Microbial Genetic Resources Research Articles

THE IMPORTANCE OF MICROBIAL GENETIC RESOURCES FOR FOOD AND AGRICULTURE IN THE BIOECONOMY

The main purpose of the Biotechnology field in the food and agriculture sector is to create Knowledge Based Bioeconomy. Bioeconomy is an economic process that deals with the commercial distribution and consumption of products such as goods, energy and services produced from biomaterials (plants, animals, microorganisms) and covers all kinds of industries and economic sectors that produce, manage and spread biological resources. It is among the sustainability features of the Biotechnology science and modern bioeconomy. Biotechnology is the driving force of the bioeconomy. Biology Science, Life Sciences and Biotechnology work in harmony with other technologies. Common goals; To provide the knowledge-based for sustainable management, production and use of biological resources, to provide new, safe, lower cost and eco-efficient products, to promote competitiveness and sustainability in the industry (Ünal, 2020). Microorganisms are biological power and rich gene potentials, the most basic for the bioeconomy and the most practical biological systems in transferring to the economy. The developing technology changes the environment and conditions that microorganisms encounter with people. With microorganisms, which were previously considered only as an infectious agent (microbe), today many fields are studied, from education to health, from industry to production, from agriculture to food, environment, industry to biological weapon. The monitoring of microbial biodiversity and genetic resources of microorganisms has been performed by culture and taxonomic evaluation of microorganisms in samples taken from ecosystems. It has been determined that the number of prokaryotic microorganisms on earth, which can be cultured until today, is over 5.000. It has been calculated that the total number of prokaryotes will be around 2.000.000 microorganisms in the nature.

INTEGRATION OF RUSSIAN MICROBIAL GENETIC RESOURCES IN EUROPEAN SYSTEM HORISON 2020

A scheme of organizing the integration of information flows about microbial genetic resources supported by the European Biological Resource Centers (MBRC) with biological databases of the Life Science system is presented.

Diplodia africana causing twig death on Araucaria araucana, a new host and first record for Chile

Araucaria araucana (monkey puzzle tree) is an endemic conifer restricted to the temperate subantarctic forests of South America, with most of the world population concentrated in Chile, covering an area of 253,715 hectares. As a native forest species, A. araucana has been the object of ongoing phytosanitary surveys by the Servicio Agrícola y Ganadero (SAG), the National Plant Protection Organization of Chile. During surveillance activities in 2018, a botryosphaeriaceous fungus was isolated from a sample of partially dead branches from a tree in Conguillio National Park, located in the Andes, Araucanía Region (38°39'00“ S, 71°37'6” W). Pycnidia and conidia produced in vitro on pine needles on water agar after 14 days were identified as Diplodia sp., with conidia hyaline after discharge from pycnidia, non-septate, measuring (26-)31-34.5(-36) × (7-)9.5-12(-13.5) μm (Fig. 1). To identify the species of Diplodia, sequences of the rDNA ITS region, β-tubulin (BT), and translation-elongation factor 1α (TEF1) gene were obtained using the universal primers ITS1/ITS4, EF1-728/EF2 (Carbone & Kohn, 2; O'Donnell et al., 5) and TUB2Fd/TUB4Rd (Aveskamp et al., 1). The sequences were submitted to GenBank with the Accession Nos. MN046380 (ITS), MN046381 (TEF1) and MN046382 (BT). BLAST analysis limited to type material showed 99.5-100% identities with Diplodia africana (MH863094, KF766397 and KF766129). A multi-locus phylogenetic analysis using maximum parsimony confirmed that the specimen clustered with the D. africana clade (bootstrap = 96%) (Fig. 2). An isolate (SAG-102744-18) was deposited in the Chilean Microbial Genetic Resources Collection, INIA Quilamapu, Chillán, Chile, with the accession number RGM 2718. The pathogenicity of the fungi was tested by inoculating six three-year-old A. araucana seedlings (approximately 40 cm in height) in April 2019. The stems of the seedlings were wounded using a sterile scalpel 5 cm above the collar root and inoculated with a mycelial plug (5 mm diameter) from a seven-day-old culture grown on 2% malt extract agar. Two seedlings used as control were inoculated with sterile agar plugs. The plugs were sealed with paraffin film. Seedlings were kept outdoors with average minimum and maximum temperatures of 5.4 and 21.5°C, and watered as needed. After four weeks, brown phloem lesions ranging from 7-30 mm in length were observed on the inoculated seedlings and the fungus was consistently re-isolated from all lesions. Additionally, all inoculated seedlings showed foliar necrosis affecting between a few leaves to 50% of the foliage. Control seedlings remained healthy (Fig. 3-4). The genus Diplodia includes species that are pathogens, endophytes and saprobes of mostly woody hosts. Some of the pathogenic species include D. africana, which was initially found on stone fruit of Prunus spp. in South Africa (Damm et al., 3) and later reported causing dieback on Phoenicean juniper in Italy (Linaldeddu et al., 4). To our knowledge, the current identification of D. africana on Araucaria araucana in Chile constitutes a new host-distribution of the fungus. The author wishes to thank SAG colleagues Diego Rupaillan for sampling, Mariana Llanos and Abraham Aburto for their technical support.

