Technological Microbiology: Development and Applications

Synthetic extremophiles via species-specific formulations improve microbial therapeutics

Microorganisms typically used to produce food and pharmaceuticals are now being explored as medicines and agricultural supplements. However, maintaining high viability from manufacturing until use remains an important challenge, requiring sophisticated cold chains and packaging. Here we report synthetic extremophiles of industrially relevant gram-negative bacteria (Escherichia coli Nissle 1917, Ensifer meliloti), gram-positive bacteria (Lactobacillus plantarum) and yeast (Saccharomyces boulardii). We develop a high-throughput pipeline to define species-specific materials that enable survival through drying, elevated temperatures, organic solvents and ionizing radiation. Using this pipeline, we enhance the stability of E. coli Nissle 1917 by more than four orders of magnitude over commercial formulations and demonstrate its capacity to remain viable while undergoing tableting and pharmaceutical processing. We further show, in live animals and plants, that synthetic extremophiles remain functional against enteric pathogens and as nitrogen-fixing plant supplements even after exposure to elevated temperatures. This synthetic, material-based stabilization enhances our capacity to apply microorganisms in extreme environments on Earth and potentially during exploratory space travel.

Harnessing bacterial endophytes for environmental resilience and agricultural sustainability

In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.

Sustainable agriculture: leveraging microorganisms for a circular economy

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.

A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation

Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.

Gut microbiota and traumatic central nervous system injuries: Insights into pathophysiology and therapeutic approaches

Traumatic brain injury and spinal cord injury are two distinct but fundamentally similar types of acute insults to the central nervous system (CNS) that often culminate in death or cognitive and motor impairment. Over the past decade, researchers have tapped into research to discover the potential role being played by gut bacteria in CNS. After an acute CNS injury, the altered composition of the gut microbiota disturbs the balance of the bidirectional gut-brain axis, aggravating secondary CNS injury, motor dysfunctions, and cognitive deficits, which worsens the patient's prognosis. Some of the well-known therapeutic interventions which can also be used as adjuvant therapy for alleviating CNS injuries include, the use of pro and prebiotics, fecal microbiota transplantation, and microbial engineering. In this review, we aim to discuss the importance of gut microbes in our nervous system, anatomy, and signaling pathways involved in regulating the gut-brain axis, the alteration of the gut microbiome in CNS injuries, and the therapeutic strategies to target gut microbiomes in traumatic CNS injuries.

Single-Cell Proteins Obtained by Circular Economy Intended as a Feed Ingredient in Aquaculture

The constant increment in the world's population leads to a parallel increase in the demand for food. This situation gives place the need for urgent development of alternative and sustainable resources to satisfy this nutritional requirement. Human nutrition is currently based on fisheries, which accounts for 50% of the fish production for human consumption, but also on agriculture, livestock, and aquaculture. Among them, aquaculture has been pointed out as a promising source of animal protein that can provide the population with high-quality protein food. This productive model has also gained attention due to its fast development. However, several aquaculture species require considerable amounts of fish protein to reach optimal growth rates, which represents its main drawback. Aquaculture needs to become sustainable using renewable source of nutrients with high contents of proteins to ensure properly fed animals. To achieve this goal, different approaches have been considered. In this sense, single-cell protein (SCP) products are a promising solution to replace fish protein from fishmeal. SCP flours based on microbes or algae biomass can be sustainably obtained. These microorganisms can be cultured by using residues supplied by other industries such as agriculture, food, or urban areas. Hence, the application of SCP for developing innovative fish meal offers a double solution by reducing the management of residues and by providing a sustainable source of proteins to aquaculture. However, the use of SCP as aquaculture feed also has some limitations, such as problems of digestibility, presence of toxins, or difficulty to scale-up the production process. In this work, we review the potential sources of SCP, their respective production processes, and their implementation in circular economy strategies, through the revalorization and exploitation of different residues for aquaculture feeding purposes. The data analyzed show the positive effects of SCP inclusion in diets and point to SCP meals as a sustainable feed system. However, new processes need to be exploited to improve yield. In that direction, the circular economy is a potential alternative to produce SCP at any time of the year and from various cost-free substrates, almost without a negative impact.

