Effect of yeast extract on microbiologically influenced corrosion of X70 pipeline steel by Desulfovibrio bizertensis SY-1

Microbiologically influenced corrosion (MIC) is a complicated process that happens ubiquitously and quietly in many fields. As a useful nutritional ingredient in microbial culture media, yeast extract (YE) is a routinely added in the MIC field. However, how the YE participated in MIC is not fully clarified. In the present work, the effect of YE on the growth of sulfate reducing prokaryotes (SRP) Desulfovibrio bizertensis SY-1 and corrosion behavior of X70 pipeline steel were studied. It was found that the weight loss of steel coupons in sterile media was doubled when YE was removed from culture media. However, in the SRP assays without YE the number of planktonic cells decreased, but the attachment of bacteria on steel surfaces was enhanced significantly. Besides, the corrosion rate of steel in SRP assays increased fourfold after removing YE from culture media. MIC was not determined for assays with planktonic SRP but only for biofilm assays. The results confirm the effect of YE on D. bizertensis SY-1 growth and also the inhibitory role of YE on MIC.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO₄. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.

Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data

In this article, we present our novel pipeline for analysis of metabolic activity using a microbial community's metatranscriptome sequence data set for validation. Our method is based on expectation-maximization (EM) algorithm and provides enzyme expression and pathway activity levels. Further expanding our analysis, we consider individual enzymatic activity and compute enzyme participation coefficients to approximate the metabolic pathway activity more accurately. We apply our EM pathways pipeline to a metatranscriptomic data set of a plankton community from surface waters of the Northern Gulf of Mexico. The data set consists of RNA-seq data and respective environmental parameters, which were sampled at two depths, six times a day over multiple 24-hour cycles. Furthermore, we discuss microbial dependence on day-night cycle within our findings based on a three-way correlation of the enzyme expression during antipodal times-midnight and noon. We show that the enzyme participation levels strongly affect the metabolic activity estimates: that is, marginal and multiple linear regression of enzymatic and metabolic pathway activity correlated significantly with the recorded environmental parameters. Our analysis statistically validates that EM-based methods produce meaningful results, as our method confirms statistically significant dependence of metabolic pathway activity on the environmental parameters, such as salinity, temperature, brightness, and a few others.

Physiological studies of the Pediococcus pentosaceus biofilm

Pediococcus pentosaceus, a bacterium recently used in human and animal probiotics, was used in combination with supports made from polylactic acid composite soybean meal was used to study biofilm formation, and it was found that dense biofilms developed by Day 1. Proteomic comparison between planktonic and biofilm cultures of P. pentosaceus showed distinct expression patterns of intracellular and extracellular proteins. Type I glyceraldehyde-3-phosphate dehydrogenase was upregulated in biofilm cultures and mediated cell adhesion and encouraged biofilm production. GMP synthase, which regulates GMP synthesis and acts as an intracellular signal molecule to control cell mechanisms and has been exploited in the development of new therapeutic agents, was also upregulated in the biofilm mode of growth. The present work serves as a basis for future studies examining the complex network of systems that regulate lactic acid bacterial (LAB) biofilm formation and can serve as a framework for studies of production of therapeutic agents from LAB.

Biofilm dynamics: linking in situ biofilm biomass and metabolic activity measurements in real-time under continuous flow conditions

The tools used to study biofilms generally involve either destructive, end-point analyses or periodic measurements. The advent of the internet of things (IoT) era allows circumvention of these limitations. Here we introduce and detail the development of the BioSpec; a modular, nondestructive, real-time monitoring system, which accurately and reliably track changes in biofilm biomass over time. The performance of the system was validated using a commercial spectrophotometer and produced comparable results for variations in planktonic and sessile biomass. BioSpec was combined with the previously developed carbon dioxide evolution measurement system (CEMS) to allow simultaneous measurement of biofilm biomass and metabolic activity and revealed a differential response of these interrelated parameters to changing environmental conditions. The application of this system can facilitate a greater understanding of biofilm mass-function relationships and aid in the development of biofilm control strategies.

Metatranscriptomic identification of polyamine-transforming bacterioplankton in the Gulf of Mexico

The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.