Terrestrial and marine Antarctic fungi extracts active against Xanthomonas citri subsp. citri.

This manuscript makes an impact on the study of micro-organisms from extreme habitats and their possible contribution in discovering new active molecules against pathogens of agricultural interest. Studies on the Antarctic continent and its communities have attracted the scientific community due to the long period of isolation and low levels of disturbance that surrounds the region. Knowing the potential of fungi in this region to produce active secondary metabolites, we aim to contribute to the discovery of compounds with antibacterial action in Xanthomonas citri subsp. citri, a plant pathogen present in several regions around the globe.

Identity of biocrust species and microbial communities drive the response of soil multifunctionality to simulated global change

Increasing N inputs and changing rainfall regimes will lead to drastic changes in multiple ecosystem functions such as nutrient cycling, organic matter decomposition and gas exchange in dryland ecosystems. As fundamental components of drylands, biological soil crusts (biocrusts) play important roles in the regulation of responses of multiple ecosystem functions to global environmental changes. Biocrusts are home to highly functional microbial communities; however little is known on the role of microbial communities associated with different biocrust species in regulating the response of multiple ecosystem functions to global change. Here, we conducted a microcosm experiment to evaluate the roles of biocrust-forming lichens (Diploschistes thunbergianus, Psora crystallifera and Xanthoparmelia reptans) in mediating the effects of simulated changes in rainfall frequency and nitrogen (N) addition on soil multifunctionality involving nutrient availability, greenhouse gas flux and enzyme activities. The three biocrust species supported different levels of soil bacterial diversity, and specific community composition as revealed by MiSeq sequencing. Biocrust species always promoted multiple functions related to carbon, nitrogen and phosphorus cycling compared to bare ground, with X. reptans having the highest effect on multifunctionality. Most importantly, the relative abundance of specific microbial communities associated with different lichen species modulates the response of multifunctionality to impacts of water frequency (negative) and N addition (positive). Our results suggest that biocrust species could regulate global change impacts on soil multifunctionality in drylands, although the strength and direction vary among the biocrust species. These findings highlight the importance of preserving biocrusts as hotspots of microbial genetic resources and ecosystem functioning in drylands.