Characterization of symbiotic and nitrogen fixing bacteria

Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.

Fermented Foods, Health and the Gut Microbiome

Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.

What Drives a Future German Bioeconomy? A Narrative and STEEPLE Analysis for Explorative Characterisation of Scenario Drivers

A future bioeconomy pursues the transformation of the resource base from fossil to renewable materials in an effort to develop a holistic, sustainable production and provision system. While the significance of this change in the German context is not yet entirely explored, scenarios analysing possible pathways could support the understanding of these changes and their systemic implications. Bioeconomy in detail depends on respective framework conditions, such as the availability of biomass or technological research priorities. Thus, for scenario creation, transferable methods for flexible input settings are needed. Addressing this issue, the study identifies relevant bioeconomy scenario drivers. With the theoretical approach of narrative analysis, 92 statements of the German National Bioeconomy Strategy 2020 have been evaluated and 21 international studies in a STEEPLE framework were assessed. For a future German bioeconomy 19 important drivers could be determined and specific aspects of the resource base, production processes and products as well as overarching issues were exploratively characterised on a quantitative and qualitative basis. The developed method demonstrate an approach for a transparent scenario driver identification that is applicable to other strategy papers. The results illustrate a possible future German bioeconomy that is resource- and technology-driven by following a value-based objective, and which is supplied by biogenic residue and side product feedstocks. As such, the bioeconomy scenario drivers can be used as a starting point for future research like scenario development or modelling of a future German bioeconomy.

Advantages and disadvantages of non-starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics

Traditional fermented foods are a significant source of starter and/or non-starter lactic acid bacteria (nsLAB). Moreover, these microorganisms are also known for their role as probiotics. The potential of nsLAB is huge; however, there are still challenges to be overcome with respect to characterization and application. In the present review, the most important steps that autochthonous lactic acid bacteria isolated from fermented foods need to overcome, to qualify as novel starter cultures, or as probiotics, in food technology and biotechnology, are considered. These different characterization steps include precise identification, detection of health-promoting properties, and safety evaluation. Each of these features is strain specific and needs to be accurately determined. This review highlights the advantages and disadvantages of nsLAB, isolated from traditional fermented foods, discussing safety aspects and sensory impact.

Recent Development of Ruminant Vaccine Against Viral Diseases

Pathogens of viral origin produce a large variety of infectious diseases in livestock. It is essential to establish the best practices in animal care and an efficient way to stop and prevent infectious diseases that impact animal husbandry. So far, the greatest way to combat the disease is to adopt a vaccine policy. In the fight against infectious diseases, vaccines are very popular. Vaccination's fundamental concept is to utilize particular antigens, either endogenous or exogenous to induce immunity against the antigens or cells. In light of how past emerging and reemerging infectious diseases and pandemics were handled, examining the vaccination methods and technological platforms utilized for the animals may provide some useful insights. New vaccine manufacturing methods have evolved because of developments in technology and medicine and our broad knowledge of immunology, molecular biology, microbiology, and biochemistry, among other basic science disciplines. Genetic engineering, proteomics, and other advanced technologies have aided in implementing novel vaccine theories, resulting in the discovery of new ruminant vaccines and the improvement of existing ones. Subunit vaccines, recombinant vaccines, DNA vaccines, and vectored vaccines are increasingly gaining scientific and public attention as the next generation of vaccines and are being seen as viable replacements to conventional vaccines. The current review looks at the effects and implications of recent ruminant vaccine advances in terms of evolving microbiology, immunology, and molecular biology.

