Safeguarding bacterial resources promotes biotechnological innovation

Usage of ectoine as a cryoprotectant for cryopreservation of lactic acid bacteria

Streptococcus thermophilus, the only Streptococcus species considered "Generally Recognized Safe", has been used widely in the food industry. This bacterium is one of the most valuable industrial lactic acid bacterial species. Due to the importance of this bacterium in industrial applications, it should be stored for a long time without losing its metabolic properties. The present study aimed to investigate the cryoprotectant effect of three compatible solutes (ectoine, trehalose, and sucrose) on bacterial cells stored at different temperatures (frozen at -80 °C or freeze-dried and subsequently stored at +4, -20, and -80 °C) for three months. The bacterial cells were tested for cell viability, bile salt tolerance, and lactic acid production before and after processing. The highest cell viability, bile salt tolerance, and lactic acid production were obtained with ectoine and under frozen (storage at -80 °C) conditions. In freeze-dried and subsequently stored at various temperatures, the best preservation was obtained at -80 °C, followed by -20 °C and +4 °C. Moreover, when ectoine's preservation potential was compared to other cryoprotectants, ectoine showed the highest preservation, followed by trehalose and sucrose. Although ectoine has a variety of qualities that have been proven, in the current work, we have shown for the first time that ectoine has cryoprotectant potential in yogurt starter cultures (S. thermophilus).

Systematic optimization of fermentation conditions for in vitro fermentations with fecal inocula

In vitro fermentation strategies with fecal inocula are considered cost-effective methods to gain mechanistic insights into fecal microbiota community dynamics. However, all in vitro approaches have their limitations due to inherent differences with respect to the in vivo situation mimicked, introducing possible biases into the results obtained. Here, we aimed to systematically optimize in vitro fermentation conditions to minimize drift from the initial inoculum, limit growth of opportunistic colonizers, and maximize the effect of added fiber products (here pectin) when compared to basal medium fermentations. We evaluated the impact of varying starting cell density and medium nutrient concentration on these three outcomes, as well as the effect of inoculation with fresh vs. stored fecal samples. By combining GC-MS metabolite profiling and 16 s rRNA gene-based amplicon sequencing, we established that starting cell densities below 1010 cells/ml opened up growth opportunities for members the Enterobacteriaceae family. This effect was exacerbated when using fecal samples that were stored frozen at -80°C. Overgrowth of Enterobacteriaceae resulted in lowered alpha-diversity and larger community drift, possibly confounding results obtained from fermentations in such conditions. Higher medium nutrient concentrations were identified as an additional factor contributing to inoculum community preservation, although the use of a less nutrient dense medium increased the impact of fiber product addition on the obtained metabolite profiles. Overall, our microbiome observations indicated that starting cell densities of 1010 cells/ml limited opportunities for exponential growth, suppressing in vitro community biases, whilst metabolome incubations should preferably be carried out in a diluted medium to maximize the impact of fermentable substrates.

A cryopreservation method to recover laboratory- and field-derived bacterial communities from mosquito larval habitats

Mosquitoes develop in a wide range of aquatic habitats containing highly diverse and variable bacterial communities that shape both larval and adult traits, including the capacity of adult females of some mosquito species to transmit disease-causing organisms to humans. However, while most mosquito studies control for host genotype and environmental conditions, the impact of microbiota variation on phenotypic outcomes of mosquitoes is often unaccounted for. The inability to conduct reproducible intra- and inter-laboratory studies of mosquito-microbiota interactions has also greatly limited our ability to identify microbial targets for mosquito-borne disease control. Here, we developed an approach to isolate and cryopreserve bacterial communities derived from lab and field-based larval rearing environments of the yellow fever mosquito Aedes aegypti-a primary vector of dengue, Zika, and chikungunya viruses. We then validated the use of our approach to generate experimental microcosms colonized by standardized lab- and field-derived bacterial communities. Our results overall reveal minimal effects of cryopreservation on the recovery of both lab- and field-derived bacteria when directly compared with isolation from non-cryopreserved fresh material. Our results also reveal improved reproducibility of bacterial communities in replicate microcosms generated using cryopreserved stocks over fresh material. Communities in replicate microcosms further captured the majority of total bacterial diversity present in both lab- and field-based larval environments, although the relative richness of recovered taxa as compared to non-recovered taxa was substantially lower in microcosms containing field-derived bacteria. Altogether, these results provide a critical next step toward the standardization of mosquito studies to include larval rearing environments colonized by defined microbial communities. They also lay the foundation for long-term studies of mosquito-microbe interactions and the identification and manipulation of taxa with potential to reduce mosquito vectorial capacity.

