Single-species microbial biofilm screening for industrial applications

Transcriptional organization and regulation of the Pseudomonas putida flagellar system

A single region of the Pseudomonas putida genome, designated the flagellar cluster, includes 59 genes potentially involved in the biogenesis and function of the flagellar system. Here, we combine bioinformatics and in vivo gene expression analyses to clarify the transcriptional organization and regulation of the flagellar genes in the cluster. We have identified 11 flagellar operons and characterized 22 primary and internal promoter regions. Our results indicate that synthesis of the flagellar apparatus and core chemotaxis machinery is regulated by a three-tier cascade in which fleQ is a Class I gene, standing at the top of the transcriptional hierarchy. FleQ- and σ⁵⁴ -dependent Class II genes encode most components of the flagellar structure, part of the chemotaxis machinery and multiple regulatory elements, including the flagellar σ factor FliA. FliA activation of Class III genes enables synthesis of the filament, one stator complex and completion of the chemotaxis apparatus. Accessory regulatory proteins and an intricate operon architecture add complexity to the regulation by providing feedback and feed-forward loops to the main circuit. Because of the high conservation of the gene arrangement and promoter motifs, we believe that the regulatory circuit presented here may also apply to other environmental pseudomonads.

Physiology of microalgal biofilm: a review on prediction of adhesion on substrates

In view of high energy cost and water consumption in microalgae cultivation, microalgal-biofilm-based cultivation system has been advocated as a solution toward a more sustainable and resource friendlier system for microalgal biomass production. Algal-derived extracellular polymeric substances (EPS) form cohesive network to interconnect the cells and substrates; however, their interactions within the biofilm are poorly understood. This scenario impedes the biofilm process development toward resource recovery. Herein, this review elucidates on various biofilm cultivation modes and contribution of EPS toward biofilm adhesion. Immobilized microalgae can be envisioned by the colloid interactions in terms of a balance of both dispersive and polar interactions among three interfaces (cells, mediums and substrates). Last portion of this review is dedicated to the future perspectives and challenges on the EPS; with regard to the biopolymers extraction, biopolymers’ functional description and cross-referencing between model biofilms and full-scale biofilm systems are evaluated. This review will serve as an informative reference for readers having interest in microalgal biofilm phenomenon by incorporating the three main players in attached cultivation systems: microalgae, EPS and supporting materials. The ability to mass produce these miniature cellular biochemical factories via immobilized biofilm technology will lay the groundwork for a more sustainable and feasible production.

Current Understanding on Adhesion and Biofilm Development in Actinobacteria

Biofilm formation and microbial adhesion are two related and complex phenomena. These phenomena are known to play an important role in microbial life and various functions with positive and negative aspects. Actinobacteria have wide distribution in aquatic and terrestrial ecosystems. This phylum is very large and diverse and contains two important genera Streptomyces and Mycobacteria. The genus Streptomyces is the most biotechnologically important, while the genus Mycobacteria contains the pathogenic species of Mycobacteriaceae. According to the literature, the majority of studies carried out on actinomycetes are focused on the detection of new molecules. Despite the well-known diversity and metabolic activities, less attention has been paid to this phylum. Research on adhesion and biofilm formation is not well developed. In the present review, an attempt has been made to review the literature available on the different aspects on biofilm formation and adhesion of Actinobacteria. We focus especially on the genus Streptomyces. Furthermore, a brief overview about the molecules and structures involved in the adhesion phenomenon in the most relevant genus is summarized. We mention the mechanisms of quorum sensing and quorum quenching because of their direct association with biofilm formation.

Biofilms and nanoparticles: applications in agriculture

A profound need to explore eco-friendly methods to practice sustainable agriculture leads to the research and exploration of plant growth-promoting rhizobacteria (PGPRs). Biofilms are assemblages of microbial communities within a self-secreted exopolymeric matrix, adhering to different biotic and abiotic surfaces and performing a variety of desired and undesired functions. Biofilm formation by PGPRs is governed by effective root colonization of the host plant in providing plant growth promotion and stress management. Biofilms can also provide a suitable environment for the synthesis and entrapment of nanoparticles. Together, nanoparticles and PGPRs may contribute towards biocontrol and crop management. This review discusses the significance of biofilms in agriculture and their confluence with different types of nanoparticles for plant protection and improved crop production.

