From bacterial genomics to metagenomics: concept, tools and recent advances

Bioremediation of an industrial soil contaminated by hydrocarbons in microcosm system, involving bioprocesses utilizing co-products and agro-industrial wastes

The present study describes practical implication of bioaugmentation and biostimulation processes for bioremediation of an industrial soil chronically contaminated by hydrocarbons. For this purpose, biomass production of six autochthonous hydrocarbon-degrading bacteria were evaluated as inoculum of bioaugmentation strategy, by testing carbon and nitrogen sources included co-products and agro-industrial waste as sustainable and low-cost components of the growth medium. Otherwise, biostimulation was approached by the addition of optimized concentration of nitrogen and phosphorus. Microcosm assays showed that total hydrocarbons (TH) were significantly removed from chronically contaminated soil undergoing bioremediation treatment. Systems Mix (bioaugmentation); N,P (biostimulation) and Mix + N,P (bioaugmentation and biostimulation) reached higher TH removal, being 89.85%, 91.00%, 93.04%, respectively, comparing to 77.83% of system C (natural attenuation) at 90 days. The increased heterotrophic aerobic bacteria and hydrocarbon degrading bacteria counts were according to TH biodegrading process during the experiments. Our results showed that biostimulation with nutrients represent a valuable alternative tool to treat a chronically hydrocarbon-contaminated industrial soil, while bioaugmentation with a consortium of hydrocarbon degrading bacteria would be justified when the soil has a low amount of endogenous degrading microorganisms. Furthermore, the production of inoculum for application in bioaugmentation using low-cost substrates, such as industrial waste, would lead to the development of an environmentally friendly and attractive process in terms of cost-benefit.

Microbial Technologies Employed for Biodegradation of Neonicotinoids in the Agroecosystem

Neonicotinoids are synthetic pesticides widely used for the control of various pests in agriculture throughout the world. They mainly attack the nicotinic acetylcholine receptors, generate nervous stimulation, receptor clot, paralysis and finally cause death. They are low volatile, highly soluble and have a long half-life in soil and water. Due to their extensive use, the environmental residues have immensely increased in the last two decades and caused many hazardous effects on non-target organisms, including humans. Hence, for the protection of the environment and diversity of living organism's the degradation of neonicotinoids has received widespread attention. Compared to the other methods, biological methods are considered cost-effective, eco-friendly and most efficient. In particular, the use of microbial species makes the degradation of xenobiotics more accessible fast and active due to their smaller size. Since this degradation also converts xenobiotics into less toxic substances, the various metabolic pathways for the microbial degradation of neonicotinoids have been systematically discussed. Additionally, different enzymes, genes, plasmids and proteins are also investigated here. At last, this review highlights the implementation of innovative tools, databases, multi-omics strategies and immobilization techniques of microbial cells to detect and degrade neonicotinoids in the environment.

Bacterial community analysis on Sclerotium-suppressive soil

Difficulties in controlling the soil-borne plant pathogenic fungus Sclerotium rolfsii favoured the analysis of its suppressive soil for better understanding. In the present study, culture-independent molecular technique was used to analyse the bacterial communities of suppressive soil and conducive soil. Hence, metagenomic DNAs from both kinds of soils were directly extracted and their sequence polymorphism was analysed by targeting hypervariable domains, V4 + V5, of the 16S rRNA gene. The results of 16S rRNA gene-driven bacterial community diversity analysis along with soil physicochemical and biological properties clearly discriminated S. rolfsii suppressive soil from conducive soil. The dominant phylogenetic group of suppressive soil is Actinobacteria followed by Proteobacteria. The other groups include Acidobacteria, Firmicutes and Cyanobacteria. In contrast, conducive soil had very few Actinobacterial sequences and was dominated by Gamma- and Betaproteobacteria. Based on the relative proportion of different bacterial communities, their diversity and species richness were observed more in suppressive soil than in conducive soil. The present study identifies the dominant bacterial community which shares S. rolfsii suppressiveness.

Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples

Metagenomics is the study of gene pool of an entire community in a particular niche. This provides valuable information about the functionality of host-microbe interaction in a biological ecosystem. Efficient metagenomic DNA extraction is a critical pre-requisite for a successful sequencing run in a metagenomic study. Although isolation of human stool metagenomic DNA is fairly standardized, the same protocol does not work as efficiently in fecal DNA from other organisms. In this study, we report a comparison of manual and commercial DNA extraction methods for diverse samples such as human stool, fish gut and soil. Fishes are known to have variable microbial diversity based on their food habits, so the study included two different varieties of fishes. A modified protocol for effective isolation of metagenomic DNA from human milk samples is also reported, highlighting critical precautions. Recent studies have emphasized the importance of studying functionality of human milk metagenome to understand its influence on infants' health. While manual method works well with most samples and therefore can be a method of choice for testing new samples, broad-range commercial kit offers advantage of high purity and quality. DNA extraction of different samples would go a long way in unraveling the unexplored association between microbes and host in a biological system.

Pakchoi Antioxidant Improvement and Differential Rhizobacterial Community Composition under Organic Fertilization

A high level of antioxidants in organic-produced vegetables has been attributed to soil conditions; however, little is known about the relationships between antioxidants and rhizobacteria under different fertilization treatments. A pot trial for pakchoi (Brassica campestris ssp. chinensis L.) was conducted under greenhouse conditions with: (1) control; (2) chemical fertilizer; and (3) organic fertilizer. The responses of the plant, soil properties, and rhizobacterial community were measured after 45 days of cultivation. Fertilization increased soil nutrient levels and pakchoi productivity and the reshaped rhizobacterial community structure, while no differences in rhizobacterial abundance and total diversity were observed. Generally, most plant antioxidants were negatively correlated with inorganic nitrogen (N) and positively correlated to organic N in soil. The genera of Arthrospira and Acutodesmus contained differential rhizobacteria under chemical fertilizer treatment, which are known as copiotrophs. In addition, the addition of a chemical fertilizer may stimulate organic substance turnover by the enrichment of organic compound degraders (e.g., Microbacterium and Chitinophaga) and the promotion of predicted functional pathways involved in energy metabolism. Several beneficial rhizobacteria were associated with organic fertilizer amended rhizosphere including the genera Bacillus, Mycobacterium, Actinomycetospora, and Frankia. Furthermore, Bacillus spp. were positively correlated with plant biomass and phenolic acid. Moreover, predictive functional profiles of the rhizobacterial community involved in amino acid metabolism and lipid metabolism were significantly increased under organic fertilization, which were positively correlated with plant antioxidant activity. Overall, our study suggests that the short-term application of chemical and organic fertilizers reshapes the rhizobacterial community structure, and such changes might contribute to the plant’s performance.

Cell Therapies in Tendon, Ligament, and Musculoskeletal System Repair

In the last few decades, several techniques have been used to optimize tendon, ligament, and musculoskeletal healing. The evidence in favor of these techniques is still not proven, and level I studies are lacking. We performed an analysis of the therapeutic strategies and tissue engineering projects recently published in this field. Here, we try to give an insight into the current status of cell therapies and the latest techniques of bioengineering applied to the field of orthopedic surgery. The future areas for research in the management of musculoskeletal injuries are outlined. There are emerging technologies developing into substantial clinical treatment options that need to be critically evaluated. Mechanical stimulation of the constructs reproduces a more propitious environment for effective healing.

Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches

The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).

Insights in Waste Management Bioprocesses Using Genomic Tools

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development

The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.

Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.

Metagenome-based analysis: a promising direction for plankton ecological studies

The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870 s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.