Enhancing cell resistance for production of mixed microbiological reference materials with Salmonella and coliforms by freeze-drying

The reference material (RM) is a technical requirement for the quality assurance of analytical results and proficiency tests or interlaboratory comparisons. Microbiological RMs are most available in the dehydrated form, mainly by freeze-drying, and maintaining bacterial survival after preparation is a challenge. Thus, obtaining the most resistant cells is essential. Considering that bacteria present cross-response to dehydration after being submitted to an array of stress conditions, this study aimed to evaluate the influence of growth conditions on enterobacteria for the production of mixed microbiological RMs by freeze-drying in skim milk powder. Salmonella enterica serovar Enteritidis, Cronobacter sakazakii, Escherichia coli, and Citrobacter freundii were grown in a minimal medium with 0.5 M NaCl and 0 to 5.0 mM of manganese sulfate (MnSO4) until stationary phase. Salmonella Enteritidis presented an increased resistance to dehydration in the presence of Mn, while C. sakazakii was the most resistant to freeze-drying and further storage for 90 days. Mixed microbiological RMs were produced by freeze-drying and containing Salmonella Enteritidis and coliforms in skim milk powder with 100 mM of trehalose and the Salmonella survival rate was 91.2 to 93.6%. The mixed RM was stable after 30 days at -20 °C, and Salmonella and coliforms were detected by different methods being, the Rambach Agar the best for the bacterial differentiation. The results showed that the culture conditions applied in this study resulted in bacterial cells being more resistant to dehydration, freeze-drying, and stabilization for the production of mixed microbiological RMs more stable and homogeneous.

Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions

In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.

Distribution of Sulfate-Reducing Bacteria in the Environment: Cryopreservation Techniques and Their Potential Storage Application

Sulfate-reducing bacteria (SRB) are a heterogeneous group of anaerobic microorganisms that play an important role in producing hydrogen sulfide not only in the natural environment, but also in the gastrointestinal tract and oral cavity of animals and humans. The present review was written with the inclusion of 110 references including the time period from 1951 to 2021. The following databases were evaluated: Web of Science, Scopus and Google Scholar. The articles chosen to be included in the review were written mainly in the English and Czech languages. The molecular mechanisms of microbial cryoprotection differ depending on the environment where microorganisms were initially isolated. It was observed that the viability of microorganisms after cryopreservation is dependent on a number of factors, primarily colony age, amount of inoculum, cell size or rate of cooling, and their molecular inventory. Therefore, this paper is devoted to assessing the performance and suitability of various cryopreservation methods of intestinal bacteria, including molecular mechanisms of their protection. In order to successfully complete the cryopreservation process, selecting the correct laboratory equipment and cryopreservation methodology is important. Our analysis revealed that SRB should be stored in glass vials to help mitigate the corrosive nature of hydrogen sulfide, which can affect their physiology on a molecular level. Furthermore, it is recommended that their storage be performed in distilled water or in a suspension with a low salt concentration. From a molecular biological and bioengineering perspective, this contribution emphasizes the need to consider the potential impact associated with SRB in the medical, construction, and environmental sectors.

Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration

Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA P = 0.035) and specific increases in the relative abundances of donor Lachnospiraceae, Bacteroidaceae, and Porphyromonadaceae (P ≤ 0.033). Lower relative abundances of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.

Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.

A new protectant medium preserving bacterial viability after freeze drying

Freeze-drying technology has been widely considered for decades as a suitable technique to preserve microorganisms. However, protective agents must be added prior to freeze drying to improve the survival and storage stability of the bacteria. The objective of our study was to evaluate the effect of a new protectant medium containing sucrose (10 %), trehalose (10 %), skimmed milk (10 %) and antioxidants on the viability of gut bacteria under different storage conditions. Two strains were tested, Escherichia coli and Akkermansia muciniphila, as examples of facultative aerobic and anaerobic bacteria, respectively. We studied the cell viability and bacterial morphology in 5 fecal samples in the presence and absence of this protectant medium using plating technique, flow cytometry and scanning electron microscopy. The results of bacterial viability assessed by plating method showed that the protectant medium yielded higher survival rates for both strains whatever the storage conditions (85-93 %) compared to normal saline solution (0.36-37.50 %). It also showed its effectiveness on fecal samples, where bacterial viability after freeze-drying was 89.47 ± 7.63 % and 84.01 ± 7.44 %, as evidenced by flow cytometry analysis and plating method. However unprotected samples showed the lowest cell viability at 19.01 ± 12.88 % and 13.23 ± 9.56 %, as measured by flow cytometry and plating method. In addition, bacterial size and shape were conserved in the protectant medium. In contrast, storage without protectant medium severely damaged bacterial morphology. In conclusion, our study is the first to use morphological features as well as culture-dependant and culture-independent tests to evaluate the effectiveness of a new protectant medium.

Low-moisture food matrices as probiotic carriers

To exert a beneficial effect on the host, adequate doses of probiotics must be administered and maintaining their viability until consumption is thus essential. Dehydrated probiotics exhibit enhanced long-term viability and can be incorporated into low-moisture food matrices, which also possess high stability at refrigeration and ambient temperature. However, several factors associated with the desiccation process, the physicochemical properties of the matrix and the storage conditions can affect probiotic survival. In the near future, an increased demand for probiotics based on functionally dominant members of the gut microbiome ('next-generation probiotics', NGP) is expected. NGPs are very sensitive to oxygen and efficient encapsulation protocols are needed. Strategies to improve the viability of traditional probiotics and particularly of NGPs involve the selection of a suitable carrier as well as proper desiccation and protection techniques. Dehydrated probiotic microcapsules may constitute an alternative to improve the microbial viability during not only storage but also upper gastrointestinal tract passage. Here we review the main dehydration techniques that are applied in the industry as well as the potential stresses associated with the desiccation process and storage. Finally, low- or intermediate-moisture food matrices suitable as carriers of traditional as well as NGPs will be discussed.