Economic Valuation of Microbial Genetic Resources: The Case of Rhizobia Bio-fertilizer in Some Regions of Ethiopia

Economic valuation of microbial genetic resources was conducted in three Zones, Arsi from Oromia, East Shoa from Amhara and Wolhyta from Southern Nations Nationalities and People’s Region (SNNPR) of Ethiopia. Willingness to pay (WTP) bids to use Rhizobia bio-fertilizer for production of different legumes was calculated. The average willingness to pay for bio-fertilizer in haricot bean production was 201.76 USD (at existing exchange rate) /household/ year. When bio-fertilizer was used for faba bean production, increase by 1 hectare of land, increased the willingness to pay for bio-fertilizer by 667 USD/quintal/year. Moreover, Higher income is significantly related to higher WTP at (F=72.17, sig. = 0.000). In general the study showed that those farmers who have gained benefits from using Rhizobia biofertilizers in all the studied Sub-districts (kebels) indicated highest WTP for the bio-fertilizers in the study. There were certain factors like size of land holding, yield per hectare and herbicides that affected the total yield and thereby the WTP. Although there might be other factors that contributed for yield increases of the leguminous plants in the studied area, it may be possible to conclude that the benefit from the use of the bio-fertilizer was significantly higher compared to those gains obtained without using bio-fertilizers. Despite that there has been certain controversy on methodological issues involving willingness-to-pay, the support of WTP in determining the economic value of genetic resources widely increased. Thus the current economic value estimate of the rhizobia bacteria may be indicated by the WTP of the studied farmers.

Metagenomics insights into food fermentations.

SummaryThis review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

Molecular, morphological and pathogenic characterization of six strains of Metarhizium spp. (Deuteromycotina: Hyphomycetes) for the control of Aegorhinus superciliosus (Coleoptera: Curculionidae)

Aegorhinus superciliosus is an important pest on blueberry (Vaccinium corymbosum L.) and other fruit trees. The use of entomopathogenic fungi as Metarhizium spp. has been evaluated for the control of this insect, but variability has been observed among different strains. The aim of this study was to characterize six promising strains of Metarhizium spp. for the control of A. superciliosus. The studied strains were QuM173c, Qu-M363, Qu-M171a, Qu-M156a, Qu-M421, and Qu-M430, all of which belonged to the Chilean Collection of Microbial Genetic Resources (ChCMGR) of the Instituto de Investigaciones Agropecuarias (INIA), Chile. Molecular characterization was made by sequencing the ITS region (Internal Transcribed Spacers, ITS-5.8S rDNA). The morphology of conidia was evaluated through scanning electron microscopy and radial colony growth was evaluated in potato dextrose agar (PDA), Sabouraud dextrose agar (SDA), agar enriched with larvae of Galleria mellonella (Lepidoptera: Pyralidae) (GA), and agar enriched with adults of A. superciliosus (AA). Pathogenicity was studied based on mortality of adults of A. superciliosus inoculated with conidia. Sequencing of the ITS-5.8S rDNA region indicates that the strains belong to the clade of M. anisopliae var. anisopliae, except for Qu-M171a, which was identified as M. anisopliae var. lepidiotum. Conidia average length for the six strains was 5.09 µm and average conidia width was 1.92 µm. Radial colony growth differences were observed between strains (p < 0.01) and between different growth media (p < 0.01). The strains exhibited the highest colony growth in the GA medium, while in the AA medium they showed the lowest (p < 0.01). Pathogenicity tests show that Qu-M430 reached a 90% mortality rate (p < 0.01). Results show that there is variability between the studied strains, which is expressed in their morphology, molecular characteristics and pathogenicity towards A. superciliosus.

Development of a National Center of Genetic Resources Passport Database: Managing Agriculture, Forestry, Livestock, Microbial, and Aquatic Genetic Resources with an Integrated Schema

Development of a National Center of Genetic Resources Passport Database: Managing Agriculture, Forestry, Livestock, Microbial, and Aquatic Genetic Resources with an Integrated Schema

GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.