Growth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis

Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured metal packing for biofilm formation. A strong and poor biofilm forming B. subtilis 168 strain due to restored exopolysaccharides (EPS) production or not were cultivated in the system to study the growth behavior of the planktonic and biofilm population for the establishment of a growth model. A high dilution rate was used in order to promote biofilm formation on the packing and wash out unwanted planktonic cells. Biofilm development kinetics on the packing were assessed through a total organic carbon mass balance. The EPS⁺ strain showed a significantly improved performance in terms of adhesion capacity and surfactin production. The mean surfactin productivity of the EPS⁺ strain was about 37% higher during the continuous cultivation compared to the EPS^- strain. The substrate consumption together with the planktonic cell and biofilm development were properly predicted by the model (α = 0.05). The results show the efficiency of the biofilm bioreactor for continuous surfactin production using an EPS producing strain.

Biofilm Forming Antibiotic Resistant Gram-Positive Pathogens Isolated From Surfaces on the International Space Station

The International Space Station (ISS) is a closed habitat in a uniquely extreme and hostile environment. Due to these special conditions, the human microflora can undergo unusual changes and may represent health risks for the crew. To address this problem, we investigated the antimicrobial activity of AGXX®, a novel surface coating consisting of micro-galvanic elements of silver and ruthenium along with examining the activity of a conventional silver coating. The antimicrobial materials were exposed on the ISS for 6, 12, and 19 months each at a place frequently visited by the crew. Bacteria that survived on the antimicrobial coatings [AGXX® and silver (Ag)] or the uncoated stainless steel carrier (V2A, control material) were recovered, phylogenetically affiliated and characterized in terms of antibiotic resistance (phenotype and genotype), plasmid content, biofilm formation capacity and antibiotic resistance transferability. On all three materials, surviving bacteria were dominated by Gram-positive bacteria and among those by Staphylococcus, Bacillus and Enterococcus spp. The novel antimicrobial surface coating proved to be highly effective. The conventional Ag coating showed only little antimicrobial activity. Microbial diversity increased with increasing exposure time on all three materials. The number of recovered bacteria decreased significantly from V2A to V2A-Ag to AGXX®. After 6 months exposure on the ISS no bacteria were recovered from AGXX®, after 12 months nine and after 19 months three isolates were obtained. Most Gram-positive pathogenic isolates were multidrug resistant (resistant to more than three antibiotics). Sulfamethoxazole, erythromycin and ampicillin resistance were most prevalent. An Enterococcus faecalis strain recovered from V2A steel after 12 months exposure exhibited the highest number of resistances (n = 9). The most prevalent resistance genes were ermC (erythromycin resistance) and tetK (tetracycline resistance). Average transfer frequency of erythromycin, tetracycline and gentamicin resistance from selected ISS isolates was 10⁻⁵ transconjugants/recipient. Most importantly, no serious human pathogens such as methicillin resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococci (VRE) were found on any surface. Thus, the infection risk for the crew is low, especially when antimicrobial surfaces such as AGXX® are applied to surfaces prone to microbial contamination.

Microalgal biofilms: A further step over current microalgal cultivation techniques

The scientific community has turned its interest to microalgae lately, because of their countless applications such as wastewater treatment and pharmaceutical industry. Nevertheless, so far applied cultivation methods are still prohibitive. Ordinary cultivation techniques in which microalgae are suspended in liquid medium suffer from many bottlenecks, such as low biomass productivities, difficulty in biomass harvesting and recovery, high installation and operating cost, high water requirements etc. Although, microalgal biofilms are known to be a nuisance because of surfaces fouling, they have emerged as an innovative technology with which microalgae are developed attached to a solid surface. This technique seems to be advantageous as compared to conventional cultivation systems. Microalgal biofilm systems could resolve the problematic aspects of ordinary cultivation techniques such as low biomass productivities, water management and biomass recovery. A detailed description of this technique with respect to the parameters affecting them is reviewed in this work.

Fly ash based robust biocatalyst generation: a sustainable strategy towards enhanced green biosurfactant production and waste utilization

Biosurfactants have been well recognized as an environmentally friendly alternative to chemical surfactants. However, their production remains challenging due to low productivity, short-term microbe stability and the potentially toxic by-products generated in the growth media. To overcome these challenges, the emerging biofilm-based biosynthesis was investigated in this study. A fresh insight into the biosynthesis process was provided through using waste fly ash as a carrier material. The biofilm produced by biosurfactant producer B. subtilis N3-1P attached onto the surface of fly ash acted as a robust and effective biocatalyst. Zeta potential analysis and scanning electron microscope (SEM) characterization were conducted to help unravel the biocatalyst formation. High-value biosurfactant products were then produced in an efficient and sustainable manner. Stimulation by a fly ash assisted biocatalyst on biosurfactant production was confirmed. The biosurfactant yield was boosted over ten times after 24 hours, at a fly ash dosage of 0.5%. The highest biosurfactant yield was achieved after five days, with a final productivity of 305 critical micelle dilution. The underlying mechanism of fly ash assisted biosurfactant production was tracked through it exerting an effect on the quorum sensing system. Fourier-transform infrared (FTIR) spectroscopy and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis demonstrated that the final biosurfactant product belonged to the lipopeptides. This research output is expected to accelerate the development of more effective bioreactors, and make a continuous contribution to high-value product generation and waste reduction.