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses

The use of bioinformatic tools for read-based taxonomic and functional analyses of metagenomic data sets, including their assembly and management, is rather fragmentary due to the absence of an accepted gold standard. Moreover, most currently available software tools need input of millions of reads and rely on approximations in data analysis in order to reduce computing times. These issues result in suboptimal results in terms of accuracy, sensitivity, and specificity when used either for the reconstruction of taxonomic or functional profiles through read analysis or analysis of genomes reconstructed by metagenomic assembly. Moreover, the recent introduction of novel DNA sequencing technologies that generate long reads, such as Nanopore and PacBio, represent a valuable data resource that still suffers from a lack of dedicated tools to perform integrated hybrid analysis alongside short read data. In order to overcome these limitations, here we describe a comprehensive bioinformatic platform, METAnnotatorX2, aimed at providing an optimized user-friendly resource which maximizes output quality, while also allowing user-specific adaptation of the pipeline and straightforward integrated analysis of both short and long read data. To further improve performance quality and accuracy of taxonomic assignment of reads and contigs, custom preprocessed and taxonomically revised genomic databases for viruses, prokaryotes, and various eukaryotes were developed. The performance of METAnnotatorX2 was tested by analysis of artificial data sets encompassing viral, archaeal, bacterial, and eukaryotic (fungal) sequence reads that simulate different biological matrices. Moreover, real biological samples were employed to validate in silico results. IMPORTANCE We developed a novel tool, i.e., METAnnotatorX2, that includes a number of new advanced features for analysis of deep and shallow metagenomic data sets and is accompanied by (regularly updated) customized databases for archaea, bacteria, fungi, protists, and viruses. Both software and databases were developed so as to maximize sensitivity and specificity while including support for shallow metagenomic data sets. Through extensive tests performed on Illumina and Nanopore artificial data sets, we demonstrated the high performance of the software to not only extract taxonomic and functional information from sequence reads but also to assemble and process genomes from metagenomic data. The robustness of these functionalities was validated using "real-life" data sets obtained from Illumina and Nanopore sequencing of biological samples. Furthermore, the performance of METAnnotatorX2 was compared to other available software tools for analysis of shotgun metagenomics data.

Biotechnological potential of bacteria from genera Bacillus Paraburkholderia and Pseudomonas to control seed fungal pathogens

Fungal pathogens are important determinants of plant dynamics in the environment. These pathogens can cause plant death and occasionally yield losses in crops, even at low initial densities in the soil. The objective of this study was to select and evaluate fungal antagonistic bacteria and to determine their biological control capacity in soybean seedlings. A total of 877 strains from the genera Pseudomonas, Bacillus, and Paraburkholderia/Burkholderia were screened, and their antagonistic effects on fungi frequently found in seeds were evaluated using four methods: quadruple plating, paired culture confrontation, strain containment, and inoculation of soybean seeds. The experimental design was completely randomized, with three replications for the first three methods and five replications in a 3 × 9 factorial scheme for the fourth treatment. The strains with the highest biotechnological potential were inoculated into soybean seeds to evaluate the biological control of fungi that attack this crop at germination. Seventy-nine strains presented some type of antagonistic effect on the tested fungi, with two strains presenting a broader antagonistic action spectrum in the seed test. In addition to the antagonistic potential, strains BR 10788 and BR 11793, when simultaneously inoculated or alone, significantly increased the seedling dry matter mass, and promoted the growth of soybean seedlings even in the presence of most fungi. Thus, this study demonstrated the efficiency of the antagonistic activity of these strains in relation to the target fungi, which proved to be potential agents for biological control.

Kluyveromyces marxianus: a potential biocatalyst of renewable chemicals and lignocellulosic ethanol production

Kluyveromyces marxianus is an ascomycetous yeast which has shown promising results in cellulosic ethanol and renewable chemicals production. It can survive on a variety of carbon sources under industrially favorable conditions due to its fast growth rate, thermotolerance, and acid tolerance. K. marxianus, is generally regarded as a safe (GRAS) microorganism, is widely recognized as a powerhouse for the production of heterologous proteins and is accepted by the US Food and Drug Administration (USFDA) for its pharmaceutical and food applications. Since lignocellulosic hydrolysates are comprised of diverse monomeric sugars, oligosaccharides and potential metabolism inhibiting compounds, this microorganism can play a pivotal role as it can grow on lignocellulosic hydrolysates coping with vegetal cell wall derived inhibitors. Furthermore, advancements in synthetic biology, for example CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, will enable development of an engineered yeast for the production of biochemicals and biopharmaceuticals having a myriad of industrial applications. Genetic engineering companies such as Cargill, Ginkgo Bioworks, DuPont, Global Yeast, Genomatica, and several others are actively working to develop designer yeasts. Given the important traits and properties of K. marxianus, these companies may find it to be a suitable biocatalyst for renewable chemicals and fuel production on the large scale. This paper reviews the recent progress made with K. marxianus biotechnology for sustainable production of ethanol, and other products utilizing lignocellulosic sugars.

