Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Simple Summary

Lignocellulosic material and substrate formulations affect mushroom productivity. The microbial community in cultivation substrates affects the quality of the substrates and the efficiency of mushroom production. The elucidation of the key microbes and their biochemical function can serve as a useful guide in the development of a more effective system for mushroom cultivation.

Abstract

Lignocellulosic materials commonly serve as base substrates for mushroom production. Cellulose, hemicellulose, and lignin are the major components of lignocellulose materials. The composition of these components depends upon the plant species. Currently, composted and non-composted lignocellulosic materials are used as substrates in mushroom cultivation depending on the mushroom species. Different substrate compositions can directly affect the quality and quantity of mushroom production yields. Consequently, the microbial dynamics and communities of the composting substrates can significantly affect mushroom production. Therefore, changes in both substrate composition and microbial diversity during the cultivation process can impact the production of high-quality substrates and result in a high degree of biological efficiency. A brief review of the current findings on substrate composition and microbial diversity for mushroom cultivation is provided in this paper. We also summarize the advantages and disadvantages of various methods of mushroom cultivation by analyzing the microbial diversity of the composting substrates during mushroom cultivation. The resulting information will serve as a useful guide for future researchers in their attempts to increase mushroom productivity through the selection of suitable substrate compositions and their relation to the microbial community.

Dynamics of fungal species related to nitrogen transformation and their network patterns during cattle manure-corn straw with biochar composting

Fungi are reputed to play a significant role in the composting matrix as decomposers of recalcitrant organic materials like cellulose and lignin. However, information on the fungi communities' roles in nitrogen transformation under a compost-biochar mixture is scarce. This study investigated shifts in fungal species mediating N transformation and their network patterns in cattle manure-corn straw (CMCS) and CMCS plus biochar (CMCB) composting using high-throughput sequencing data. The results revealed that the addition of biochar altered fungal richness and diversity and significantly influenced their compositions during composting. Biochar also altered the compost fungal network patterns; CMCS had a more complex network with higher positive links than CMCB, suggesting stable niche overlap. The consistent agreement of multivariate analyses (redundancy, network, regression, Mantel and path analyses) indicated that Ciliophora_sp in CMCS and unclassified_norank_Pleosporales in CMCB were the key fungal species mediating total N transformation, whereas Scedosporium_prolificans in CMCS and unclassified_Microascaceae in CMCB were identified as major predictive indices determining NO₃^--N transformation. Also, Coprinopsis cinerea and Penicillium oxalicum were the predictive factors for NH₄⁺-N transformation in CMCS and CMCB during composting. These results indicated that the effects of biochar on N conversions in composting could be unraveled using multivariate analyses on fungi community evolution, network patterns, and metabolism.

Finding a Balance in the Vaginal Microbiome: How Do We Treat and Prevent the Occurrence of Bacterial Vaginosis?

Bacterial vaginosis (BV) has been reported in one-third of women worldwide at different life stages, due to the complex balance in the ecology of the vaginal microbiota. It is a common cause of abnormal vaginal discharge and is associated with other health issues. Since the first description of anaerobic microbes associated with BV like Gardnerella vaginalis in the 1950s, researchers have stepped up the game by incorporating advanced molecular tools to monitor and evaluate the extent of dysbiosis within the vaginal microbiome, particularly on how specific microbial population changes compared to a healthy state. Moreover, treatment failure and BV recurrence rate remain high despite the standard antibiotic treatment. Consequently, researchers have been probing into alternative or adjunct treatments, including probiotics or even vaginal microbiota transplants, to ensure successful treatment outcomes and reduce the colonization by pathogenic microbes of the female reproductive tract. The current review summarizes the latest findings in probiotics use for BV and explores the potential of vaginal microbiota transplants in restoring vaginal health.