Biosurfactants have been well recognized as an environmentally friendly alternative to chemical surfactants.

Recombinant Escherichia coli BL21-pET28a-egfp Cultivated with Nanomaterials in a Modified Microchannel for Biofilm Formation

The application of whole cells as catalytic biofilms in microchannels has attracted increasing scientific interest. However, the excessive biomass formation and structure of biofilms in a reactor limits their use. A microchannel reactor with surface modification was used to colonize recombinant Escherichia coil BL21-pET28a-egfp rapidly and accelerated growth of biofilms in the microchannel. The segmented flow system of 'air/culture medium containing nanomaterials' was firstly used to modulate the biofilms formation of recombinant E. coil; the inhibitory effects of nanomaterials on biofilm formation were investigated. The results indicated that the segmental flow mode has a significant impact on the structure and development of biofilms. Using the channels modified by silane reagent, the culture time of biofilms (30 h) was reduced by 6 h compared to unmodified channels. With the addition of graphene sheets (10 mg/L) in Luria-Bertani (LB) medium, the graphene sheets possessed a minimum inhibition rate of 3.23% against recombinant E. coil. The biofilms cultivated by the LB medium with added graphene sheets were stably formed in 20 h; the formation time was 33.33% shorter than that by LB medium without graphene. The developed method provides an efficient and simple approach for rapid preparation of catalytic biofilms in microchannel reactors.

Preparation of Biocomposite Microfibers Ready for Processing into Biologically Active Textile Fabrics for Bioremediation

Biocomposites, i.e., materials consisting of metabolically active microorganisms embedded in a synthetic extracellular matrix, may find applications as highly specific catalysts in bioproduction and bioremediation. 3D constructs based on fibrous biocomposites, so-called "artificial biofilms," are of particular interest in this context. The inability to produce biocomposite fibers of sufficient mechanical strength for processing into bioactive fabrics has so far hindered progress in the area. Herein a method is proposed for the direct wet spinning of microfibers suitable for weaving and knitting. Metabolically active bacteria (either Shewanella oneidensis or Nitrobacter winogradskyi (N. winogradskyi)) are embedded in these fibers, using poly(vinyl alcohol) as matrix. The produced microfibers have a partially crystalline structure and are stable in water without further treatment, such as coating. In a first application, their potential for nitrite removal (N. winogradskyi) is demonstrated, a typical challenge in potable water treatment.

Environmentally sustainable biogenic fabrication of AuNP decorated-graphitic g-C3N4 nanostructures towards improved photoelectrochemical performances

Proposed schematic model for the biogenic synthesis of Au-g-C₃N₄ nanostructures using an environment-friendly approach.

Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach

According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.

Analyzing the influence of microstructured surfaces on the lactic acid production of Lactobacillus delbrueckii lactis in a flow-through cell system

Microorganisms growing in biofilms might be possible biocatalysts for future biotechnological production processes. Attached to a surface and embedded in an extracellular polymeric matrix, they create their preferred environment and form robust cultures for continuous systems. With the objective of implementing highly efficient processes, productive biofilms need to be understood comprehensively. In this study, the influence of microstructured metallic surfaces on biofilm productivity was researched. To conduct this study, titanium and stainless steel sheets were polished, micromilled, as well as coated with particles. Subsequently, the metal sheets were exposed to the lactic acid producing Lactobacillus delbrueckii subsp. lactis under laminar and homogeneous flow conditions in a custom-built flow cell. A proof-of-concept showed that biofilm formation in the system only occurred on the designated substratum. Following a 24-h batch cultivation for primary biofilm development, the culture was continuously provided with glucose containing medium. As different experimental series have indicated, the process resulted to be stable for up to eleven days. Primary metabolite productivity averaged around 6-7 g/(L h). Interestingly, the productivity was shown to be affected neither by the type of metal, nor by the applied microstructures. Nevertheless, a higher dry biomass weight determined on micro-milled substratum indicates a complementary differentiation of biofilm components in future experiments.

