Genomic and Physiological Investigation of Heavy Metal Resistance from Plant Endophytic Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum

Functional differences of cultivable leaf-associated microorganisms in the native Andean tree Gevuina avellana Mol. (Proteaceae) exposed to atmospheric contamination

AIMS

This study aimed to evaluate and describe the functional differences of cultivable bacteria and fungi inhabiting the leaves of Gevuina avellana Mol. (Proteaceae) in an urban area with high levels of air pollution and in a native forest in the southern Andes.

METHODS AND RESULTS

Phyllosphere microorganisms were isolated from the leaves of G. avellana, their plant growth-promoting capabilities were estimated along with their biocontrol potential and tolerance to metal(loid)s. Notably, plants from the urban area showed contrasting culturable leaf-associated microorganisms compared to those from the native area. The tolerance to metal(loid)s in bacteria range from 15 to 450 mg l-1 of metal(loid)s, while fungal strains showed tolerance from 15 to 625 mg l-1, being especially higher in the isolates from the urban area. Notably, the bacterial strain Curtobacterium flaccumfaciens and the fungal strain Cladosporium sp. exhibited several plant-growth-promoting properties along with the ability to inhibit the growth of phytopathogenic fungi.

CONCLUSIONS

Overall, our study provides evidence that culturable taxa in G. avellana leaves is directly influenced by the sampling area. This change is likely due to the presence of atmospheric pollutants and diverse microbial symbionts that can be horizontally acquired from the environment.

Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation

Natural and anthropogenic causes are continually growing sources of metals in the ecosystem; hence, heavy metal (HM) accumulation has become a primary environmental concern. HM contamination poses a serious threat to plants. A major focus of global research has been to develop cost-effective and proficient phytoremediation technologies to rehabilitate HM-contaminated soil. In this regard, there is a need for insights into the mechanisms associated with the accumulation and tolerance of HMs in plants. It has been recently suggested that plant root architecture has a critical role in the processes that determine sensitivity or tolerance to HMs stress. Several plant species, including those from aquatic habitats, are considered good hyperaccumulators for HM cleanup. Several transporters, such as the ABC transporter family, NRAMP, HMA, and metal tolerance proteins, are involved in the metal acquisition mechanisms. Omics tools have shown that HM stress regulates several genes, stress metabolites or small molecules, microRNAs, and phytohormones to promote tolerance to HM stress and for efficient regulation of metabolic pathways for survival. This review presents a mechanistic view of HM uptake, translocation, and detoxification. Sustainable plant-based solutions may provide essential and economical means of mitigating HM toxicity.

Copper removal capability and genomic insight into the lifestyle of copper mine inhabiting Micrococcus yunnanensis GKSM13

Heavy metal pollution in mining areas is a serious environmental concern. The exploration of mine-inhabiting microbes, especially bacteria may use as an effective alternative for the remediation of mining hazards. A highly copper-tolerant strain GKSM13 was isolated from the soil of the Singhbhum copper mining area and characterized for significant copper (Cu) removal potential and tolerance to other heavy metals. The punctate, yellow-colored, coccoid strain GKSM13 was able to tolerate 500 mg L^-1 Cu²⁺. Whole-genome sequencing identified strain GKSM13 as Micrococcus yunnanensis, which has a 2.44 Mb genome with 2176 protein-coding genes. The presence of putative Cu homeostasis genes and other heavy metal transporters/response regulators or transcription factors may responsible for multi-metal resistance. The maximum Cu²⁺ removal of 89.2% was achieved at a pH of 7.5, a temperature of 35.5 °C, and an initial Cu²⁺ ion concentration of 31.5 mg L^-1. Alteration of the cell surface, deposition of Cu²⁺ in the bacterial cell, and the involvement of hydroxyl, carboxyl amide, and amine groups in Cu²⁺ removal were observed using microscopic and spectroscopic analysis. This study is the first to reveal a molecular-based approach for the multi-metal tolerance and copper homeostasis mechanism of M. yunnanensis GKSM13.

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

Secondary metabolites from methylotrophic bacteria: their role in improving plant growth under a stressed environment

Climate change is considered a natural disaster that causes the ecosystem to fluctuate and increase temperature, as well as the amount of UV radiation (UV-A and UV-B) on the Earth's surface. Consequently, greenhouse gases such as chlorofluorocarbons, methane, nitrogen oxide, and carbon dioxide have become obstacles to the development of sustainable agriculture. To overcome environmental stress such as phytopathogens, drought, salinity, heavy metals, and high-low temperatures, the utilization of microorganisms is a viable option. The synthesis of secondary metabolites by methylotrophic bacteria improves plant metabolism, enhances tolerance, and facilitates growth. The genus Methylobacterium is a pink-pigmented facultative methylotrophs which abundantly colonizes plants, especially young leaves, owing to the availability of methanol. Secondary metabolites such as amino acids, carotenoids, hormones, antimicrobial compounds, and other compounds produced by methylotrophic bacteria enhance plant metabolism under stress conditions. Therefore, in this review, we discuss the role of secondary metabolites produced by methylotrophic bacteria and their role in promoting plant growth under stress.