A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme

An actinomycete strain CSR-4 was isolated from the rhizosphere soil of Zingiber montanum. Taxonomic characterization revealed strain CSR-4 was a member of the genus Microbispora. Whole-genome sequence analysis exhibited the highest average nucleotide identity (ANI) value (95.34%) and digital DNA–DNA hybridization (DDH) value (74.7%) between strain CSR-4 and the closest relative M. hainanensis DSM 45428^T, which was in line with the assignment to same species. In addition, a new diterpene compound, 2α-hydroxy-8(14), 15-pimaradien-17, 18-dioic acid, and nine known compounds were isolated from the ethyl acetate crude extract of fermentation broth. Interestingly, a new diterpene displayed the suppressive effect on the recombinant human acetylcholinesterase (rhAChE) enzymes (IC₅₀ 96.87 ± 2.31 μg/ml). In silico studies based on molecular docking and molecular dynamics (MD) simulations were performed to predict a binding mode of the new compound into the binding pocket of the rhAChE enzyme and revealed that some amino acids in the peripheral anions site (PAS), anionic subsite, oxyanion site and catalytic active site (CAS) of the rhAChE have interacted with the compound. Therefore, our new compound could be proposed as a potential active human AChE inhibitor. Moreover, the new compound can protect significantly the neuron cells (% neuron viability = 88.56 ± 5.19%) from oxidative stress induced by serum deprivation method at 1 ng/ml without both neurotoxicities on murine P19-derived neuron cells and cytotoxicity against Vero cells.

Bioremediation of malachite green dye by two bacterial strains isolated from textile effluents

Globally, water pollution from the textile industries is an alarming issue. Malachite Green dye of the triphenylmethane group is an extensively used dye in the fabric industries that is emitted through textile wastewater. This study aimed to isolate and characterize potential Malachite Green (MG) dye degrading bacteria from textile effluents. Different growth and culture parameters such as temperature, pH and dye concentration were optimized to perform the dye-degradation assay using different concentrations of MG dye in the mineral salt medium. A photo-electric-colorimeter was used to measure the decolorizing activity of bacteria at different time intervals after aerobic incubation. Two potential bacterial strains of Enterobacter spp. CV-S1 (accession no: MH450229) and Enterobacter spp. CM-S1 (accession no: MH447289) were isolated from textile effluents exhibiting potential MG dye decoloring efficiency. Further, the RAPD analysis and 16S rRNA sequencing confirmed the genetic differences of the isolated strains. Enterobacter sp CV-S1 and Enterobacter sp CM-S1 can completely decolor MG dye up to 15 mg/L under shaking condition without any requirement of sole carbon source. Thus, these two bacteria have the potency to be utilized in the textile wastewater treatment plant.

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

Biotransformation strategies for steroid estrogen and androgen pollution

The common steroid hormones are estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2), and testosterone (T). These steroids are reported to contaminate the environment through wastewater treatment plants. Steroid estrogens are widespread in the aquatic environment and therefore pose a potential risk, as exposure to these compounds has adverse impacts on vertebrates. Excessive exposure to steroid estrogens causes endocrine disruption in aquatic vertebrates, which affects the normal sexual life of these animals. Steroid pollutants also cause several health problems in humans and other animals. Microbial degradation is an efficient method for removing hormone pollutants from the environment by remediation. Over the last two decades, microbial metabolism of steroids has gained considerable attention due to its higher efficiency to reduce pollutants from the environment. The present review is focused on the major causes of steroid pollution, concentrations of these pollutants in surface water, groundwater, drinking water, and wastewater, their effect on humans and aquatic animals, as well as recent efforts by various research groups that seek better ways to degrade steroids by aerobic and anaerobic microbial systems. Detailed overview of aerobic and anaerobic microbial biotransformation of steroid estrogens and testosterone present in the environment along with the active enzyme systems involved in these biotransformation reactions is described in the review article, which helps readers to understand the biotransformation mechanism of steroids in depth. Other measures such as co-metabolic degradation, consortia degradation, algal, and fungal steroid biotransformation are also discussed in detail.

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

BACKGROUND

Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.

RESULTS

Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.

CONCLUSIONS

Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.