Microbial Resource Management Research Articles

Construction and application of standard system for the preservation of pathogenic microorganism resources

Standards are the technical support for economic activities and social development. The construction and standardization of the pathogenic microorganism preservation standard system is an important technical foundation for the high-quality development of preservation work. Establishing a pathogenic microorganism resource standard system is also important to the national biosafety standards. Through the standardization of pathogenic microbial resource preservation, we can ensure the effective management and sustainable utilization of pathogenic microbial resources, promote the transformation of resources, and serve as an important new element of new productivity to assist the innovative development of biosafety science and technology. This article elaborates and analyzes the establishment background, construction framework, standardization process, and application effects of the standard system for preserving pathogenic microbial resources, providing stronger support for further improving the standard system and promoting the standardization of pathogenic microbial resource preservation.

Microbial Resources and Sparkling Wine Differentiation: State of the Arts

Consumers’ increasing interest in sparkling wine has enhanced the global market’s demand. The pro-technological yeasts strains selected for the formulation of microbial starter cultures are a fundamental parameter for exalting the quality and safety of the final product. Nowadays, the management of the employed microbial resource is highly requested by stakeholders, because of the increasing economic importance of this oenological sector. Here, we report an overview of the production processes of sparkling wine and the main characterisation criteria to select Saccharomyces and non-Saccharomyces strains appropriate for the preparation of commercial starter cultures dedicated to the primary and, in particular, the secondary fermentation of sparkling wines. We also focused on the possible uses of selected indigenous strains to improve the unique traits of sparkling wines from particular productive areas. In summary, the sparkling wine industry will get an important advantage from the management of autochthonous microbial resources associated with vineyard/wine microbial diversity.

Engineering microbial technologies for environmental sustainability: choices to make.

SummaryMicrobial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long‐term effects of climate change. The key to the success of microbial technologies is an effective, target‐oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi‐natural or even entirely human‐made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.

Heritage hands and tastes of the pandemic

AbstractThe revitalization of fermentation projects during COVID-19 raises questions about the preservation of the pandemic’s material and ephemeral effects – a topic that heritage policy is well equipped to engage. These activities also emphasize the necessity of engaging with heritage practices as a kind of care, encompassing both methods of safekeeping and practices of empathy. In addition, heritage ferments prove “good to think” around themes of loss and preservation, the interpretation of novel viruses through traditional food practices, and the coupling of heritage to microbes. Connecting microbes with heritage allows us to consider points of overlap: as bearers of patrimony with cultural and material lineages, as central to heritage tastes, and as open to geographical indications or other protections to further a kind of microbial resource management. Despite the pandemic’s devastating impact, consideration of heritage ferments points to both emancipatory and constraining outcomes for our post-pandemic future.

Microbiological Safety and the Management of Microbial Resources in Artisanal Foods and Beverages: The Need for a Transdisciplinary Assessment to Conciliate Actual Trends and Risks Avoidance.

Current social and environmental trends explain the rising popularity of artisanal fermented foods and beverages. In contrast with their marketing success, several studies underline a lack of regulations necessary to claim differences occurred from the farm to the fork and to certify high quality and safety standards. Microbial-based fermentative processes represent the crucial phase in the production of fermented foods and beverages. Nevertheless, what are the effects of the application of the “artisanal” category to the management of food fermentations? This opinion paper is built up on this issue by analyzing microbial aspects, instances of innovation, safety issues, and possible solutions. Evidence indicates: (i) a global curiosity to exploit food fermentations as drivers of innovation in artisanal contexts and (ii) an increasing interest of the artisanal producers into management of fermentation that relies on native microbial consortia. Unfortunately, this kind of revamp of “artisanal food microbiology,” rather than re-establishing artisanal content, can restore the scarce hygienic conditions that characterized underdeveloped food systems. We highlight that in the scientific literature, it is possible to underline existing approaches that, surpassing the dichotomy between relying on spontaneous fermentation and the use of commercial starter cultures, depict a “third way” to conjugate interest in enhancing the artisanal attributes with the need for correct management of microbial-related risks in the final products.

A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine.

This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.

