Biofilm formation, sodium hypochlorite susceptibility and genetic diversity of Vibrio parahaemolyticus

Vibrio parahaemolyticus is a marine oriented pathogen; and biofilm formation enables its survival and persistence on seafood processing plant, complicating the hygienic practice. The objectives of this study are to assess the ability of V. parahaemolyticus isolated from seafood related environments to form biofilms, to determine the effective sodium hypochlorite concentrations required to inactivate planktonic and biofilm cells, and to evaluate the genetic diversity required for strong biofilm formation. Among nine isolates, PFR30J09 and PFR34B02 isolates were identified as strong biofilm forming strains, with biofilm cell counts of 7.20, 7.08 log10 CFU/cm2, respectively, on stainless steel coupons after incubation at 25 °C. Free available chlorine of 1176 mg/L and 4704 mg/L was required to eliminate biofilm cells of 1.74-2.28 log10 CFU/cm2 and > 7 log10 CFU/cm2, respectively, whereas 63 mg/L for planktonic cells, indicating the ineffectiveness of sodium hypochlorite in eliminating V. parahaemolyticus biofilm cells at recommended concentration in the food industry. These strong biofilm-forming isolates produced more polysaccharides and were less susceptible to sodium hypochlorite, implying a possible correlation between polysaccharide production and sodium hypochlorite susceptibility. Genetic diversity in mshA, mshC and mshD contributed to the observed variation in biofilm formation between isolates. This study identified strong biofilm-forming V. parahaemolyticus strains of new multilocus sequence typing (MLST) types, showed a relationship between polysaccharide production and sodium hypochlorite resistance.fals

Exploring rumen microbe-derived fibre-degrading activities for improving feed digestibility

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evolved with their ruminant hosts over millions of years to perform this task, their enzymes are hypothesised to be optimally suited for activity at the temperature, pH range, and anaerobic environment of the rumen. However, fibre-rich diets are not fully digested, which represents a loss in potential animal productivity. Thus, there is opportunity to improve fibre utilisation through treating feeds with rumen microbe-derived fibrolytic enzymes and associated activities that enhance fibre degradation. This research aims to gain a better understanding of the key rumen microbes involved in fibre degradation and the mechanisms they employ to degrade fibre, by applying cultivation-based and culture-independent genomics approaches to rumen microbial communities of New Zealand dairy cattle. Using this knowledge, we aim to identify new opportunities for improving fibre degradation to enhance dairy productivity. Rumen content samples were taken over the course of a year from a Waikato dairy production herd. Over 1,000 rumen bacterial cultures were obtained from the plant-adherent fraction of the rumen contents. Among these cultures, two, 59 and 103 potentially new families, genera and species of rumen bacteria were identified, respectively. Many of the novel strains are being genome sequenced within the Hungate 1000 rumen microbial reference genome programme, which is providing deeper insights into the range of mechanisms used by the individual strains for fibre degradation. This information has been used to guide the selection of rumen bacterial strains with considerable potential as fibrolytic enzyme producers in vitro, with the intent of developing the strains so that their enzymes may be used as feed pre-treatments for use on farm. Culture-independent metagenomic approaches were also used to explore the activities involved in fibre degradation from the rumen microbial communities. Functional screening has revealed a range of novel enzymes and a novel fibre disrupting activity. Enrichment for the cell-secreted proteins from the community revealed evidence of a diverse range of cellulosomes, which are cell-surface associated multi-enzyme complexes that efficiently degrade plant cell wall polysaccharides. Biochemical and structural characterisation of these proteins has been conducted. In conclusion, cultivation and culture-independent genomic approaches have been applied to New Zealand bovine rumen microbial communities, and have provided considerable new insights into ruminal fibre degradation processes. Novel activities and bacterial species that display desirable activities on fibrous substrates in vitro are now being explored for their potential to improve ruminal fibre degradation, to allow the development of new technologies that will enhance dairy productivity

Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.

Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.fals

Efficacy of commercial peroxyacetic acid on Vibrio parahaemolyticus planktonic cells and biofilms on stainless steel and Greenshell™ mussel (Perna canaliculus) surfaces.