Genetic and virulence characterisation of Vibrio parahaemolyticus isolated from Indian coast

BACKGROUND

V. parahaemolyticus is autochthonous to the marine environment and causes seafood-borne gastroenteritis in humans. Generally, V. parahaemolyticus recovered from the environment and/or seafood is thought to be non-pathogenic and the relationship between environmental isolates and acute diarrhoeal disease is poorly understood. In this study, we explored the virulence potential of environmental V. parahaemolyticus isolated from water, plankton and assorted seafood samples collected from the Indian coast.

RESULTS

Twenty-two V. parahaemolyticus isolates from seafood harboured virulence associated genes encoding the thermostable-direct haemolysin (TDH), TDH-related haemolysin (TRH), and Type 3 secretion systems (T3SS) and 95.5% of the toxigenic isolates had pandemic strain attributes (toxRS/new+). Nine serovars, with pandemic strain traits were newly identified and an O4:K36 tdh-trh+V. parahaemolyticus bearing pandemic marker gene was recognised for the first time. Results obtained by reverse transcription PCR showed trh, T3SS1 and T3SS2β to be functional in the seafood isolates. Moreover, the environmental strains were cytotoxic and could invade Caco-2 cells upon infection as well as induce changes to the tight junction protein, ZO-1 and the actin cytoskeleton.

CONCLUSION

Our study provides evidence that environmental isolates of V. parahaemolyticus are potentially invasive and capable of eliciting pathogenic characteristics typical of clinical strains and present a potential health risk. We also demonstrate that virulence of this pathogen is highly complex and hence draws attention for the need to investigate more reliable virulence markers in order to distinguish the environmental and clinical isolates, which will be crucial for the pathogenomics and control of this pathogen.

Prolonged inhibitory effects against planktonic growth, adherence, and biofilm formation of pathogens causing ventilator-associated pneumonia using a novel polyamide/silver nanoparticle composite-coated endotracheal tube

Microbial cells can rapidly form biofilm on endotracheal tubes (ETT) causing ventilator-associated pneumonia, a serious complication in patients receiving mechanical ventilation. A novel polyamide with a good balance of hydrophilic/hydrophobic moieties was used for the embedment of green-reduction silver nanoparticles (AgNPs) for the composite-coated ETT. The films were conformal with a thickness of ∼ 17 ± 3 µm accommodating high loading of 60 ± 35 nm spherical-shaped AgNPs. The coated ETT resulted in a significant difference in reducing both planktonic growth and microbial adhesion of single and mixed-species cultures, compared with uncoated ETT (p < 0.05). A time-kill assay demonstrated rapid bactericidal effects of the coating on bacterial growth and cell adhesion to ETT surface. Biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus, commonly encountered pathogens, was inhibited by > 96% after incubation for 72 h. Polyamide/AgNP composite-coated ETT provided a broad-spectrum activity against both Gram-positive and Gram-negative bacteria as well as Candida albicans and prolonged antimicrobial activity.

In vitro activity of the antimicrobial peptide AP7121 against the human methicillin-resistant biofilm producers Staphylococcus aureus and Staphylococcus epidermidis

In vitro activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis biofilm producers from blood cultures of patients with prosthetic hip infections was evaluated. The Minimum Inhibitory Concentration (MIC) for AP7121 was determined and the bactericidal activity of AP7121 (MICx1, MICx4) against planktonic cells was studied at 4, 8 and 24 h. The biofilms formed were incubated with AP7121 (MICx1, MICx4) for 1 and 24 h. The anti-adhesion effect of an AP7121-treated inert surface over the highest MIC isolate was studied with scanning electron microscopy (SEM). The bactericidal activity of AP7121 against all the planktonic staphylococcal cells was observed at 4 h at both peptide concentrations. Dose-dependent anti-biofilm activity was detected. AP7121 (MICx4) showed bactericidal activity at 24 h in all isolates. SEM confirmed prevention of biofilm formation. This research showed the in vitro anti-biofilm activity of AP7121 against MRSA and S. epidermidis and the prevention of biofilm formation by them on an abiotic surface.

