The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling

Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem

Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.

Understanding the bacterial community structure associated with the Eichhornia crassipes rootzone

BACKGROUND

Plant microbiome acts as an interface between plants and their environment, aiding in the functioning of the ecosystem, such as protection against abiotic and biotic stress along with improving nutrient uptake. The rhizosphere is an essential interface for the interaction between plants and microbes and plays a substantial part in the removal as well as uptake of heavy metals and antibiotics from contaminated locations. Eichhornia crassipes is a promising plant that contains a rich community of microbes in its rhizosphere. Microorganism's association with plants embodies a crucial pathway via which humans can also be exposed to antibiotic-resistant genes and bacteria.

METHODS AND RESULTS

In our earlier study enhanced removal of ciprofloxacin was observed by plant growth-promoting Microbacterium sp. WHC1 in the presence of E. crassipes root exudates. Therefore, the V3-V4, hypervariable region of the 16 S rRNA gene was studied to assess the bacterial diversity and functional profiles of the microbiota associated with plant roots. Using the QIIME software program, 16 S rRNA data from the Next Generation Sequencing (NGS) platform was examined. Alpha diversity including Chao1, Observed Shannon, and Simpson index denote significantly higher bacterial diversity. Proteobacteria (79%) was the most abundant phylum which was present in the root samples followed by Firmicutes (8%) and Cyanobacteria (8%). Sulfuricurvum (36%) is the most abundant genus belonging to the family Helicobacteraceae and the species kujiense in the genus Sulfuricurvum is the most abundant species present in the root sample. Also, the bacterial communities in the rhizoplane of Eichhornia crassipes harbor the genes conferring resistance to beta-lactams, tetracycline, fluoroquinolones, and penams.

CONCLUSION

Metagenomic studies on the E. crassipes microbiome showed that the bacterial communities constituting the root exudates of the Eichhornia aid them to survive in a polluted environment.

Vallisneria natans decreased CH4 fluxes in wetlands: Interactions among plant physiological status, nutrients and epiphytic bacterial community

Submerged macrophytes provide niches for epiphytic microbes (including aerobic methanotrophs) growth. However, little is known about the impacts of submerged macrophytes growth status and nutrients loadings on methanotroph community and methane release in wetlands. In the present study, methane fluxes, bacterial and methanotroph community in epiphytic biofilm, and environmental parameters were investigated during Vallisneria natans senescence in wetlands under low (VnL) and high (VnH) nutrients for seven weeks. Relative conductivity and concentration of H₂O₂, total chlorophyll and malondialdehyde were higher in leaves of V. natans in VnH than VnL at the same sampling time. Nutrients loading increased methane fluxes in treatments with or without (Control) macrophytes, while healthy V. natans plants reduced the methane flux and nutrients concentration in water columns. CH₄ fluxes were positively correlated to temperature and COD (p < 0.05). Methane oxidation rates were 3.04-31.68 μmol methane mg^-1 fresh weight of V. natans leaves - epiphytic biofilm within 1 h. Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Actinobacteria and Acidobacteria were dominant phylum in all epiphytic biofilms. The mean abundances of pmoA/16S rRNA were higher in VnL than VnH. According to Illumina sequencing results of pmoA gene, γ-proteobacteria and α-proteobacteria were the dominant methanotroph class in epiphytic biofilm from VnH and VnL, respectively. Among seven detected methanotrophic genera, Methylomonas was significantly higher in VnH than VnL. Network analysis revealed that there were much closer relationships between the environmental parameters and epiphytic bacterial community in VnH than in VnL. COD and MDA were negatively correlated with Methyloglobulus, Methylosarcina, Methylobacter and Methylocystis, but positively correlated with Methylomonas and Methylosinus. This study highlights that methanotrophs in epiphytic biofilm play important roles in methane-oxidizing, which can be affected by plant physiological status and environmental parameters.

