Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces

Microbial dynamics of South Korean beef and surroundings along the supply chain based on high-throughput sequencing

Microbiological safety and quality of beef is crucial as beef can serve as a reservoir for a variety of bacteria, including spoilage-related and foodborne pathogens. Controlling microbial contamination is a critical aspect of food quality and safety, but it is difficult to prevent as there are several potential sources of contamination from production to distribution. In this study, the microbiological ecology of cattle/beef and associated environmental samples (n = 69) were trace-investigated to reveal microbiome shifts in cattle/beef and possible cross-contaminants throughout the entire supply chain using 16S rRNA gene sequencing. Pseudomonas, Psychrobacter, and Acinetobacter, known as spoilage bacteria, opportunistic pathogens, or antibiotic-resistant bacteria, were the main microorganisms present in cattle/beef, and Staphylococcus became abundant in the final products. The dominance of Acinetobacter and Pseudomonas was noticeable in the slaughtered carcasses and slaughterhouse environment, indicating that the slaughterhouse is a critical site where hygienic practices are required to prevent further contamination. Taxonomic similarities between cattle/beef and several environmental samples, as well as diversity analysis, presented a high potential for microbial transmission. Source tracking identified environmental samples that primarily contributed to the microbiota of cattle/beef. Farm floor (48%), workers' gloves (73%), and carcass splitters (20%) in the slaughterhouse were found to be major sources influencing the microbiome of cattle/beef at the farm, slaughterhouse, and processing plant, respectively. These findings demonstrated the dynamics of bacterial communities in cattle/beef according to stage and detected potential contamination sources, which may aid in a better understanding and control of microbial transmission in beef production.

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems

Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.

Bacteria of eleven different species isolated from biofilms in a meat processing environment have diverse biofilm forming abilities

Biofilms are formed by microorganisms protected by a self-produced matrix, most often attached to a surface. In the food processing environments biofilms endanger the product safety by the transmission of spoilage and pathogenic bacteria. In this study, we characterised the biofilm formation of the following eleven strains isolated from biofilms in a meat-processing environment: Acinetobacter harbinensis BF1, Arthrobacter sp. BF1, Brochothrix thermosphacta BF1, Carnobacterium maltaromaticum BF1, Kocuria salsicia BF1, Lactococcus piscium BF1, Microbacterium sp. BF1, Pseudomonas fragi BF1, Psychrobacter sp. BF1, Rhodococcus erythropolis BF1, Stenotrophomonas sp. BF1. We applied whole- genome sequencing and subsequent genome analysis to elucidate genetic features associated with the biofilm lifestyle. We furthermore determined the motility and studied biofilm formation on stainless steel using a static mono-species biofilm model mimicking the meat processing environment. The biomass and the EPS components carbohydrates, proteins and extracellular DNA (eDNA) of the biofilms were investigated after seven days at 10 °C. Whole-genome analysis of the isolates revealed that all strains except the Kocuria salsicia BF1 isolate, harboured biofilm associated genes, including genes for matrix production and motility. Genes involved in cellulose metabolism (present in 82% of the eleven strains) and twitching motility (present in 45%) were most frequently found. The capacity for twitching was confirmed using plate assays for all strains except Lactococcus piscium BF1, which showed the lowest motility behaviour. Differences in biofilm forming abilities could be demonstrated. The bacterial load ranged from 5.4 log CFU/cm² (Psychrobacter sp. isolate) to 8.7 log CFU/cm² (Microbacterium sp. isolate). The amount of the matrix components varied between isolates. In the biofilm of six strains we detected all three matrix components at different levels (carbohydrates, proteins and eDNA), in two only carbohydrates and eDNA, and in three only carbohydrates. Carbohydrates were detected in biofilms of all strains ranging from 0.5 to 4.3 μg glucose equivalents/cm². Overall, the Microbacterium sp. strain showed the highest biofilm forming ability with high bacterial load (8.7 log CFU/cm²) and high amounts of carbohydrates (2.2 μg glucose equivalents/cm²), proteins (present in all experiments) and eDNA (549 ng/cm²). In contrast, Brochothrix thermosphacta was a weak biofilm former, showing low bacterial load and low levels of carbohydrates in the matrix (6.2 log CFU/cm² and 0.5 μg glucose equivalents/cm²). This study contributes to our understanding of the biofilm forming ability of bacteria highly abundant in the meat processing environment, which is crucial to develop strategies to prevent and reduce biofilm formation in the food producing environment.

Effect of exopolysaccharides produced by dairy starter cultures on biofilms formed on reverse osmosis membranes

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Not all EPS-producing starter cultures have an advantage in regard to their ability to form biofilm on membrane separation surfaces.

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Variations between different EPS modify adhesive behavior to reverse osmosis membranes.

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Cell hydrophobicity is critical for initial adhesion to RO membrane separation surface and thus biofilm formation.