Vitamin C Enhances the Antibacterial Activity of Honey against Planktonic and Biofilm-Embedded Bacteria

Multifactorial antibacterial action is an important feature of honey; however, its bactericidal efficacy against biofilm-embedded bacteria is limited. The aim of this study was to investigate the impact of vitamin C (Vit C) on the antibacterial activity of natural honeys against planktonic as well as biofilm-embedded bacterial pathogens. The antibacterial activity of four honey samples supplemented with Vit C was expressed as the minimum inhibitory concentration (MIC). At sub-MICs, Vit C significantly increased the antibacterial activity of the tested honeys against Pseudomonas aeruginosa in planktonic cultures. However, after supplementation, honeydew honey, the most active honey, was ineffective against Staphylococcus aureus. On the other hand, when 100% honeydew honey was supplemented with Vit C (100 mg/g of honey) in a multispecies wound biofilm model, complete eradication of almost all bacterial isolates, including S. aureus, was observed. Furthermore, a mixture of honey and Vit C was partially effective against Enterococcus faecalis, whereas honey alone exhibited no antibacterial activity against this bacterium. Vit C counteracted hydrogen peroxide in honey solution and, thus, eliminated the major antibacterial compound present in honey. It is likely that a combination of honey with Vit C may trigger the intracellular production of reactive oxygen species in bacterial cells, but the exact cellular mechanisms warrant further investigations.

Synergistic effects of vorinostat (SAHA) and azoles against Aspergillus species and their biofilms

BACKGROUND

Invasive aspergillosis is a fungal infection that occurs mainly in immunocompromised patients. It is responsible for a high degree of mortality and is invariably unresponsive to conventional antifungal treatments. Histone deacetylase inhibitors can affect the cell cycle, apoptosis and differentiation. The histone deacetylase inhibitor vorinostat (SAHA) has recently received approval for the treatment of cutaneous T cell lymphoma. Here, we investigated the interactions of SAHA and itraconazole, voriconazole, and posaconazole against Aspergillus spp. in vitro using both planktonic cells and biofilms.

RESULTS

We investigated 20 clinical strains using broth microdilution checkerboard methods. The results showed synergy between SAHA and itraconazole, voriconazole, and posaconazole against 60, 40, and 25% of tested isolates of planktonic Aspergillus spp., respectively. Similar synergy was also observed against Aspergillus biofilms. The expression of the azole-associated multidrug efflux pumps MDR1, MDR2, MDR3 and MDR4, as well as that of HSP90, was measured by RT-PCR. The results indicated that the molecular mechanism of the observed synergistic effects in Aspergillus fumigatus may be partly associated with dampened expression of the efflux pump genes and, furthermore, that HSP90 suppression may be a major contributor to the observed synergistic effects of the drugs.

CONCLUSIONS

SAHA has potential as a secondary treatment to enhance the effects of azoles against both biofilm and planktonic cells of Aspergillus spp. in vitro. This effect occurs mostly by inhibition of HSP90 expression.

Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype

Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.

Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence

The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

BACKGROUND

The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.

RESULTS

Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.

CONCLUSIONS

This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.

Natural and non-toxic products from Fabaceae Brazilian plants as a replacement for traditional antifouling biocides: an inhibition potential against initial biofouling

In this study, we screened for the antifouling activity of 15 species plant extracts from Brazilian the Brazilian Caatinga Fabaceae against the initial colonization of natural marine bacterial biofilm. We also investigated the potential toxicity of extracts against planktonic and benthic non-target organisms. Aqueous extracts of plants collected in the Caatinga biome (PE, Brazil) were prepared and tested at different concentration levels (0, 0.5, 1, 2, 4, and 8 mg mL^-1). Natural marine bacterial consortium was inoculated in multi-well plates and incubated with the different treatments for 48 h. The biofilm and planktonic bacterial density and biomass inhibition were evaluated along with biofilm biomass eradication. The extracts that showed the highest bacterial biofilm inhibition were evaluated for toxicity against microalgae and crustaceans. The biofilm and planktonic bacterial inhibition potential were evaluated through flow cytometry and spectrophotometry. The selected treatments were evaluated for their toxicity using the microalgae Chaetoceros calcitrans, the copepod Nitokra sp., and the brine shrimp Artemia salina as bioindicators. Our work demonstrates the biotechnological potential of Fabaceae plant compounds as a safe antifouling alternative. Anadenanthera colubrina var. cebil fruits and Apuleia leiocarpa leaf extracts showed antibiofilm activity (≥ 80%), while Myroxylon peruiferum and Dioclea grandiflora leaf extracts showed antibiotic activity. These extracts were safe to planktonic and benthic non-target organisms. The results of this study point to potential substitutes to highly toxic antifouling paints and shed light on the prospect of a yet to be explored biome for more sustainable alternatives in biofouling research.

Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs

BACKGROUND

Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea.

RESULTS

The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high.

CONCLUSIONS

The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.

Algae-bacteria interactions that balance the planktonic microbiome

Phytoplankton communities within the photic zones of the oceans and lakes are characterised by highly complex assemblages of unicellular microalgae and associated bacteria. The interconnected evolutionary history of algae and bacteria allowed the formation of a wide spectrum of associations defined by orchestrated nutrient exchange, mutual support with growth factors, quorum sensing mediation, and episodic killing of the partners to obtain more resources. In this review, we discuss how these cross-kingdom interactions shape plankton communities that undergo annual, seasonal switching between alternative states with balanced multispecies consortia. We illustrate how these microscopic interactions can have consequences that scale up to influence global element cycling.

Development of an autonomous biosampler to capture in situ aquatic microbiomes

The importance of planktonic microbial communities is well acknowledged, since they are fundamental for several natural processes of aquatic ecosystems. Microorganisms naturally control the flux of nutrients, and also degrade and recycle anthropogenic organic and inorganic contaminants. Nevertheless, climate change effects and/or the runoff of nutrients/pollutants can affect the equilibrium of natural microbial communities influencing the occurrence of microbial pathogens and/or microbial toxin producers, which can compromise ecosystem environmental status. Therefore, improved microbial plankton monitoring is essential to better understand how these communities respond to environmental shifts. The study of marine microbial communities typically involves highly cost and time-consuming sampling procedures, which can limit the frequency of sampling and data availability. In this context, we developed and validated an in situ autonomous biosampler (IS-ABS) able to collect/concentrate in situ planktonic communities of different size fractions (targeting prokaryotes and unicellular eukaryotes) for posterior genomic, metagenomic, and/or transcriptomic analysis at a home laboratory. The IS-ABS field prototype is a small size and compact system able to operate up to 150 m depth. Water is pumped by a micropump (TCS MG2000) through a hydraulic circuit that allows in situ filtration of environmental water in one or more Sterivex filters placed in a filter cartridge. The IS-ABS also includes an application to program sampling definitions, allowing pre-setting configuration of the sampling. The efficiency of the IS-ABS was tested against traditional laboratory filtration standardized protocols. Results showed a good performance in terms of DNA recovery, as well as prokaryotic (16S rDNA) and eukaryotic (18S rDNA) community diversity analysis, using either methodologies. The IS-ABS automates the process of collecting environmental DNA, and is suitable for integration in water observation systems, what will contribute to substantially increase biological surveillances. Also, the use of highly sensitive genomic approaches allows a further study of the diversity and functions of whole or specific microbial communities.

Seasonal dynamics of the coastal bacterioplankton at intensive fish-farming areas of the Yellow Sea, China revealed by high-throughput sequencing

Marine aquaculture areas are facing stressed environmental challenges, especially the degradation of coastal ecosystems. Here a coordinated time-series study was used to investigate the coastal bacterioplankton biodiversity dynamics of the Yellow Sea, China. Bacterial 16S rRNA gene sequencing revealed a temporal pattern of decreasing of diversity in summer. Functional prediction indicated that metabolic pathways related to the adenosine triphosphate (ATP)-binding cassette transporters and other membrane transporters were significantly enriched in May, while the genetic information processing category was most abundant in March. The May microbiomes showed most significant positive correlation with phosphate concentration, while the August and November microbiomes correlated with temperature and chemical oxygen demand (COD) most, and the March microbiomes showed significant correlation with Cu²⁺ level, pH and salinity. The correlations between representative bacteria and environmental parameters revealed in this study may provide insights into the potential influences of human aquaculture activities, on the biodiversity of coastal bacterioplankton.

Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production

There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.