Eichhornia crassipes-rhizospheric biofilms contribute to nutrients removal and methane oxidization in wastewater stabilization ponds receiving simulative sewage treatment plants effluents

Wastewater stabilization ponds (WSPs) have been used in treating sewage treatment plants (STPs) effluents. However, little is known about the role of rhizospheric biofilms on methane release in WSPs with floating plants. In the present study, the nutrient removal, CH₄ fluxes, CH₄ oxidization potential and rhizospheric bacterial community were investigated in WSPs with Eichhornia crassipes under simulate STPs effluents for 31 days. At the end of the experiment, E. crassipes biomass was 5.60-8.81 times of initial weight and increased with increasing nutrients concentration. E. crassipes effectively reduced methane release and nutrients. Compared to control, E. crassipes reduced 52.30%-83.21% of CH₄ fluxes at water-atmosphere interface and had better inhibition effect on CH₄ fluxes in treatments with high nutrients. However, methane oxidization rates of E. crassipes roots were higher in low nutrients (0.83 ± 0.046 mg CH₄ (kg fresh plant)^-1 day^-1) than high nutrients (0.12 ± 0.04 mg CH₄ (kg fresh plant)^-1 day^-1). Structural equation modeling revealed that biomass of E. crassipes has negative effect on CH₄ fluxes (-0.453, p = 0.000). Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi and Actinobacteria were the predominant phyla in the rhizospheric biofilm of E. crassipes and contributed to nutrients removal. Aerobic methanotrophs and pomA abundances were higher in rhizospheric biofilm exposed to high nutrients than low nutrients and aerobic methanotrophs had close interactions with other microorganisms and participated in the carbon and nitrogen cycle, demonstrating that many bacteria harboring pmoA gene did not fully involve in methane oxidization. These data highlight plants E. crassipes have an important role in both reducing methane release and nutrients removal.

Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake

Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.

Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed

Bacterial communities associated with aquatic macrophytes largely influence host primary production and nutrient cycling in freshwater environments; however, little is known about how specific bacteria migrate to and proliferate at this unique habitat. Here, we separately identified bacterial genes involved in the initial colonization and overall fitness on plant surface, using the genome-wide transposon sequencing (Tn-seq) of Aquitalea magnusonii H3, a plant growth-promoting bacterium of the floating macrophyte, duckweed. Functional annotation of identified genes indicated that initial colonization efficiency might be simply explained by motility and cell surface structure, while overall fitness was associated with diverse metabolic and regulatory functions. Genes involved in lipopolysaccharides and type-IV pili biosynthesis showed different contributions to colonization and fitness, reflecting their metabolic cost and profound roles in host association. These results provide a comprehensive genetic perspective on aquatic-plant-bacterial interactions, and highlight the potential trade-off between bacterial colonization and proliferation abilities on plant surface.

Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch

The rivers in the megacities face a constant inflow of extremely polluted wastewaters from various sources, and their influence on the connected peri-urban river is still poorly understood. The riverine system in Pune consists of Rivers Mula, Ramnadi, Pawana, Mutha, and Mula-Mutha, traversing through the urban settlements of Pune before joining River Bhima in the peri-urban region. We used MinION-based metagenomic sequencing to generate a comprehensive understanding of the microbial diversity differences between the urban and peri-urban zones, which has not been explored at the meta scale until date. The taxonomic analysis revealed significant enrichment of pollution indicators microbial taxa (Welsch's t-test, p < 0.05, Benjamini-Hochberg FDR test) such as Bacteriodetes, Firmicutes, Spirochaetes, Synergistetes, Euryarcheota in the urban waters as compared to peri-urban waters. Further, the peri-urban waters showed a significantly higher prevalence of ammonium oxidising archaeal groups such as Nitrososphaeraceae (Student's t-test p-value <0.05 with FDR correction), thereby probably suggesting the influence of agricultural runoffs. Besides, the microbial community diversity assessment also indicated the significant dissimilarity in the microbial community of urban and peri-urban waters. Overall, the analysis predicted 295 virulence genes mapping to 38 different pathogenic bacteria in the riverine system. Moreover, the higher genome coverage (at least 60%) for priority pathogens such as Pseudomonas, Klebsiella, Acinetobacter, Escherichia, Aeromonas in the sediment metagenome consolidates their dominance in this riverine system. To conclude, our investigation showed that the unrestrained anthropogenic and related activities could potentially contribute to the overall dismal conditions and influence the connected riverine stretches on the outskirts of the city.