Biofilm production by Zymomonas mobilis enhances ethanol production and tolerance to toxic inhibitors from rice bran hydrolysate

Microorganisms play a significant role in bioethanol production from lignocellulosic material. A challenging problem in bioconversion of rice bran is the presence of toxic inhibitors in lignocellulosic acid hydrolysate. Various strains of Zymomonas mobilis (ZM4, TISTR 405, 548, 550 and 551) grown under biofilm or planktonic modes were used in this study to examine their potential for bioconversion of rice bran hydrolysate and ethanol production efficiencies. Z. mobilis readily formed bacterial attachment on plastic surfaces, but not on glass surfaces. Additionally, the biofilms formed on plastic surfaces steadily increased over time, while those formed on glass were speculated to cycle through accumulation and detachment phases. Microscopic analysis revealed that Z. mobilis ZM4 rapidly developed homogeneous biofilm structures within 24 hours, while other Z. mobilis strains developed heterogeneous biofilm structures. ZM4 biofilms were thicker and seemed to be more stable than other Z. mobilis strains. The percentage of live cells in biofilms was greater than that for planktonic cells (54.32 ± 7.10% vs. 28.69 ± 3.03%), suggesting that biofilms serve as a protective niche for growth of bacteria in the presence of toxic inhibitors in the rice bran hydrolysate. The metabolic activity of ZM4 grown as a biofilm was also higher than the same strain grown planktonically, as measured by ethanol production from rice bran hydrolysate (13.40 ± 2.43 g/L vs. 0.432 ± 0.29 g/L, with percent theoretical ethanol yields of 72.47 ± 6.13% and 3.71 ± 5.24% respectively). Strain TISTR 551 was also quite metabolically active, with ethanol production by biofilm and planktonically grown cells of 8.956 ± 4.06 g/L and 0.0846 ± 0.064 g/L (percent theoretical yields were 48.37 ± 16.64% and 2.046 ± 1.58%, respectively). This study illustrates the potential for enhancing ethanol production by utilizing bacterial biofilms in the bioconversion of a readily available and normally unusable low value by-product of rice farming.

Application of biofilm bioreactors in white biotechnology

The production of valuable compounds in industrial biotechnology is commonly done by cultivation of suspended cells or use of (immobilized) enzymes rather than using microorganisms in an immobilized state. Within the field of wastewater as well as odor treatment the application of immobilized cells is a proven technique. The cells are entrapped in a matrix of extracellular polymeric compounds produced by themselves. The surface-associated agglomerate of encapsulated cells is termed biofilm. In comparison to common immobilization techniques, toxic effects of compounds used for cell entrapment may be neglected. Although the economic impact of biofilm processes used for the production of valuable compounds is negligible, many prospective approaches were examined in the laboratory and on a pilot scale. This review gives an overview of biofilm reactors applied to the production of valuable compounds. Moreover, the characteristics of the utilized materials are discussed with respect to support of surface-attached microbial growth.

Application of the adhesive bacterionanofiber AtaA to a novel microbial immobilization method for the production of indigo as a model chemical

The toluene-degrading bacterium Acinetobacter sp. Tol 5 shows high adhesiveness mediated by the bacterionanofiber protein AtaA, which is a new member of the trimeric autotransporter adhesin (TAA) family. In contrast to other reported TAAs, AtaA mediates the adhesion of Tol 5 to various abiotic surfaces ranging from hydrophobic plastics to hydrophilic glass and stainless steel. The expression of ataA in industrially relevant bacteria improves their adhesiveness and enables immobilization directly onto support materials. This represents a new method that can be alternated with conventional immobilization via gel entrapment and chemical bonding. In this study, we demonstrate the feasibility of this immobilizing method by utilizing AtaA. As a model case for this method, the indigo producer Acinetobacter sp. ST-550 was transformed with ataA and immobilized on a polyurethane support. The immobilized ST-550 cells were transferred directly to a reaction solution containing indole as the substrate. The immobilized ST-550 cells showed a faster indigo production rate at high concentrations of indole compared with planktonic ST-550 not expressing the ataA gene, implying that immobilization enhanced the tolerance of ST-550 to the substrate indole. As a result, the immobilized ST-550 produced fivefold higher levels of indigo than planktonic ST-550. These results proved that AtaA is useful for bacterial immobilization.