The potential of using commercial peroxyacetic acid (PAA) for Vibrio parahaemolyticus sanitization was evaluated. Commercial PAA of 0.005 % (v/v, PAA: 2.24 mg/L, hydrogen peroxide: 11.79 mg/L) resulted in a planktonic cell reduction of >7.00 log10 CFU/mL when initial V. parahaemolyticus cells averaged 7.64 log10 CFU/mL. For cells on stainless steel coupons, treatment of 0.02 % PAA (v/v, PAA: 8.96 mg/L, hydrogen peroxide: 47.16 mg/L) achieved >5.00 log10 CFU/cm2 reductions in biofilm cells for eight strains but not for the two strongest biofilm formers. PAA of 0.05 % (v/v, PAA: 22.39 mg/L, hydrogen peroxide: 117.91 mg/L) was required to inactivate >5.00 log10 CFU/cm2 biofilm cells from mussel shell surfaces. The detection of PAA residues after biofilm treatment demonstrated that higher biofilm production resulted in higher PAA residues (p < 0.05), suggesting biofilm is acting as a barrier interfering with PAA diffusing into the matrices. Based on the comparative analysis of genomes, robust biofilm formation and metabolic heterogeneity within niches might have contributed to the variations in PAA resistance of V. parahaemolyticus biofilms.fals

Differential Responses of Bird Species to Habitat Condition in a Coastal Kenyan Forest Reserve: Implications for Conservation

The management of assemblages of species across many taxa is a common concern in conservation. Consequently, the use of one or a few surrogate or indicator species to represent an entire assemblage has become an increasingly important tool in conservation science. However, conservation schemes based on the needs of one or two focal species often fail to account for individualistic responses of larger assemblages of species. Data from bird point counts along with vegetation characteristics from a coastal tropical dry forest in Kenya that is subject to elephant disturbance were used to explore the differential responses of bird species to environmental conditions in a forest reserve where wildlife management includes both endangered birds and mammals. Results revealed that even birds with similar foraging habits had idiosyncratic responses to both environmental traits and elephant disturbance. While overall species responded to important characteristics such as percent canopy cover and leaf litter depth, individualistic responses of different species trait diversity defied easy characterization of optimal forest management schemes. Taken together, our analyses highlight the difficulty in basing the development of management plans for entire assemblages of species on the response of a single or a few species. Implications for wildlife conservation in Arabuko-Sokoke Forest and similar forest reserves are discussed, emphasizing the need for a better understanding of individual species’ responses to forest conditions

Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield

How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture

The use of natural products in the leather industry: Depilation without damage

Content: Sheepskin, a by-product of the meat industry, is then often processed to leather, primarily for the clothing industry. Where the tanneries are distant from the abattoirs and freezing works, the raw skins have to be transported long distances to be processed. In warm weather, there is the potential for putrefaction of the skins which then have to be disposed of at a cost. Depilation, the first step of leather processing, is designed to remove the wool from the skin without damaging it. Conventional depilation involves the use of strong alkali and sulfides, that are harmful to both the environment and the personnel carrying out the process due to the potential production of hydrogen sulfide, a toxic, flammable gas. To solve this problem, scientists have been looking to depilate skins using enzymes as these are environmentally friendly. Various enzymes, such as collagenase, keratinase, protease and lipase have been shown to be able to remove hair from skin, but unfortunately usually damage it. Furthermore, at present, they are not cost effective at an industrial level. We have found a simple solution, a derivative of a dairy by-product, that prevents putrefaction, preserving the skin for days at room temperature. In addition, it allows easy removal of the wool from the skin. Scanning electron microscopy showed there was no obvious damage to the surface of the depilated skin and that the wool is cleanly removed from the hair follicle. To assess any less visible damage that may have occurred as a result of soaking the skin, biochemical analyses were carried out to measure the changes to the amino acid composition, collagen crosslinks and proteoglycan concentrations of the depilated skins. Sheepskin depilated with this method was processed to leather and its physical properties such as tear, and tensile strength analysed. Culture dependent methods were used to isolate the microorganisms present in the solution after depilation, showed that only four main species were consistently found in the depilation fluid and on the skins. Metagenomic analysis, confirmed these findings and was used to follow the changes in the microbiome during the course of depilation. This presentation will describe the progress that has been made to understand the science behind these observations and compare the properties of skins depilated using this method with those depilated using the traditional beamhouse process. Take-Away: We are using a natural product to depilate sheepskin. The sheepskin is also preserved while depilation. Microscopy, chemical analyses, physical tests, and metagenomics analysis were done to understand the process

Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium Xylanibacter ruminicola.