Storing of exoelectrogenic anolyte for efficient microbial fuel cell recovery

Starting up a microbial fuel cell (MFC) requires often a long-term culture enrichment period, which is a challenge after process upsets. The purpose of this study was to develop low-cost storage for MFC enrichment culture to enable prompt process recovery after upsets. Anolyte of an operating xylose-fed MFC was stored at different temperatures and for different time periods. Storing the anolyte for 1 week or 1 month at +4°C did not significantly affect power production, but the lag time for power production was increased from 2 days to 3 or 5 days, respectively. One month storing at -20°C increased the lag time to 7 days. The average power density in these MFCs varied between 1.2 and 1.7 W/m³. The share of dead cells (measured by live/dead staining) increased with storing time. After 6-month storage, the power production was insignificant. However, xylose removal remained similar in all cultures (99-100%) while volatile fatty acids production varied. The results indicate that fermentative organisms tolerated the long storage better than the exoelectrogens. As storing at +4°C is less energy intensive compared to freezing, anolyte storage at +4°C for a maximum of 1 month is recommended as start-up seed for MFC after process failure to enable efficient process recovery.

Ice Recrystallization Inhibiting Polymers Enable Glycerol-Free Cryopreservation of Microorganisms

All modern molecular biology and microbiology is underpinned by not only the tools to handle and manipulate microorganisms but also those to store, bank, and transport them. Glycerol is the current gold-standard cryoprotectant, but it is intrinsically toxic to most microorganisms: only a fraction of cells survive freezing and the presence of glycerol can impact downstream applications and assays. Extremophile organisms survive repeated freeze/thaw cycles by producing antifreeze proteins which are potent ice recrystallization inhibitors. Here we introduce a new concept for the storage/transport of microorganisms by using ice recrystallization inhibiting poly(vinyl alcohol) in tandem with poly(ethylene glycol). This cryopreserving formulation is shown to result in a 4-fold increase in E. coli yield post-thaw, compared to glycerol, utilizing lower concentrations, and successful cryopreservation shown as low as 1.1 wt % of additive. The mechanism of protection is demonstrated to be linked not only to inhibiting ice recrystallization (by comparison to a recombinant antifreeze protein) but also to the significantly lower toxicity of the polymers compared to glycerol. Optimized formulations are presented and shown to be broadly applicable to the cryopreservation of a panel of Gram-negative, Gram-positive, and mycobacteria strains. This represents a step-change in how microorganisms will be stored by the design of new macromolecular ice growth inhibitors; it should enable a transition from traditional solvent-based to macromolecular microbiology storage methods.

Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes

Strict anaerobic gut microbes have been suggested as ‘next‐generation probiotics’ for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (−80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant‐free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03–2% in protectant‐free cultures to 11–37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process‐ and species‐specific.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

BACKGROUND

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions.

RESULTS

High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms.

CONCLUSIONS

A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.

PERN: an EU-Russia initiative for rhizosphere microbial resources

Millions of microbial taxa inhabit the rhizosphere and could be used as biofertilizers, biopesticides, and/or for bioremediation. Only a fraction of these microbes have been described and/or are being utilized. Most are dispersed in collections, but coordination of their accessibility and availability is challenging. Here, we present the Pan-European Rhizosphere Resource Network (PERN), which is a transnational repository of microorganisms whose objectives are to facilitate access to rhizosphere resources and information and help users with technical and legal issues.

Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity

The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.

Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria for the scientific community

Long-term storage of the fastidious ammonia-oxidizing bacteria has proven difficult, which limits their public availability and results in a loss of cultured biodiversity. To enable their accessibility to the scientific community, an effective protocol for cryopreservation of ammonia-oxidizing cultures at -80 °C and in liquid nitrogen was developed. Long-term storage could be achieved using 5% DMSO as cryoprotectant, preferably in a cryoprotective preservation medium containing tenfold-diluted trypticase soy broth and 1% trehalose. As such, successful activity and growth recovery was observed for a diverse set of ammonia-oxidizing cultures.

Microbial cultivation and the role of microbial resource centers in the omics era

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.

Rapid and simple cryopreservation of anaerobic ammonium-oxidizing bacteria

A quick and simple protocol for long-term cryopreservation of anaerobic ammonium-oxidizing bacteria (anammox bacteria) was developed. After 29 weeks of preservation at -80°C, activity recovery for all tested cultures under at least one of the applied sets of preservation conditions was observed. Growth recovery was also demonstrated for a single-cell culture of "Candidatus Kuenenia stuttgartiensis."