Picoliter nDEP traps enable time-resolved contactless single bacterial cell analysis in controlled microenvironments

We present a lab-on-a-chip device, the Envirostat 2.0, which allows for the first time contactless cultivation of a single bacterial cell by negative dielectrophoresis (nDEP) in a precisely controllable microenvironment. Stable trapping in perfusing growth medium was achieved by a miniaturization of octupole electrode geometries, matching the dimensions of bacteria. Temperature sensitive fluorescent measurements showed that these reductions of microelectrode distances led to reduced Joule heating during cell manipulation. The presented miniaturization is not possible with conventional manufacturing processes. Therefore, we present a novel bonding technology, which permits miniaturization of 3D octupole electrode geometry with biocompatible materials. To exclude the influence of other cells and to enable sampling of perfusion medium from the isolated living bacterium under study, computer aided flow simulations were used to develop a microfluidic nDEP isolation procedure. The developed microchannel and microelectrode design integrates for the first time well characterized nDEP cell sorting mechanisms and time-resolved contactless single bacterial cell cultivation in a 1.7 picoliter bioreactor system. The cell type independent trapping is demonstrated with singularized Bacillus subtilis, Escherichia coli, Corynebacterium glutamicum and other industrially relevant microbes. The static and precisely controlled microenvironment resulted in a consistent and significant faster growth compared to maximal growth rates observed on population level. Preventing the influence of surfaces and cell-cell interactions, the Envirostat 2.0 chip permits total microenvironmental control by the experimenter and therefore provides major opportunities for microfluidic based cell analysis of bacteria and small eukaryotes.

Isolated microbial single cells and resulting micropopulations grow faster in controlled environments

Singularized cells of Pichia pastoris, Hansenula polymorpha, and Corynebacterium glutamicum displayed specific growth rates under chemically and physically constant conditions that were consistently higher than those obtained in populations. This highlights the importance of single-cell analyses by uncoupling physiology and the extracellular environment, which is now possible using the Envirostat 2.0 concept.

Maximizing the productivity of catalytic biofilms on solid supports in membrane aerated reactors

A new solid support membrane aerated biofilm reactor was designed for the synthesis of enantiopure (S)-styrene oxide utilizing Pseudomonas sp. strain VLB120DeltaC growing in a biofilm as biocatalyst. In analogy to traditional packed bed systems, maximizing the volumetric oxygen mass transfer capability (k(L)a) was identified as the most critical issue enabling a consistent productivity, as this parameter was shown to directly influence biofilm growth and biotransformation performance. A microporous ceramic unit was identified as an ideal microenvironment for biofilm growth and for efficient oxygen transfer. A uniform and dense biofilm developed on this matrix. Due to this dual function, the reactor configuration could be significantly simplified by eliminating additional packing materials, as used in traditional packed bed reactors. Up to now, a maximum productivity of 28 g L(ab) (-1) day(-1) was achieved by integrating an in situ substrate feed and an in situ product recovery technique based on a silicone membrane. The system was stable for more than 30 days before it was actively terminated.

Cell immobilization for production of lactic acid biofilms do it naturally

Interest in natural cell immobilization or biofilms for lactic acid fermentation has developed considerably over the last few decades. Many studies report the benefits associated with biofilms as industrial methods for food production and for wastewater treatment, since the formation represents a protective means of microbial growth offering survival advantages to cells in toxic environments. The formation of biofilms is a natural process in which microbial cells adsorb to a support without chemicals or polymers that entrap the cells and is dependent on the reactor environment, microorganism, and characteristics of the support. These unique characteristics enable biofilms to cause chronic infections, disease, food spoilage, and devastating effects as in microbial corrosion. Their distinct resistance to toxicity, high biomass potential, and improved stability over cells in suspension make biofilms a good tool for improving the industrial economics of biological lactic acid production. Lactic acid bacteria and specific filamentous fungi are the main sources of biological lactic acid. Over the past two decades, studies have focused on improving the lactic acid volumetric productivity through reactor design development, new support materials, and improvements in microbial production strains. To illustrate the operational designs applied to the natural immobilization of lactic acid producing microorganisms, this chapter presents the results of a search for optimum parameters and how they are affected by the physical, chemical, and biological variables of the process. We will place particular emphasis upon the relationship between lactic acid productivity attained by various types of reactors, supports, media formulations, and lactic acid producing microorganisms.

Microbial biofilms: a concept for industrial catalysis?

Biofilm reactors have long been commercially used in the treatment of wastewater and off-gas. New opportunities are arising with the rapid expansion of our understanding of biofilm biology over the last few years. Biofilms have great potential as industrial workhorses for the sustainable production of chemicals because of their inherent characteristics of self-immobilization, high resistance to reactants and long-term activity, which all facilitate continuous processing. A variety of biofilm reactor configurations have been explored for productive catalysis and some reactors have been operated continuously for months. Sectors that might particularly benefit from this biofilm approach include synthetic chemistry (ranging from specialty to bulk chemicals), bioenergy, biologics and the food industry.