Removal of NH3 and H2S from odor causing tannery emissions using biological filters: Impact of operational strategy on the performance of a pilot-scale bio-filter

Deodorization of gases emitted from Tanneries using eco-friendly and cost-effective approaches is necessary for the safe disposal of industrial emissions. There is limited research available on the treatment of odorous gases emitted from tanneries using bio-filter. In this endeavor, pilot-scale studies were performed in a 2.7 m³ bio-filter with synthetic gas mixture containing hydrogen sulfide (H₂S) and ammonia (NH₃) as input gas to study the impact of bedding material for the removal of H₂S and NH₃ using bio-filter and identification of various design parameters for scale-up. The pilot-scale studies showed that the removal efficacy of both NH₃ and H₂S was about 90-99% at an empty bed residence time of 55 seconds at an inlet concentration (NH₃ and H₂S) of 200 to 210 ppmV and microbial count enhanced from 3.5 × 10³ to 8.9 × 10⁹ in 210 days. The microbial biodiversity analysis revealed the dominance of proteobacteriaas as well as Firmicutes and Acinetobacter. A full-scale bio-filter (13.75 m³) was designed, installed, and commissioned in a tannery and observed that the removal efficiency of >99% since last three years.

Biological characteristics and salt-tolerant plant growth-promoting effects of an ACC deaminase-producing Burkholderia pyrrocinia strain isolated from the tea rhizosphere

Plant growth-promoting rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase can promote plant growth and enhance abiotic stress tolerance. In this study, Burkholderia pyrrocinia strain P10, with an ACC deaminase activity of 33.01-µmol/h/mg protein, was isolated from the tea rhizosphere and identified based on morphological, biochemical, and molecular characteristics. In addition to its ACC deaminase activity at pH 5.0-9.0 and in response to 5% NaCl and 20% polyethylene glycol, strain P10 can also solubilize phosphorus compounds, produce indole-3-acetic acid, and secrete siderophores. Pot experiments revealed that strain P10 can significantly enhance peanut seedling growth under saline conditions (100- and 170-mmol/L NaCl). Specifically, it increased the fresh weight and root length of plants by 90.12% and 79.22%, respectively, compared with high-salt stress. These results provide new insights into the biological characteristics of Burkholderia pyrrocinia, which may be useful as a bio-fertilizer.

Alkaline lipase production by novel meso-tolerant psychrophilic Exiguobacterium sp. strain (AMBL-20) isolated from glacier of northeastern Pakistan

Lipase is an important commercial enzyme with unique and versatile biotechnological applications. This study was conducted to biosynthesize and characterizes alkaliphilic lipase by Exiguobacterium sp. strain AMBL-20^T isolated from the glacial water samples of the northeastern (Gilgit-Baltistan) region of Pakistan. The isolated bacterium was identified as Exiguobaterium sp. strain AMBL-20^T on the basis of morphological, biochemical, and phylogenetic analysis of 16S rRNA sequences with GenBank accession number MW229267. The bacterial strain was further screened for its lipolytic activity, biosynthesis, and characterization by different parameters with the aim of maximizing lipase activity. Results showed that 2% Olive oil, 0.2% peptone at 25 °C, pH 8, and 24 h of incubation time found optimal for maximum lipase production. The lipase enzyme was partially purified by ammonium sulphate precipitation and its activity was standardized at pH 8 under 30 °C temperature. The enzyme showed functional stability over a range of temperature and pH. Hence, extracellular alkaliphilic lipase from Exiguobacterium sp. is a potential candidate with extraordinary industrial applications, particularly in bio-detergent formulations.