In 2008, the platform "GenoSol" ( http://www.dijon.inra.fr/plateforme_genosol ) was created at the INRA (French National Institute for Agronomic Research) of Dijon. This platform was launched by several soil microbial ecologist senior scientists to provide a logistics and technical structure dedicated to the acquisition, conservation, characterization, and supply of genetic resources (DNA) of soils from very large-scale samplings (several hundred to several thousand corresponding to large spatial and/or temporal scales). Thanks to this structure metagenomic analysis of soil microbial communities has been standardized as well as a reliable reference system for analysis of the microbial genetic resources of the collected soils (more than 10,000 soil samples to date). This platform also illustrates the usefulness of existing soil archives in providing a readily available source of ecological information that is relevant to microbial ecology, probably more than we can currently fathom.

Microbial diversity and its importance in microbial genetic resources preservation and its role in natural

Biodiversity has been very common to almost every one. However, a comprehensive understanding on the concept of biodiversity might be less common to many discussing parties. Likewise, microbial diversity is even less common to most of academician, ex-cept of course to microbiologists. In fact, a correct and clear concept of biodiversity is prerequisite for serious and appropriate discussion of the matter. In this paper, the concept and understanding of microbial diversity is fundamentally described as well as their genetic potential by reviewing the development and application of species concept based on molecular biological approach. It is an undeniable fact that molecular biology has provided a powerful tool for microbiologists as well as evolutionists to unravel the biodiversity of microbial world which play a paramount important to conserve the basic function of any natural environments in the biosphere since microbes live and flourish in all ecosystems, including extreme habitats. The ubiquity of microbes clearly underpins by their diversity, including physiological and metabolic diversity, ability to live in anaerobic environments, and their small size. Molecular biology development and application in microbiology have transformed the three areas in microbiology, namely microbial ecology, microbial diversity, and microbial evolution from weakness into the strength, in unraveling and understanding microbial diversity and its genetic potential as well as its role in nature, especially their role to keep work the biogeochemical cycle in the Earth. Only by having an adequate understanding of microbial critical role in preserving nature that the environmental conservation issue could be carried out, understood and realized meaningfully.

Promoting the utilization of plant, animal and microbial genetic resources for research and development in biotechnology: evidence on researchers' preferences for specific attributes from Korean genebanks

With regard to the survey data of Korean researchers using genetic resources from three genebanks administered by the Korea Research Institute of Bioscience and Biotechnology, we conducted conjoint and cluster analyses to estimate the relative importance of genetic resource (microbial, plant and animal) attributes among the researchers. Our results indicate that Korean researchers view price (cost of acquiring an accession), high new functionality (functional properties of germplasms for specific applications and uses) and completely uncovered genomic information (about mutation, genetic transformation, genomic function and pathways) as far more important in decision-making about R&amp;D use of microbial, plant and animal genetic resources, respectively, than other attributes. Furthermore, this study shows that researchers conducting R&amp;D in the microbial and plant genetic resource sectors especially prefer resources from specific domestic environments and Korean indigenous species, respectively. The study also sheds light on different patterns of researcher segments in terms of utilities of attributes and subgroups of researchers who have common needs in the three genetic resource sectors. We proposed some policy and strategic implications based on the results of this study.

Crowdsourcing to Create National Repositories of Microbial Genetic Resources: Fungi as a Model

To address the challenging task of identifying, obtaining and cataloging the different microbes in a country with wide-ranging environments and habitats, we present a crowdsourcing model. With fungi as the prototype, we discuss approaches for rapid collection and identification of strains from environments and habitats that might lead to novel genes of industrial importance. Also, we expect the use of easy culture preservation methods to promote colleges as mini culture-collection centres and serve as the initial focal point in a national research initiative. Our model envisions the concerted involvement of undergraduate students, faculty, industries, national laboratories and culture- collection repositories to rapidly build a large assemblage of rare fungal strains and enhance the biodiversity resource of a country.

Phylogenetically and spatially close marine sponges harbour divergent bacterial communities.

Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family - Sarcotragus spinosulus and Ircinia variabilis – in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of S. spinosulus and I. variabilis differed markedly from each other – with higher number of ribotypes observed in S. spinosulus – and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria). Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria), respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis. These findings suggest a pivotal host-driven effect on the shape of the marine sponge microbiome, bearing implications to our current understanding of the distribution of microbial genetic resources in the marine realm.

Microsatellite variability in nutria (Myocastor coypus) genetic resource in the Czech Republic

Nutria (Myocastor coypus) is a large rodent native to South America which was introduced worldwide originally with the intention of fur farming. Three colour forms (Standard, Moravian Silver, and Prestice Multicolour) fall into the Farm Animal Genetic Resources of the Czech Republic protected by the National Programme on Conservation and Utilization of Plant, Animal and Microbial Genetic Resources for Food and Agriculture coordinated by the National Focal Point. The objective of our investigation in the Czech Republic was to establish microsatellite panel for nutria and determine microsatellite variability in the local nutria population, levels of genetic diversity within and among subpopulations with respect to colour form and the levels of inbreeding within subpopulations. The genetic variability was studied in 64 animals by investigating 11 microsatellite markers (McoD214, McoD217, McoD59, McoD69, McoC124, McoC203, McoD60, McoB17, McoC118, McoA04, and McoD228) analysed by multicoloured capillary electrophoresis. The whole population showed a moderate level of genetic variability in terms of number of alleles (5 alleles per locus) or heterozygosity (50.4%) and the Prestice Multicolour form exhibited the highest level of diversity. Particular attention should be paid to organizing mate to minimise inbreeding, especially in the Standard colour form (F&lt;sub&gt;IS&lt;/sub&gt; = 0.238) which showed the highest level of inbreeding out of the three colour forms. High combined exclusion probability (CEP) values (99.5, 94.5, and 99.9%) implied that the panel of microsatellite markers established in this study was usable for individual identification or routine parentage testing in nutria population in the Czech Republic. &amp;nbsp;

Biodiversity of Qatari Bacillusthuringiensisstrains and molecular prediction of their biological activities and bioassays: for a safer and clean environment

Abstract Qatar's soil and environment are sources of beneficial bacterial strains and bacterial resources that should be first of all, identified, isolated, studied, used and valorized. In fact, the Qatari environment should be elective for many microbial genetic resources tolerant to high temperature, drought, salinity and hydrocarbon rich soil. Isolating microbial strains having biotechnological applications would be very beneficial not only for Qatar, but also for the Gulf region and other countries in the world. B. thuringiensis is a Gram-positive bacterium which produces, during sporulation, crystalline inclusions containing one or more deltaendotoxins, that are considered as the best biological insecticides as they are harmless for man and animal and act specifically against a wide variety of pathogenic insects, including pests and disease vectors. In this research project, we studied 31 crystal producing Qatari B. thuringiensis isolates, by the investigation of their plasmid patterns, crystal morphology, deltaendotoxin identification by SDS-PAGE, prediction of gene nature by PCR and insecticidal activities. The crystal morphology comparison showed that 22.5 % were spherical, 32.2 % were amorphous, 38.7 % were pyramidal and 6.4 % were bipyramidal. Based on the isolates plasmid patterns, 11 representative strains of the different classes were deeply studied. We used their molecular ribotyping and bioinformatic tools of sequence and BLAST alignment, to confirm that the studied isolates are B. thuringiensis strains. By SDS-PAGE, we showed that the deltaendotoxins produced by the different strains have different molecular weights. The PCR screening of these strains, using oligonucleotides specific for the genes cry1 and cry4, showed the presence of genes cry1A in two strains and allowed us to predict their potential insecticidal activities against lepidopteran larvae. Moreover, we used a B. thuringiensis israelensis in bioassay experiments against local mosquito Culex pipiens larveae and demonstrated the efficacy of such biological bioinsecticides on Qatari mosquitoes. These results are very encouraging and favour the use of B. thuringiensis local strain bioinsecticides for environmentally safe integrated pest management in this region.

