observed for MC-RR, followed by MC-LR. No statistically significant decrease in the concentration of MC-LF was noted. Products of MC decomposition were detected via the HPLC method, and their highest number was found for MC-RR (six products with the retention time between 5.6 and 16.2 min), followed by MC-LR (two products with the retention time between 19.3 and 20.2 min). Although the decrease in MC-LF concentration was not significant, four MC-LF degradation products were detected with the retention time between 28.9 and 33.0 min. The results showed that MC-LF was the most stable and resistant MC variant under experimental conditions. No accumulation of MCs or their biodegradation products in S. polyrhiza was found. The findings suggest that the microorganisms (bacteria and algae) associated with S. polyrhiza could be responsible for the MC biodegradation observed. Therefore, there is a need to broaden the research on the biodegradation products detected and potential MC-degraders associated with plants.

Growth Promotion of Giant Duckweed Spirodela polyrhiza (Lemnaceae) by Ensifer sp. SP4 Through Enhancement of Nitrogen Metabolism and Photosynthesis

Duckweeds (Lemnaceae) are representative producers in fresh aquatic ecosystems and also yield sustainable biomass for animal feeds, human foods, and biofuels, and contribute toward effective wastewater treatment; thus, enhancing duckweed productivity is a critical challenge. Plant-growth-promoting bacteria (PGPB) can improve the productivity of terrestrial plants; however, duckweed-PGPB interactions remain unclear and no previous study has investigated the molecular mechanisms underlying duckweed-PGPB interaction. Herein, a PGPB, Ensifer sp. strain SP4, was newly isolated from giant duckweed (Spirodela polyrhiza), and the interactions between S. polyrhiza and SP4 were investigated through physiological, biochemical, and metabolomic analyses. In S. polyrhiza and SP4 coculture, SP4 increased the nitrogen (N), chlorophyll, and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) contents and the photosynthesis rate of S. polyrhiza by 2.5-, 2.5-, 2.7-, and 2.4-fold, respectively. Elevated photosynthesis increased the relative growth rate and biomass productivity of S. polyrhiza by 1.5- and 2.7-fold, respectively. Strain SP4 significantly altered the metabolomic profile of S. polyrhiza, especially its amino acid profile. N stable isotope analysis revealed that organic N compounds were transferred from SP4 to S. polyrhiza. These N compounds, particularly glutamic acid, possibly triggered the increase in photosynthetic and growth activities. Accordingly, we propose a new model for the molecular mechanism underlying S. polyrhiza growth promotion by its associated bacteria Ensifer sp. SP4, which occurs through enhanced N compound metabolism and photosynthesis. Our findings show that Ensifer sp. SP4 is a promising PGPB for increasing biomass yield, wastewater purification activity, and CO₂ capture of S. polyrhiza.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Synthetic Bacterial Community of Duckweed: A Simple and Stable System to Study Plant-microbe Interactions

A complete understanding of the plant microbiome has not yet been achieved due to its complexity and temporal shifts in the community structure. To overcome these issues, we created a synthetic bacterial community of the aquatic plant, duckweed. The synthetic community established with six bacterial strains showed a stable composition for 50 days, which may have been because duckweed maintains a similar physiological status through its clonal reproduction. Additionally, the synthetic community reflected the taxonomic structure of the natural duckweed microbiome at the family level. These results suggest the potential of a duckweed-based synthetic community as a useful model system for examining the community assembly mechanisms of the plant microbiome.