Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis

Insights into the community structure and environmental functions of water hyacinth rhizobiome in urban river ecosystem

Water hyacinth (WH) is a widespread floating invasive aquatic plant with a prolific reproductive and dispersion rate. With the aid of its root-associated microbes, WH significantly modulates the ecosystem's functioning. Despite their irrevocable importance, the WH microbiome remains unexplored in detail. Here, we present a shotgun sequencing analysis of WH rhizobiome predominant in urban rivers and their surrounding water to unveil the diversity drivers and functional relationship. The core microbiome of the WH mainly consisted of the methane-metabolizing archaebacteria and sulfate-reducing bacteria, which are probably driving the methane and sulfur metabolic flux along the vegetative zone in the water. The beta diversity analysis revealed temporal variations (River WH_2020 vs. WH_2022) (R of 0.8 to 1 and R2 of 0.17 to 0.41), which probably could be attributed to the transient taxa as there was a higher sharing of core bacteria (48%). Also, the WH microbiome significantly differed (R = 0.46 to 1.0 and R2 of 0.18 to 0.52) from its surrounding water. Further, the functional analysis predicted 140 pollutant-degrading enzymes (PDEs) well-implicated in various xenobiotic pollutant degradation, including hydrocarbons, plastics, and aromatic dyes. These PDEs were mapped to bacterial genera such as Hydrogenophaga, Ideonella, Rubrivivax, Dechloromonas, and Thauera, which are well-reported for facilitating the metabolism of xenobiotic compounds. The higher prevalence of metal and biocide resistance genes further highlighted the persistence of resistant microbes assisting WH in bioremediation applications.

AlphaFun: Structural-Alignment-Based Proteome Annotation Reveals why the Functionally Unknown Proteins (uPE1) Are So Understudied

With the rapid expansion of sequencing of genomes, the functional annotation of proteins becomes a bottleneck in understanding proteomes. The Chromosome-centric Human Proteome Project (C-HPP) aims to identify all proteins encoded by the human genome and find functional annotations for them. However, until now there are still 1137 identified human proteins without functional annotation, called uPE1 proteins. Sequence alignment was insufficient to predict their functions, and the crystal structures of most proteins were unavailable. In this study, we demonstrated a new functional annotation strategy, AlphaFun, based on structural alignment using deep-learning-predicted protein structures. Using this strategy, we functionally annotated 99% of the human proteome, including the uPE1 proteins and missing proteins, which have not been identified yet. The accuracy of the functional annotations was validated using the known-function proteins. The uPE1 proteins shared similar functions to the known-function PE1 proteins and tend to express only in very limited tissues. They are evolutionally young genes and thus should conduct functions only in specific tissues and conditions, limiting their occurrence in commonly studied biological models. Such functional annotations provide hints for functional investigations on the uPE1 proteins. This proteome-wide-scale functional annotation strategy is also applicable to any other species.

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.

The Multifaceted Function of Water Hyacinth in Maintaining Environmental Sustainability and the Underlying Mechanisms: A Mini Review

Water hyacinth (Eichhornia crassipes) (WH) is a widespread aquatic plant. As a top invasive macrophyte, WH causes enormous economic and ecological losses. To control it, various physical, chemical and biological methods have been developed. However, multiple drawbacks of these methods limited their application. While being a noxious macrophyte, WH has great potential in many areas, such as phytoremediation, manufacture of value-added products, and so on. Resource utilization of WH has enormous benefits and therefore, is a sustainable strategy for its control. In accordance with the increasing urgency of maintaining environmental sustainability, this review concisely introduced up to date WH utilization specifically in pollution remediation and curbing the global warming crisis and discussed the underlying mechanisms.

Phytochemicals and Allelopathy of Induced Water Hyacinth against Microcystis aeruginosa

Induced water hyacinth with purple roots (PRWH) exerts a significant inhibitory effect on the growth of blue-green algae. Interestingly, its chemical constituents differ from those of wild-type water hyacinth and have not yet been reported. This study aimed to explore the chemical constituents of PRWH and its bioactive components serving as allelopathic agents against blue-green algae. Phytochemical investigation of the bioactive ethyl acetate fraction of a crude methanol extract from PRWH led to the isolation of 56 compounds, including 11 new phenylphenalene derivatives. The structures of these compounds were elucidated by comprehensive analyses through NMR, HRMS, and X-ray techniques. Bioactivity evaluation against Microcystis aeruginosa indicated that compounds 7, 12, 15, 37, 39, 45, and 47 potently inhibited blue-green algae growth.

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.

Autoactivation of Translation Causes the Bloom of Prorocentrum donghaiense in Harmful Algal Blooms

Harmful algal blooms (HABs) are symptomatic of ecosystem imbalance, leading to major worldwide marine natural disasters, and seriously threaten the human health. Some HAB algae's exceptional genome size prohibited the genomic investigations on molecular mechanisms, for example, Prorocentrum. This study performed translatome sequencing (RNC-seq) for Prorocentrum donghaiense to assemble the translatome reference sequences on appropriate cost to enable the global molecular study at translatome and proteome levels. By analyzing the translatome and proteome of P. donghaiense in phosphor-rich, phosphor-deficient, and phosphor-restored media, we found massive up-regulation of energy and material production pathways in phosphor-rich conditions that enables autoactivation of translation, which is the key to its exponential growth in HABs. To break down the autoactivation, we demonstrated that mild translation delay using very low concentrations of cycloheximide efficiently controls the blooming without harming other aquatic organisms and humans. Our result provides a novel hint for controlling HABs and demonstrated the RNC-seq as an economic strategy on investigating functions of organisms with large and unknown genomes.

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.

IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

Smut fungi as a stratagem to characterize rust effectors: opportunities and challenges

The rust pathogens are one of the most complex fungi in the Basidiomycetes. The development of genomic resources for rust and other plant pathogens has opened the opportunities for functional genomics of fungal genes. Despite significant progress in the field of fungal genomics, functional characterization of the genome components has lacked, especially for the rust pathogens. Their obligate nature and lack of standard stable transformation protocol are the primary reasons for rusts to be one of the least explored genera despite its significance. In the recently sequenced rust genomes, a vast catalogue of predicted effectors and pathogenicity genes have been reported. However, most of these candidate genes remained unexplored due to the lack of suitable characterization methods. The heterologous expression of putative effectors in Nicotiana benthamiana and Arabidopsis thaliana has proved to be a rapid screening method for identifying the role of these effectors in virulence. However, no fungal system has been used for the functional validation of these candidate genes. The smuts, from the evolutionary point of view, are closely related to the rust pathogens. Moreover, they have been widely studied and hence could be a suitable model system for expressing rust fungal genes heterologously. The genetic manipulation methods for smuts are also well standardized. Complementation assays can be used for functional validation of the homologous genes present in rust and smut fungal pathogens, while the species-specific proteins can be expressed in the mutant strains of smut pathogens having reduced or no virulence for virulence analysis. We propose that smuts, especially Ustilago maydis, may prove to be a good model system to characterize rust effector proteins in the absence of methods to manipulate the rust genomes directly.

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

Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.