Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems

Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.

Characterization of the composition, structure, and functional potential of bamboo rhizosphere archaeal communities along a chromium gradient

Introduction

Bamboo can be used in the phytoremediation of heavy metal pollution. However, the characteristics of the bamboo rhizosphere archaeal community in Cr-contaminated soil under field conditions remain unclear.

Methods

In this study, high-throughput sequencing was used to examine the rhizosphere soil archaeal communities of Lei bamboo (Phyllostachys precox) plantations along a Cr pollution gradient.

Results

The results revealed U-shaped relationships between Cr [total Cr (TCr) or HCl-extractable Cr (ACr)] and two alpha indices (Chao1 and Shannon) of archaea. We also established that high Cr concentrations were associated with a significant increase in the abundance of Thaumarchaeota and significant reductions in the abundances of Crenarchaeota and Euryarchaeota. The archaeal co-occurrence networks reduced in complexity with Cr pollution, decreasing the community's resistance to environmental disturbance. Candidatus nitrosotalea and Nitrososphaeraceae_unclassified (two genera of Thaumarchaeota) were identified as keystone taxa. The community structure of soil archaeal communities was also found to be affected by TCr, ACr, pH, total organic C, and available nutrient (N, P, and K) concentrations, with pH being identified as the most reliable predictor of the archaeal community in assessed soils.

Discussion

These findings enhance our understanding of microbial responses to Cr pollution and provide a basis for developing more refined approaches for the use of bamboo in the remediation of Cr-contaminated soils.

Metatranscriptomic insight into the possible role of clay microbiome in skin disease management

Even though the scientific documentation is limited, microbiome of healing clay is gradually gaining attention of the scientific community, as a therapeutic force playing an indispensable role in skin disease management. The present study explores the metatranscriptome profile of the Chamliyal clay, widely known for its efficacy in managing various skin problems, using Illumina NextSeq sequencing technology. The gene expression profile of the clay microbial community was analyzed through SEED subsystems of the MG-RAST server. Due to the unavailability of metatranscriptomic data on other therapeutic clays, Chamliyal's profile was compared to non-therapeutic soils, as well as healthy and diseased human skin microbiomes. The study identified Firmicutes, Proteobacteria, and Actinobacteria as the primary active microbial phyla in Chamliyal clay. These resemble those abundant in a healthy human skin microbiome. This is significant as lower levels of these phyla in the skin are linked to inflammatory skin conditions like psoriasis. Interestingly, pathogenic microbes actively metabolizing in the clay were absent. Importantly, 6% of the transcripts annotated to sulfur and iron metabolism, which are known to play a major role in skin disease management. This study provides the most comprehensive and a novel overview of the metatranscriptome of any of the healing clay available worldwide. The findings offer valuable insights into the clay microbiome's potential in managing skin disorders, inspiring future endeavors to harness these insights for medical applications.

Biodegradation of Pollutants in the Environment: Omics Approaches

This special edition intends to highlight how omics approaches have been used in biodegradation studies to understand the mechanisms involved and improve biodegradation processes [...].

A review on control and abatement of soil pollution by heavy metals: Emphasis on artificial intelligence in recovery of contaminated soil

"Save Soil Save Earth" is not just a catchphrase; it is a necessity to protect soil ecosystem from the unwanted and unregulated level of xenobiotic contamination. Numerous challenges such as type, lifespan, nature of pollutants and high cost of treatment has been associated with the treatment or remediation of contaminated soil, whether it be either on-site or off-site. Due to the food chain, the health of non-target soil species as well as human health were impacted by soil contaminants, both organic and inorganic. In this review, the use of microbial omics approaches and artificial intelligence or machine learning has been comprehensively explored with recent advancements in order to identify the sources, characterize, quantify, and mitigate soil pollutants from the environment for increased sustainability. This will generate novel insights into methods for soil remediation that will reduce the time and expense of soil treatment.

Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture

The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.