Xylanibacter ruminicola is an abundant rumen bacterium that produces propionate in a cobalamin (vitamin B12)-dependent manner via the succinate pathway. However, the extent to which this occurs across ruminal Xylanibacter and closely related bacteria, and the effect of cobalamin supplementation on the expression of propionate pathway genes and enzymes has yet to be investigated. To assess this, we screened 14 strains and found that almost all strains produced propionate when supplemented with cobalamin. X. ruminicola KHP1 was selected for further study, including complete genome sequencing, and comparative transcriptomics and proteomics of KHP1 cultures grown with and without supplemented cobalamin. The complete KHP1 genome was searched for cobalamin-binding riboswitches and four were predicted, though none were closely located to any of the succinate pathway genes, which were dispersed at numerous genomic loci. Cobalamin supplementation led to the differential expression of 17.5% of genes, including genes encoding the cobalamin-dependent methylmalonyl-CoA mutase and some methylmalonyl-CoA decarboxylase subunits, but most propionate biosynthesis pathway genes were not differentially expressed. The effect of cobalamin supplementation on the KHP1 proteome was much less pronounced, with the only differentially abundant propionate pathway enzyme being methylmalonyl-CoA mutase, which had greater abundance when supplemented with cobalamin. Our results demonstrate that cobalamin supplementation does not result in induction of the entire propionate biosynthesis pathway, but consistently increased expression of methylmalonyl-CoA mutase at transcriptome and proteome levels. The magnitude of the differential expression of propionate pathway genes observed was minor compared to that of genes proximate to predicted cobalamin riboswitches. IMPORTANCE In ruminants, the rumen microbial community plays a critical role in nutrition through the fermentation of feed to provide vital energy substrates for the host animal. Propionate is a major rumen fermentation end-product and increasing its production is desirable given its importance in host glucose production and impact on greenhouse gas production. Vitamin B12 (cobalamin) can induce propionate production in the prominent rumen bacterium Xylanibacter ruminicola, but it is not fully understood how cobalamin regulates propionate pathway activity. Contrary to expectation, we found that cobalamin supplementation had little effect on propionate pathway expression at transcriptome and proteome levels, with minor upregulation of genes encoding the cobalamin-dependent enzyme of the pathway. These findings provide new insights into factors that regulate propionate production and suggest that cobalamin-dependent propionate production by X. ruminicola is controlled post-translationally.fals

Global expansion of Vibrio parahaemolyticus threatens the seafood industry: Perspective on controlling its biofilm formation

As global warming increases the geographical range and frequency of Vibrio parahaemolyticus infections, its formation of biofilms providing bacteria greater resistance to stress and contributing to the persistence of pathogens, is threatening the seafood industry. V. parahaemolyticus has a number of advantages leading to biofilm formation. This study reviews recent advances in understanding V. parahaemolyticus biofilm formation on biotic and abiotic surfaces, discusses research gaps in the mechanism of biofilm formation and examines promising biofilm control strategies to overcome current limitations of chemical disinfectant. This information will deepen our understanding of V. parahaemolyticus biofilm formation, as well as help design and optimize V. parahaemolyticus biofilm control strategies for the seafood industry.fals

Global expansion of Vibrio parahaemolyticus threatens the seafood industry: Perspective on controlling its biofilm formation

As global warming increases the geographical range and frequency of Vibrio parahaemolyticus infections, its formation of biofilms providing bacteria greater resistance to stress and contributing to the persistence of pathogens, is threatening the seafood industry. V. parahaemolyticus has a number of advantages leading to biofilm formation. This study reviews recent advances in understanding V. parahaemolyticus biofilm formation on biotic and abiotic surfaces, discusses research gaps in the mechanism of biofilm formation and examines promising biofilm control strategies to overcome current limitations of chemical disinfectant. This information will deepen our understanding of V. parahaemolyticus biofilm formation, as well as help design and optimize V. parahaemolyticus biofilm control strategies for the seafood industry