Plant extract mediated synthesis enhanced the functional properties of silver ferrite nanoparticles over chemical mediated synthesis

In this study, the antibacterial, antioxidant and cytotoxicity behaviour of silver ferrite nanoparticles (AgFeO2 NPs) synthesized through chemical and green routes were compared. Green synthesis (Bio) of AgFeO2 NPs were prepared by precipitation method using Amaranthus blitum leaves extract as a reducing agent. Chemical synthesis (Che) of AgFeO2 NPs was mediated by sodium borohydride as a reducing agent. [AgFeO2 (Bio)] NPs showed reduced size, better monodispersity and surface area compared to [AgFeO2 (Che)] NPs. The results showed that synthesized NPs have better antibacterial activity against E. coli than S. aureus. In addition, 250 μg of AgFeO2 (Bio) and (Che) NPs showed antioxidant efficiency of 98 and 86%. The results showed that [AgFeO2 (Bio)] NPs showed lower cytotoxicity [AgFeO2 (Che)] NPs against human human embryonic kidney (HEK 293) cells. These results suggest that [AgFeO2 (Bio)] NPs have improved physicochemical properties thereby they can be used as an effective biocatalytic material in biotechnology.

Species-specific Identification of Vibrio sp. based on 16S-23S rRNA gene internal transcribed spacer

AIMS

To explore a prokaryotic species-specific DNA marker, 16S-23S rRNA gene internal transcribed spacer (ITS) sequence for identification and classification of Vibrio.

METHODS AND RESULTS

Five hundred and seventy four ITS sequences from 60 Vibrio strains were collected, then the primary and secondary structures of ITS sequence were analysed. The ITS was divided into several subunits, and the species-specificity of these subunits were evaluated by blast. The variable subunit of ITS showed high species-specificity. A protocol to identify a Vibrio species based on ITS analysis was developed and verified. Both the specificity and sensitivity were 100%. The phylogeny analysis of Vibrio based on ITS showed that ITS devised a better classification than 16S rDNA. Finally, an identification method of Vibrio based on ITS sequencing in food samples was developed and evaluated. The results of ITS sequencing were (100%) consistent with the results identified by ISO standard.

CONCLUSIONS

Vibrio could be accurately identified at the species level by using the ITS sequences.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study suggests that the ITS can be considered as a significant DNA marker for identification and classification of Vibrio species, and it posed a new path to screen the Vibrio in food sample.

FLYCOP: metabolic modeling-based analysis and engineering microbial communities

Motivation

Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account.

Results

In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones.

Availability and implementation

Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP.

Supplementary information

Supplementary data are available at Bioinformatics online.

Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens

Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.

Metarhizium humberi sp. nov. (Hypocreales: Clavicipitaceae), a new member of the PARB clade in the Metarhizium anisopliae complex from Latin America

A new species, Metarhizium humberi, from the M. anisopliae complex and sister lineage of the M. anisopliae s.str. in the PARB clade, including M. pingshaense, M. anisopliae, M. robertsii and M. brunneum, is described based on phylogenetic analyses [translation elongation factor 1-alpha (5'TEF and 3'TEF), RNA polymerase II largest subunit (RPB1a), RNA polymerase II second largest subunit (RPB2a) and β-tubulin (BTUB)]. Metarhizium humberi was first collected in 2001 in the Central Brazilian state of Goiás, later found to be a common fungus in soils in Brazil, and since then has also been isolated from coleopteran, hemipteran and lepidopteran insects in Brazil and Mexico. This new species, named in honor of Richard A. Humber, a well-known insect pathologist and taxonomist of entomopathogenic fungi, is characterized by a high insecticidal activity against different developmental stages of arthropod pests with importance in agriculture and vectors of diseases to human and animals.

Black soldier fly larvae (Hermetia illucens) strengthen the metabolic function of food waste biodegradation by gut microbiome

