Digitalization in microbiology - Paving the path to sustainable circular bioeconomy

The piranha gut microbiome provides a selective lens into river water biodiversity

Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.

Extremophiles in a changing world

Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.

The buzz about honey-based biosurveys

Approximately 1.8 million metric tonnes of honey are produced globally every year. The key source behind this output, the honey bee (Apis mellifera), works tirelessly to create the delicious condiment that is consumed worldwide. The honey that finds its way into jars on store shelves contains a myriad of information about its biogeographical origins, such as the bees that produced it, the botanical constituents, and traces of other organisms or pathogens that have come in contact with the product or its producer. With the ongoing threat of honey bee decline and overall global biodiversity loss, access to ecological information has become an key factor in preventing the loss of species. This review delves into the various molecular techniques developed to characterize the collective DNA harnessed within honey samples, and how it can be used to elucidate the ecological interactions between honey bees and the environment. We also explore how these DNA-based methods can be used for large-scale biogeographical studies through the environmental DNA collected by foraging honey bees. Further development of these techniques can assist in the conservation of biodiversity by detecting ecosystem perturbations, with the potential to be expanded towards other critical flying pollinators.

Digitalization concepts in academic bioprocess development

Digitalization with integrated devices, digital and physical assistants, automation, and simulation is setting a new direction for laboratory work. Even with complex research workflows, high staff turnover, and a limited budget some laboratories have already shown that digitalization is indeed possible. However, academic bioprocess laboratories often struggle to follow the trend of digitalization. Due to their diverse research circumstances, high variety of team composition, goals, and limitations the concepts are substantially different. Here, we will provide an overview on different aspects of digitalization and describe how academic laboratories successfully digitalized their working environment. The key aspect is the collaboration and communication between IT-experts and scientific staff. The developed digital infrastructure is only useful if it supports the laboratory worker and does not complicate their work. Thereby, laboratory researchers have to collaborate closely with IT-experts in order for a well-developed and maintainable digitalization concept that fits their individual needs and level of complexity. This review may serve as a starting point or a collection of ideas for the transformation toward a digitalized laboratory.

Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs

The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.

Cyberbiosecurity in high-containment laboratories

High-containment laboratories (HCLs) conduct critical research on infectious diseases, provide diagnostic services, and produce vaccines for the world's most dangerous pathogens, often called high-consequence pathogens (HCPs). The modernization of HCLs has led to an increasingly cyber-connected laboratory infrastructure. The unique cyberphysical elements of these laboratories and the critical data they generate pose cybersecurity concerns specific to these laboratories. Cyberbiosecurity, the discipline devoted to the study of cybersecurity risks in conjunction with biological risks, is a relatively new field for which few approaches have been developed to identify, assess, and mitigate cyber risks in biological research and diagnostic environments. This study provides a novel approach for cybersecurity risk assessment and identification of risk mitigation measures by applying an asset-impact analysis to the unique environment of HCLs. First, we identified the common cyber and cyberphysical systems in HCLs, summarizing the typical cyber-workflow. We then analyzed the potential adverse outcomes arising from a compromise of these cyber and cyberphysical systems, broadly categorizing potential consequences as relevant to scientific advancement, public health, worker safety, security, and the financial wellbeing of these laboratories. Finally, we discussed potential risk mitigation strategies, leaning heavily on the cybersecurity materials produced by the Center for Internet Security (CIS), including the CIS Controls®, that can serve as a guide for HCL operators to begin the process of implementing risk mitigation measures to reduce their cyberbiorisk and considering the integration of cyber risk management into existing biorisk management practices. This paper provides a discussion to raise awareness among laboratory decision-makers of these critical risks to safety and security within HCLs. Furthermore, this paper can serve as a guide for evaluating cyberbiorisks specific to a laboratory by identifying cyber-connected assets and the impacts associated with a compromise of those assets.

Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans

The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.

Insights into microbial diversity on plastisphere by multi-omics

Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.

Partnership for International Development: Finland-Argentina Conference on Circular Economy and Bioeconomy with Emphasis on Food Sovereignty and Sustainability

A joint collaboration between the Cuarto region of Argentina championed by the National University of Rio Cuarto and the Arctic Centre of the University of Lapland, Finland organised a conference on several topics that are related to food sovereignty, sustainability, circular economy and bioeconomy. The efficient utilisation of natural resources in both regions is an important theme in meeting the sustainable development goals agenda. Hence, this partnership between the partner institutions will lead to the cocreation of knowledge. The topics were multidisciplinary, and the discussion focussed on research and teaching opportunities for institutions in both countries. The experts from both countries will continue to engage on the possibility of promoting the research agenda in these important areas.

Smart and Sustainable Bioeconomy Platform: A New Approach towards Sustainability

The smart and sustainable bioeconomy represents a comprehensive perspective, in which economic, social, environmental, and technological dimensions are considered simultaneously in the planning, monitoring, evaluating, and redefining of processes and operations. In this context of profound transformation driven by rapid urbanization and digitalization, participatory and interactive strategies and practices have become fundamental to support policymakers, entrepreneurs, and citizens in the transition towards a smart and sustainable bioeconomy. This approach is applied by numerous countries around the world in order to redefine their strategy of sustainable and technology-assisted development. Specifically, real-time monitoring stations, sensors, Internet of Things (IoT), smart grids, GPS tracking systems, and Blockchain aim to develop and strengthen the quality and efficiency of the circularity of economic, social, and environmental resources. In this sense, this study proposes a systematic review of the literature of smart and sustainable bioeconomy strategies and practices implemented worldwide in order to develop a platform capable of integrating holistically the following phases: (1) planning and stakeholder management; (2) identification of social, economic, environmental, and technological dimensions; and (3) goals. The results of this analysis emphasise an innovative and under-treated perspective, further stimulating knowledge in the theoretical and managerial debate on the smart and sustainable aspects of the bioeconomy, which mainly concern the following: (a) the proactive involvement of stakeholders in planning; (b) the improvement of efficiency and quality of economic, social, environmental, and technological flows; and (c) the reinforcement of the integration between smartness and sustainability.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Nexus of circular economy and sustainable business performance in the era of digitalization

Purpose

This study aims to conduct a comprehensive review and network-based analysis by exploring future research directions in the nexus of circular economy (CE) and sustainable business performance (SBP) in the context of digitalization.

Design/methodology/approach

A systematic literature review methodology was adopted to present the review in the field of CE and SBP in the era of digitalization. WOS and SCOPUS databases were considered in the study to identify and select the articles. The bibliometric study was carried out to analyze the significant contributions made by authors, various journal sources, countries and different universities in the field of CE and SBP in the era of digitalization. Further, network analysis is carried out to analyze the collaboration among authors from different countries.

Findings

The study revealed that digitalization could be a great help in developing sustainable circular products. Moreover, the customers' involvement is necessary for creating innovative sustainable circular products using digitalization. A move toward the product-service system was suggested to accelerate the transformation toward CE and digitalization.

Originality/value

The paper discusses digitalization and CE practices' adoption to enhance the SP of the firms. This work's unique contribution is the systematic literature analysis and bibliometric study to explore future research directions in the nexus of CE and SP in the context of digitalization. The present study has been one of the first efforts to examine the literature of CE and SBP integration from a digitalization perspective along with bibliometric analysis.

A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases

Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.