Institutionalizing Global Genetic Resource Commons: Towards Aternative Models for Facilitating Access in the Global Biodiversity Regime

The proliferation of intellectual property rights has lead to increasing restrictions and commercial pressures on access to and use of genetic resources. These changes present a formidable challenge for the incipient commons-based sharing practices for genetic resources on a global scale amongst scientists, breeders, and between ex-situ collections of microbial genetic material, which have been made possible by new technological breakthroughs. This paper presents a comparative analysis of three cases of global genetic-resource commons, in the fields of microbial, plant and animal genetic resources, with the aim to contribute to the understanding of the challenges faced and to analyze possible institutional solutions. The analysis in this paper shows that, under conditions of appropriate quality control, the use of standard contracts against misappropriation and an initial investment in the creation of social networks, global genetic resource commons can be a desirable and effective solution to manage and provide essential knowledge assets that contribute to conservation and sustainable use of biodiversity with major benefits both for developing and industrialized countries.

Collection of food relevant microscopic fungi under the Czech national programme of protection of genetic resources of economically significant microorganisms - a short report

A unique project exists in the Czech Republic, namely the Czech National Programme of Protection of Genetic Resources of Economically Significant Microorganisms and Tiny Animals (NPPGR), which includes nineteen Czech collections of microorganisms (bacteria, fungi), viruses, and tiny animals. It is fully financed by the Ministry of Agriculture of the Czech Republic. Under this Programme, the Culture Collection of Fungi (CCF) in Prague maintains 293 fungal strains, 225 of which are food and feed relevant fungi (e.g. toxigenic &lt;I&gt;Aspergillus flavus, Penicillium verrucosum&lt;/I&gt;, and &lt;I&gt;Fusarium sporotrichioides&lt;/I&gt;). The main aims of the Programme are to provide adequate protection of the microbial genetic resources that are of importance to the agriculture and food industries, to provide strains (free of charge) for the research and educational purposes, and to support the cooperation between Czech and foreign institutions. A database of all microorganisms is accessible online.

Governing the management and use of pooled microbial genetic resources: Lessons from the global crop commons

The paper highlights lessons learned over the last thirty years establishing a governance structure for the global crop commons that are of relevance to current champions of the microbial commons. It argues that the political, legal and biophysical situation in which microbial genetic resources (and their users) are located today are similar to the situation of plant genetic resources in the mid-1990s, before the International Treaty on Plant Genetic Resources was negotiated. Consequently, the paper suggests that it may be useful to look to the model of global network of ex situ plant genetic resources collections as a precedent to follow &ndash; even if only loosely &ndash; in developing an intergovernmentally endorsed legal substructure and governance framework for the microbial commons.

Characterization of a Deep-Sea Sediment Metagenomic Clone that Produces Water-Soluble Melanin in Escherichia coli

To access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment DNA was extracted and cloned into fosmid vector (pCC1FOS) generating a library of 39,600 clones with inserts of 24-45 kb. The clone fss6 producing red-brown pigment was isolated and characterized. The pigment was identified as melanin according to its physico-chemical characteristics. Subcloning and sequences analyses of fss6 demonstrated that one open reading frame (ORF2) was responsible for the pigment production. The deduced protein from ORF2 revealed significant amino acid similarity to the 4-hydroxyphenylpyruvate dioxygenase (HPPD) from deep-sea bacteria Idiomarina loihiensis. Further study demonstrated that the production of melanin was correlated with homogentistic acid (HGA). The p-hydroxyphenylpyruvate produced by the Escherichia coli host was converted to HGA through the oxidation reaction of introduced HPPD. The results demonstrate that expression of DNA extracted directly from the environment might generate applicable microbial gene products. The construction and analysis of the metagenomic library from deep-sea sediment contributed to our understanding for the reservoir of unexploited deep-sea microorganisms.