Isolation and screening of low-density polyethylene (LDPE) bags degrading bacteria from Addis Ababa municipal solid waste disposal site “Koshe”

Purpose

This study aims to screen bacterial isolates from the Addis Ababa municipal solid waste dumping site (Koshe) for the biodegradation of low-density polyethylene bags and analyzes their efficiency in degrading plastic bags.

Methods

In this study, low-density polyethylene bag-degrading bacteria were isolated from the Koshe municipal solid waste disposal area in Addis Ababa, Ethiopia. Screening of isolates for low-density polyethylene bag biodegradation was carried out using a clear zone method. Additionally, the efficiency of the isolates for low-density polyethylene biodegradation was evaluated using the weight loss method, scanning electron microscopy analysis, and Fourier transform infrared analysis. Finally, molecular identification of potential low-density polyethylene degrader bacterial isolates was done by 16S rDNA sequencing.

Results

Isolates KS35, KS14, and KS119 resulted in significant weight loss of low-density polyethylene film (42.87 ± 1.91%, 37.2 ± 3.06%, and 23.87 ± 0.11% weight loss, respectively). These isolates were selected for further biodegradation study using scanning electron microscopy and Fourier transform infrared analysis. Scanning electron microscopy analysis shows the formation of pores, pits, and distortion of the plastic surface. Fourier transform infrared analysis indicates the appearance of new peaks at the surface of low-density polyethylene films. Phylogenetic analysis of the three potential bacterial isolates was also carried out, and the result indicates that the sequence of isolate KS35 had 99% similarity with sequences of Methylobacterium radiotolerans MN525302. Isolate KS119 had 100% similarity with Methylobacterium fujisawaense KT720189, and the sequence of isolate KS14 had 99% similarity with species of Lysinibacillus fusiformis.

Conclusions

Weight loss, scanning electron microscopy analysis, and Fourier transform infrared analysis results show that isolates KS35, KS14, and KS119 have high potential in degrading low-density polyethylene bags.

Airborne Prokaryotic, Fungal and Eukaryotic Communities of an Urban Environment in the UK

Bioaerosols often contain human pathogens and allergens affecting public health. However, relatively little attention has been given to bioaerosols compared with non-biological aerosols. In this study, we aimed to identify bioaerosol compositions in Manchester, UK by applying high throughput sequencing methods and to find potential sources. Samples were collected at Manchester Air Quality Super Site at the Firs Environmental Research Station in November 2019 and in February 2020. Total DNA has been extracted and sequenced targeting the 16S rRNA gene of prokaryotes, ITS region of fungal DNA and 18S rRNA gene of eukaryotes. We found marine environment-associated bacteria and archaea were relatively more abundant in the February 2020 samples compared with the November 2019 samples, consistent with the North West marine origin based on wind back-trajectory analysis. In contrast, an OTU belonging to Methylobacterium, which includes many species resistant to heavy metals, was relatively more abundant in November 2019 when there were higher metal concentrations. Fungal taxa that fruit all year were relatively more abundant in the February 2020 samples while autumn fruiting species generally had higher relative abundance in the November 2019 samples. There were higher relative abundances of land plants and algae in the February 2020 samples based on 18S rRNA gene sequencing. One of the OTUs belonging to the coniferous yew genus Taxus was more abundant in the February 2020 samples agreeing with the usual pollen season of yews in the UK which is from mid-January until late April. The result from this study suggests a potential application of bioaerosol profiling for tracing the source of atmospheric particles.

Bacterial Biosorbents, an Efficient Heavy Metals Green Clean-Up Strategy: Prospects, Challenges, and Opportunities

Rapid industrialization has led to the pollution of soil and water by various types of contaminants. Heavy metals (HMs) are considered the most reactive toxic contaminants, even at low concentrations, which cause health problems through accumulation in the food chain and water. Remediation using conventional methods, including physical and chemical techniques, is a costly treatment process and generates toxic by-products, which may negatively affect the surrounding environment. Therefore, biosorption has attracted significant research interest in the recent decades. In contrast to existing methods, bacterial biomass offers a potential alternative for recovering toxic/persistent HMs from the environment through different mechanisms for metal ion uptake. This review provides an outlook of the advantages and disadvantages of the current bioremediation technologies and describes bacterial groups, especially extremophiles with biosorbent potential for heavy metal removal with relevant examples and perspectives.

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.