16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes

The rhizosphere of a plant is an important interface for the plant-microbe interaction that plays a significant role in the uptake and removal of heavy metal from contaminated sites. Eichhornia crassipes is a free-floating macrophyte and a well-known metal hyperaccumulator. It is a promising plant, which harbors a diverse microbial community in its rhizosphere. Therefore it is hypothesized that it can be a good habitat for microorganisms that supports plant growth and increases its phytoremediation potential. The rhizospheric DNA was extracted from the procured plant samples. The library was prepared and sequenced using the Illumina platform. 16S rRNA data from the Next Generation Sequencing (NGS) platform was analyzed using the QIIME software package. Alpha diversity was estimated from statistical indices i.e. Shannon index, Chao1 index, and observed species. The rarefaction plots, rank abundance curve, krona graph, and heat map were generated to study the rhizospheric community in detail. Metagenome consisted of 225,408 flash reads, 185,008 non-chimeric sequences with 17,578 Operational Taxonomic Units (OTU's), and 4622 OTU's without singletons. The data of present study are available at NCBI Bioproject (PRJNA631882). The taxonomic analysis of OTU's showed that the sequences belonged to major Phyla revealing the dominance of Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia. The most abundant Genera in the sampled rhizosphere recorded were Thiothrix and Flavobacterium.

Water hyacinth for energy and environmental applications: A review

This review is focused on the sustainable management of harvested water hyacinth (WH) via thermochemical conversion to carbonaceous materials (CMs), biofuels, and chemicals for energy and environmental applications. One of the major challenges in thermochemical conversion is to guarantee the phytoremediation performance of biochar and the energy conversion efficiency in biowaste-to-energy processes. Thus, a circular sustainable approach is proposed to improve the biochar and energy production. The co-conversion process can enhance the syngas, heat, and energy productions with high-quality products. The produced biochar should be economically feasible and comparable to available commercial carbon products. The removal and control of heavy and transition metals are essential for the safe implementation and management of WH biochar. CMs derived from biochar are of interest in wastewater treatment, air purification, and construction. It is important to control the size, shape, and chemical compositions of the CM particles for higher-value products like catalyst, adsorbent or conductor.

Responses of phytoremediation in urban wastewater with water hyacinths to extreme precipitation

Climate change not only intensifies eutrophication and enhances the rainfall, but also elevates the contents of greenhouse gases, which can further increase the intensity and frequency of extreme precipitation events. The effectivity of phytoremediation of urban wastewaters by water hyacinths under an extreme rainfall event (up to 380 mm d^-1) was investigated using self-designed fabrications with six flow rates (2-15 m³ d^-1) in situ on pilot scale for 30 days. The results suggest that water hyacinths had high N and P removal capacities even under adverse conditions such as low dissolved oxygen concentrations (DO, <1 mg L^-1) and high ammonium concentrations (NH₄⁺-N, >7 mg L^-1). Specifically, the highest removal yields of N and P were 13.14 ± 0.47 g N·m^-2·d^-1 and 2.12 ± 0.04 g P·m^-2·d^-1, respectively. The results indicate that water hyacinths can be used for water treatment to reduce the amounts of NH₄⁺-N, dissolved organic nitrogen (DON) and phosphate (PO₄^3-) even during extreme precipitation events. Moreover, DO increased due to wet deposition, runoff and surface flows during the extreme rainfall event, resulting in shifts between nitrification and denitrification processes which significantly altered nitrogen forms in urban wastewater. Results of this study suggest that water hyacinths could be recommended as a cost-effective and eco-friendly technology for urban wastewater phytoremediation in areas suffering from frequent extreme precipitation events.

Bacterial community characterization of the rhizobiome of plants belonging to Solanaceae family cultivated in desert soils

Purpose

The plant Solanaceae family is one of the most important for global agriculture and nutrition. Within this plant family, two plant species stand out for their economic importance and for human consumption, which are tomato (Solanum lycopersicum) and chili pepper (Capsicum annuum). Moreover, those plants support diverse and characteristic microbial communities that are uniquely suited to the plant habitat and intimately connected to plant health. The main objective of this work is the bacterial community characterization in the rhizobiome of tomato and chili pepper, cultivated in arid environments.

Methods

Five crop fields located in the south of the peninsula of Baja California, Mexico, were sampled. Total DNA was extracted from rhizosphere, rhizoplane, and endophytic root compartment and sequenced by Illumina MiniSeq platform technology applied to 16S rRNA gene V3 region.

Results

We were able to obtain 1,195,426 total reads and 1,725,258 total reads for tomato and chili pepper samples, respectively. The analysis of the bacterial community structures confirmed that the two plant species showed differences in their microbial community structures. Nonetheless, the microbial community structures were directly and equally influenced by the crop field localization of each plant species. Interestingly, we determined that in both plant species, the Proteobacteria was the main phylum.

Conclusion

In conclusion, we found that several bacterial families are part of the core rhizobiome (28 OTUs) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants.

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.