Pathogenic microorganism biobanking in China

Pathogenic microbial strains and specimens are crucial national and strategic biological resources. Preservation and management of the pathogenic microbial resources, as an integral component of biosafety, play an important role in the national biosafety system and in the overall framework of national security. Sound preservation and management rely on the effective designation of preservation institutions, strengthened operation and management of preservation institutions, standardized description and data specifications, establishment of preservation information management systems, and promotion of resource-sharing and utilization. Firm protection and efficient sharing and utility of pathogenic microbial resources are expected to make a unique contribution to the sustainable development of the national economy.

Metataxonomy and functionality of wood-tar degrading microbial consortia

Wood-tar is a liquid material obtained by wood gasification process, and comprises several polycyclic aromatic hydrocarbons (PAH). Tar biodegradation is a very challenging task, due to its toxicity and to its complex chemistry. The ‘microbial resource management’ concerns the use of environmental microbial communities potentially able to provide us services. We applied this concept in tar biodegradation. Tar composed by several PAH (including phenanthrene, acenaphthylene and fluorene) was subjected to a biodegradation process in triplicate microcosms spiked with a microbial community collected from PAH-rich soils. In 20 days, 98.9% of tar was mineralized or adsorbed to floccules, while negative controls showed poor PAH reduction. The dynamics of fungal and bacterial communities was assessed through Automated Ribosomal Intergenic Spacer Analysis (ARISA), 454 pyrosequencing of the fungal ITS and of the bacterial 16S rRNA. Quantification of the degrading bacterial communities was performed via quantitative Real Time PCR of the 16S rRNA genes and of the cathecol 2,3-dioxygenase genes. Results showed the importance of fungal tar-degrading populations in the first period of incubation, followed by a complex bacterial dynamical growth ruled by co-feeding behaviors.

Microbial Resources and Innovation in the Wine Production Sector

Microbial starter cultures represent a fundamental level of innovation in the wine sector. Selected yeast strains are routinely used to achieve the needed biomass preparation to accelerate and steer alcoholic fermentation in grape must. The use of starter cultures to induce malolactic fermentation in wine relies on the characterisation and propagation of suitable strains of lactic acid bacteria. Furthermore, the selection of new strains, the renewal of management of microbial resources and new technologies allow continuous improvements in oenology, which may increase the beneficial aspects of wine. In this review, with the aim to stimulate microbial-driven, consumer-oriented advances in the oenological sector, we propose an overview of recent trends in this field that are reported by following the classical separation into ‘product innovation’ and ‘process innovation’. Hence, we shall highlight i) the possible positive innovative impacts of microbial resources on the safety and the sensorial and functional properties of wine (product innovation) and ii) the potential microbial-based improvements allowing the reduction of time/costs and the environmental impacts associated with winemaking (process innovation).

Bacterial interactions and implications for oil biodegradation process in mangrove sediments

Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.

Starter Cultures for Sparkling Wine

The sparkling wine market has expanded in recent years, boosted by the increasing demand of the global market. As for other fermented beverages, technological yeasts and bacteria selected to design commercial starter cultures represent key levers to maximize product quality and safety. The increasing economic interest in the sector of sparkling wine has also implied a renewed interest in microbial resource management. In this review, after a brief introduction, we report an overview of the main characterization criteria in order to select Saccharomyces cerevisiae strains suitable for use as starter cultures for the production of base wines and to drive re-fermentation of base wines to obtain sparkling wines. Particular attention has been reserved to the technological characterization aspects of re-fermenting phenotypes. We also analysed the possible uses of selected non-Saccharomyces and malolactic strains in order to differentiate specific productions. Finally, we highlighted the main safety aspects related to microbes of enological interest and underlined some microbial-based biotechnological applications helpful to pursue product and process innovations. Overall, the sparkling wine industry may find a relevant benefit from the exploitation of the wide resources associated with vineyard/wine microbial diversity.

Management of Microbial Communities through Transient Disturbances Enhances the Functional Resilience of Nitrifying Gas-Biofilters to Future Disturbances.

Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.

Disturbance opens recruitment sites for bacterial colonization in activated sludge.

Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems.

Thermophilic and cellulolytic consortium isolated from composting plants improves anaerobic digestion of cellulosic biomass: Toward a microbial resource management approach

A cellulolytic consortium was isolated from a composting plant in order to boost the initial hydrolysis step encountered in anaerobic digestion. Improvement of the cellulose degradation, as well as biogas production, was observed for the cultures inoculated with the exogenous consortium. Metagenomics analyses pointed out a weak richness (related to the number of OTUs) of the exogenous consortium induced by the selective pressure (cellulose as sole carbon source) met during the initial isolation steps. Main microbial strains determined were strictly anaerobic and belong to the Clostridia class. During cellulose anaerobic degradation, pH drop induced a strong modification of the microbial population. Despite the fact that richness and evenness were very weak, the exogenous consortium was able to adapt and to maintain the cellulolytic degradation potential. This important result point out the fact that simplified microbial communities could be used in order to increase the robustness of mixed cultures involved in environmental biotechnology.