Two different cheese starter cultures producing exopolysaccharides (EPS⁺: Streptococcus thermophilus strain ST3534 and Lactococcus lactis ssp. cremoris strain JFR+) and their isogenic EPS-negative (EPS⁻: S. thermophilus strain ST5842 and L. lactis ssp. cremoris strain JFR–) variants were used to study the attachment of bacterial cells in the absence of growth (at 4°C) and the resultant biofilm formation on reverse osmosis membranes (at 30 or 35°C). We used M17 broth and a 10% solution of whey protein concentrate (with 35% protein) as growth media for biofilm development under static conditions. As expected, ST3534 (EPS⁺) showed significantly greater cell counts within biofilms than ST5842 (EPS⁻). In the absence of growth, however, cells of these 2 isogenic Streptococcus strains attached to the membrane in similar numbers. In contrast, JFR+ counts were significantly lower than those of JFR– under all conditions. These findings indicate that the EPS produced by S. thermophilus may play a greater role in building up the 3-dimensional structure of the biofilm, rather than only assisting during initial attachment of the cells to the membrane, whereas the EPS produced by L. lactis ssp. cremoris hampered both initial attachment to the membrane and biofilm formation. Although no differences were observed in the surface charge of the cells between the 2 EPS-producing cultures, surface hydrophobicity was associated with the different adhesive properties of these microorganisms. In conclusion, our results exclude the hypothesis that all EPS-producing starter cultures have an advantage in regard to their ability to form biofilm on membrane separation surfaces. In contrast, variations between different EPS, with hydrophobicity being an important influencing feature, modify adhesive behavior to reverse osmosis membranes.

Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.

Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B

Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.

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.

FlrA Represses Transcription of the Biofilm-Associated bpfA Operon in Shewanella putrefaciens

Manipulation of biofilm formation in Shewanella is beneficial for application to industrial and environmental biotechnology. BpfA is an adhesin largely responsible for biofilm formation in many Shewanella species. However, the mechanism underlying BpfA production and the resulting biofilm remains vaguely understood. We previously described the finding that BpfA expression is enhanced by DosD, an oxygen-stimulated diguanylate cyclase, under aerobic growth. In the present work, we identify FlrA as a critical transcription regulator of the bpfA operon in Shewanella putrefaciens CN32 by transposon mutagenesis. FlrA acted as a repressor of the operon promoter by binding to two boxes overlapping the -10 and -35 sites recognized by σ⁷⁰ DosD regulation of the expression of the bpfA operon was mediated by FlrA, and cyclic diguanylic acid (c-di-GMP) abolished FlrA binding to the operon promoter. We also demonstrate that FlhG, an accessory protein for flagellum synthesis, antagonized FlrA repression of the expression of the bpfA operon. Collectively, this work demonstrates that FlrA acts as a central mediator in the signaling pathway from c-di-GMP to BpfA-associated biofilm formation in S. putrefaciens CN32.

IMPORTANCE

Motility and biofilm are mutually exclusive lifestyles, shifts between which are under the strict regulation of bacteria attempting to adapt to the fluctuation of diverse environmental conditions. The FlrA protein in many bacteria is known to control motility as a master regulator of flagellum synthesis. This work elucidates its effect on biofilm formation by controlling the expression of the adhesin BpfA in S. putrefaciens CN32 in response to c-di-GMP. Therefore, FlrA plays a dual role in controlling motility and biofilm formation in S. putrefaciens CN32. The cooccurrence of flrA, bpfA, and the FlrA box in the promoter region of the bpfA operon in diverse Shewanella strains suggests that bpfA is a common mechanism that controls biofilm formation in this bacterial species.

Adhesins Involved in Attachment to Abiotic Surfaces by Gram-Negative Bacteria

During the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. Depending on the nature of these interactions, attachment can be transient or permanent. To achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. This article reviews the recent advances in our understanding of the secretion, assembly, and regulation of the bacterial adhesins during biofilm formation, with a particular emphasis on the fimbrial, nonfimbrial, and discrete polysaccharide adhesins in Gram-negative bacteria.

Brine assemblages of ultrasmall microbial cells within the ice cover of Lake Vida, Antarctica

The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions.

Epifluorescence, SEM, TEM and nanoSIMS image analysis of the cold phenotype of Clostridium psychrophilum at subzero temperatures

We have applied an image-based approach combining epifluorescence microscopy, electron microscopy and nanoscale secondary ion mass spectrometry (nanoSIMS) with stable isotope probing to examine directly the characteristic cellular features involved in the expression of the cold phenotype in the Antarctic bacterium Clostridium psychrophilum exposed to a temperature range from +5 to -15 °C under anoxic conditions. We observed dramatic morphological changes depending on temperature. At temperatures below -10 °C, cell division was inhibited and consequently filamentous growth predominated. Bacterial cells appeared surrounded by a remarkably thick cell wall and a capsule formed of long exopolysaccharide fibres. Moreover, bacteria were entirely embedded within a dense extracellular matrix, suggesting a role both in cryo-protection and in the cycling of nutrients and genetic material. Strings of extracellular DNA, transient cell membrane permeability and release of membrane vesicles were observed that suggest that evolution via transfer of genetic material may be especially active under frozen conditions. While at -5 °C, the bacterial population was metabolically healthy, at temperatures below -10 °C, most cells showed no sign of active metabolism or the metabolic flux was extremely slowed down; instead of being consumed, carbon was accumulated and stored in intracellular granules as in preparation for a long-term survival.