Vermicomposting using black soldier fly (BSF) larvae (Hermetia illucens) has gradually become a promising biotechnology for waste management, but knowledge about the larvae gut microbiome is sparse. In this study, 16S rRNA sequencing, SourceTracker, and network analysis were leveraged to decipher the influence of larvae gut microbiome on food waste (FW) biodegradation. The microbial community structure of BSF vermicompost (BC) changed greatly after larvae inoculation, with a peak colonization traceable to gut bacteria of 66.0%. The relative abundance of 11 out of 21 metabolic function groups in BC were significantly higher than that in natural composting (NC), such as carbohydrate-active enzymes. In addition, 36.5% of the functional genes in BC were significantly higher than those in NC. The changes of metabolic functions and functional genes were significantly correlated with the microbial succession. Moreover, the bacteria that proliferated in vermicompost, including Corynebacterium, Vagococcus, and Providencia, had strong metabolic abilities. Systematic and complex interactions between the BSF gut and BC bacteria occurred over time through invasion, altered the microbial community structure, and thus evolved into a new intermediate niche favourable for FW biodegradation. The study highlights BSF gut microbiome as an engine for FW bioconversion, which is conducive to bioproducts regeneration from wastes.

Production of lipolytic enzymes by bacteria isolated from biological effluent treatment systems

This work aimed to evaluate the production of lipolytic complexes, produced by microorganisms isolated from a biological treatment system of effluents from a hotel. To select the best lipolytic microorganism for use in biotechnological processes, we tested 45 bacterial isolates recovered from the raw effluent of the hotel's restaurant waste tank. Lipase production was assayed in culture medium supplemented with olive oil and rhodamine B, incubated at 25 °C and 30 °C for 24 h - 48 h. Results showed 22 isolates lipase producers. All isolates were inoculated on medium without yeast extract to select the ones with highest enzyme yields. Out of these, nine isolates showed high lipase activity. The strain with the larger halo was assayed in submerged culture using an orbital shaker and a bioreactor, with three different substrates (olive oil, grape seed oil, and canola oil). Isolate G40 identified as Acinetobacter baylyi was selected to run the production assays because it showed the best result in the solid medium. In the bioreactor, maximum lipase production was obtained after 12 h of culture with the three substrates evaluated: 0,358 U/mL.min-1 in olive oil, 0,352 U/mL.min-1 with grapeseed oil, and 0,348 U/mL.min-1 with canola oil.

Microbial Inoculants for Improving Crop Quality and Human Health in Africa

Current agricultural practices depend heavily on chemical inputs (such as fertilizers, pesticides, herbicides, etc.) which, all things being equal cause a deleterious effect on the nutritional value of farm product and health of farm workers and consumers. Excessive and indiscriminate use of these chemicals have resulted in food contamination, weed and disease resistance and negative environmental outcomes which together have a significant impact on human health. Application of these chemical inputs promotes the accumulation of toxic compounds in soils. Chemical compounds are absorbed by most crops from soil. Several synthetic fertilizers contain acid radicals, such as hydrochloride and sulfuric radicals, and hence increase the soil acidity and adversely affect soil and plant health. Highly recalcitrant compounds can also be absorbed by some plants. Continuous consumption of such crops can lead to systematic disorders in humans. Quite a number of pesticides and herbicides have carcinogenicity potential. The increasing awareness of health challenges as a result of consumption of poor quality crops has led to a quest for new and improved technologies of improving both the quantity and quality of crop without jeopardizing human health. A reliable alternative to the use of chemical inputs is microbial inoculants that can act as biofertilizers, bioherbicide, biopesticides, and biocontrol agents. Microorganisms are able to carry out the plant growth promotion, pest and disease and weed control. Microbial inoculants are beneficiary microorganisms applied to either the soil or the plant in order to improve productivity and crop health. Microbial inoculants are natural-based products being widely used to control pests and improve the quality of the soil and crop, and hence human health. Microbial inoculants involve a blend of microorganisms that work with the soil and the soil life to improve soil fertility and health and by extension improve human health. Microbial inoculants have the ability to minimize the negative impact of chemical input and consequently increase the quantity and quality of farm produce. Microbial inoculants are environmental-friendly and deliver plant nutrients to plants in a more sustainable manner. Microbial inoculants can help reduce chemical fertilizer application. Microbial inoculants could include bacteria, fungi and algae. This research summarizes the impact of agricultural chemical inputs on human health. The contribution of microbial inoculants in sustainable maintenance of human health will be expatiated. Advances in microbial inoculants and technology and strategies to explore this natural, user friendly biological resource for sustainable maintenance of plant health will be discussed.

An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth

The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.