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops.

Biogas is an important renewable energy carrier. It is a product of stepwise anaerobic degradation of organic materials by highly diverse microbial communities forming complex interlinking metabolic networks. Knowledge about the microbial background of long-term stable process performance in full-scale reactors is crucial for rationally improving the efficiency and reliability of biogas plants. To generate such knowledge, in the present study three parallel mesophilic full-scale reactors fed exclusively with energy crops were sampled weekly over one year. Physicochemical process parameters were determined and the microbial communities were analysed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and 454-amplicon sequencing. For investigating the methanogenic community, a high-resolution T-RFLP approach based on the mcrA gene was developed by selecting restriction enzymes with improved taxonomic resolution compared to previous studies. Interestingly, no Methanosarcina-related generalists, but rather specialized hydrogenotrophic and acetoclastic methanogenic taxa were detected. In general, the microbial communities in the non-connected reactors were remarkably stable and highly similar indicating that identical environmental and process parameters resulted in identical microbial assemblages and dynamics. Practical implications such as flexible operation schemes comprising controlled variations of process parameters for an efficient microbial resource management under fluctuating process conditions are discussed.

The manufacturing microbe.

In all industrialized countries, the manufacturing industry appears to be in difficulty: the costs of maintaining skilled workers to do complicated technical tasks are becoming a major hurdle. The fact that a majority of the young professionals will spend their whole lives just typing in front of a screen is worrying plenty of sociologists, particularly because of the simple fact that our brains apparently are sparked to creativity by being involved in complex handling – read manufacturing – exercises (Sennett, 2014).

Special Issue on “Microbial Ecology of Anaerobic Digestion”

Anaerobic digestion (AD) is an efficient and sustainable way of using organic carbon from residual biomass and organic waste for the production of renewable energy, while simultaneously recycling nutrients and cleaning up waste streams. The process relies on complex microbial communities comprised of diverse functional guilds; these communities have manifold metabolic pathways and interactions. In contrast to the conventional view of an anaerobic digester as a black box, advanced microbiological methods have paved the way for understanding and even controlling complex microbial networks. Nowadays, microbial resource management is crucial for technological progress in AD, and offers new perspectives concerning sustainable waste management, renewable energy production, resource efficiency, and advanced bio-refineries; these perspectives lead to novel applications of AD processes that go beyond biogas as the main product. [...].

Management of microbial resources in the environment

Management of microbial resources in the environment

Application of a molecular based approach for the early detection of short term 3-chloroaniline shock loads on activated sludge bacterial community and functionality

Microbial processes are central elements in wastewater treatment plants (WWTPs) to mineralize the organic matter, to degrade pollutants and to decrease the amount of suspended solids. This activity can be disrupted by organic and inorganic pollutants present in wastewater streams. Hence, it is of primary importance to investigate and monitor the structure and functionality of the sludge-resident microbial communities. We simulated a 3-chloroaniline (3-CA) shock load in 3-CA adapted and non-adapted semi-continuous activated-sludge (SCAS) reactors to selectively stress the Ammonia Oxidizing Bacteria (AOB). Recently developed setting-independent theoretical interpretation of molecular DNA and RNA fingerprinting patterns were used to evaluate the responses of the microbial populations. Ammonium accumulation in treated reactors upon 3-CA addition confirmed the disruption of the functionality under stress conditions. Molecular analyses coupled to their interpretation highlighted that shock loaded reactors clustered separately from non-treated ones, especially when AOBs community was specifically targeted. Furthermore, the interpretation of RNA-based analyses, as compared to DNA-based ones, allowed to more promptly depicting shifts in a stressed community. We showed that the use of RNA-based molecular tools in combination with a new set of parameters is a powerful tool to link functional failures with microbial structure modifications in WWTPs, providing a potential tool for a rational optimization of the processes (Microbial Resource Management - MRM).

Conceptualizing functional traits and ecological characteristics of methane‐oxidizing bacteria as life strategies

Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.