Expression of the Biofilm-Associated Genes in Methicillin-Resistant Staphylococcus aureus in Biofilm and Planktonic Conditions

The role of genes that are essential for development of Staphylococcus aureus biofilm during infection is not fully known. mRNA from two methicillin-resistant S. aureus strains that formed weak and strong biofilm on polystyrene plates were isolated at five time points from cells grown in biofilm and planktonic culture. Quantitative real-time PCR analysis showed that the expression levels of investigated genes under biofilm conditions were significantly higher than under planktonic conditions. The expression levels of the gene encoding elastin binding protein (ebps) and laminin binding protein (eno) were significantly increased in biofilm at 3 h, both in strongly and weakly adhering strain. The peak expression of fib gene encoding fibrinogen binding protein was found at 6 and 8 h in the case of strongly and weakly adhering strain, respectively. The expression of icaA and icaD genes in both strains was significantly higher under biofilm conditions when comparing to planktonic cells during 12 h. The expression level of the genes encoding binding proteins and the glucosamine polymer polysaccharide intercellular adhesin (PIA) slowly decreased after 24 h. Finally, we found that the expression levels of genes encoding binding factors in weakly adhering strain were significantly lower than in strongly adhering strain.

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

BACKGROUND

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.

RESULTS

Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.

CONCLUSIONS

These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

Morphological Observation and Comparative Transcriptomic Analysis of Clostridium perfringens Biofilm and Planktonic Cells

Bacterial biofilms can enhance survival in adverse environments and promote infection. However, little is known about biofilm formation by Clostridium perfringens. To better characterize this process, we used SEM to observe the surfaces of C. perfringens biofilms after 12, 24, 48, and 72 h of incubation. Biofilm cells appeared to be encased in a dense matrix material, and the total biomass of the biofilm increased with incubation time. To gain insight into the differentially expressed genes (DEGs) between biofilm and planktonic cells, we carried out comparative transcriptomic analysis using RNA sequencing. In total, 91 genes were significantly differentially expressed, with 40 being up-regulated and 51 down-regulated. In particular, genes encoding sortase, ribosomal proteins, and ATP synthase were up-regulated in biofilms, while genes coding for clostripain and phospholipase C were down-regulated. To validate the RNA sequencing results, qRT-PCR analysis was performed using five randomly selected DEGs. Results showed that all five genes were up-regulated, which was in accordance with the RNA sequencing results. To examine the functional differences, the DEGs were characterized by GO and KEGG pathway enrichment analyses. Results showed that the up-regulated genes were divided into 32 significantly enriched GO terms, with "macromolecular complex" being the most common. Oxidative phosphorylation was the only significantly enriched pathway, suggesting that ATP is required for biofilm stability. This study provides valuable insights into the morphology and transcriptional regulation of C. perfringens during biofilm formation, and will be useful for understanding and developing biofilm-based processes.

Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River

BACKGROUND

Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities in large rivers.

RESULTS

This study provides the first spatiotemporal pattern of bacterial communities in the Yangtze River, the largest river in Asia with a catchment area of 1,800,000 km2. We find that sedimentary bacteria made larger contributions than planktonic bacteria to the bacterial diversity of the Yangzte River ecosystem with the sediment subgroup providing 98.8% of 38,906 operational taxonomic units (OTUs) observed in 280 samples of synchronous flowing water and sediment at 50 national monitoring stations covering a 4300 km reach. OTUs within the same phylum displayed uniform seasonal variations, and many phyla demonstrated autumn preference throughout the length of the river. Seasonal differences in bacterial communities were statistically significant in water, whereas bacterial communities in both water and sediment were geographically clustered according to five types of landforms: mountain, foothill, basin, foothill-mountain, and plain. Interestingly, the presence of two huge dams resulted in a drastic fall of bacterial taxa in sediment immediately downstream due to severe riverbed scouring. The integrity of the biogeography is satisfactorily interpreted by the combination of neutral and species sorting perspectives in meta-community theory for bacterial communities in flowing water and sediment.

CONCLUSIONS

Our study fills a gap in understanding of bacterial communities in one of the world's largest river and highlights the importance of both planktonic and sedimentary communities to the integrity of bacterial biogeographic patterns in a river subject to varying natural and anthropogenic impacts.

Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria

Biofilms are surface-attached groups of microbial cells encased in an extracellular matrix that are significantly less susceptible to antimicrobial agents than non-adherent, planktonic cells. Biofilm-based infections are, as a result, extremely difficult to cure. A wide range of molecular mechanisms contribute to the high degree of recalcitrance that is characteristic of biofilm communities. These mechanisms include, among others, interaction of antimicrobials with biofilm matrix components, reduced growth rates and the various actions of specific genetic determinants of antibiotic resistance and tolerance. Alone, each of these mechanisms only partially accounts for the increased antimicrobial recalcitrance observed in biofilms. Acting in concert, however, these defences help to ensure the survival of biofilm cells in the face of even the most aggressive antimicrobial treatment regimens. This review summarises both historical and recent scientific data in support of the known biofilm resistance and tolerance mechanisms. Additionally, suggestions for future work in the field are provided.

Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli

Here, we investigated novel interactions of three global regulators of the network that controls biofilm formation in the model bacterium Escherichia coli using computational network analysis, an in vivo reporter assay and physiological validation experiments. We were able to map critical nodes that govern planktonic to biofilm transition and identify 8 new regulatory interactions for CRP, IHF or Fis responsible for the control of the promoters of rpoS, rpoE, flhD, fliA, csgD and yeaJ. Additionally, an in vivo promoter reporter assay and motility analysis revealed a key role for IHF as a repressor of cell motility through the control of FliA sigma factor expression. This investigation of first stage and mature biofilm formation indicates that biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning mechanism. Taken together, the analysis presented here shows the utility of combining computational and experimental approaches to generate a deeper understanding of the biofilm formation process in bacteria.

An early mechanical coupling of planktonic bacteria in dilute suspensions

It is generally accepted that planktonic bacteria in dilute suspensions are not mechanically coupled and do not show correlated motion. The mechanical coupling of cells is a trait that develops upon transition into a biofilm, a microbial community of self-aggregated bacterial cells. Here we employ optical tweezers to show that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion. The strength of the coupling increases with the growth of liquid bacterial culture. The matrix responsible for the mechanical coupling is composed of cell debris and extracellular polymer material. The fragile network connecting cells behaves as viscoelastic liquid of entangled extracellular polymers. Our findings point to physical connections between bacteria in dilute bacterial suspensions that may provide a mechanistic framework for understanding of biofilm formation, osmotic flow of nutrients, diffusion of signal molecules in quorum sensing, or different efficacy of antibiotic treatments at low and high bacterial densities.Planktonic bacteria are untethered to surfaces or to each other, and thus are expected to move independently when at low cell densities. Here Sretenovic et al. show, using optical tweezers, that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion.

Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean

Estimation of growth rates is crucial to understand the ecological role of prokaryotes and their contribution to marine biogeochemical cycling. However, there are only a few estimates for individual taxa. Two top-down (grazing) and bottom-up (phosphorus (P) availability) manipulation experiments were conducted under different light regimes in the NW Mediterranean Sea. Growth rate of different phylogenetic groups, including the Bacteroidetes, Rhodobacteraceae, SAR11, Gammaproteobacteria and its subgroups Alteromonadaceae and the NOR5/OM60 clade, were estimated from changes in cell numbers. Maximal growth rates were achieved in the P-amended treatments but when comparing values between treatments (response ratios), the response to predation removal was in general larger than to P-amendment. The Alteromonadaceae displayed the highest rates in both experiments followed by the Rhodobacteraceae, but all groups largely responded to filtration and P-amendment, even the SAR11 which presented low growth rates. Comparing light and dark treatments, growth rates were on average equal or higher in the dark than in the light for all groups, except for the Rhodobacteraceae and particularly the NOR5 clade, groups that contain photoheterotrophic species. These results are useful to evaluate the potential contributions of different bacterial types to biogeochemical processes under changing environmental conditions.

Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria

Biofilms are surface-attached groups of microbial cells encased in an extracellular matrix that are significantly less susceptible to antimicrobial agents than non-adherent, planktonic cells. Biofilm-based infections are, as a result, extremely difficult to cure. A wide range of molecular mechanisms contribute to the high degree of recalcitrance that is characteristic of biofilm communities. These mechanisms include, among others, interaction of antimicrobials with biofilm matrix components, reduced growth rates and the various actions of specific genetic determinants of antibiotic resistance and tolerance. Alone, each of these mechanisms only partially accounts for the increased antimicrobial recalcitrance observed in biofilms. Acting in concert, however, these defences help to ensure the survival of biofilm cells in the face of even the most aggressive antimicrobial treatment regimens. This review summarises both historical and recent scientific data in support of the known biofilm resistance and tolerance mechanisms. Additionally, suggestions for future work in the field are provided.

[Relations between Bacterioplankton, Heterotrophic Nanoflagellates, and Virioplankton in the Littoral Zone of a LarRe Plain Reservoir:. ImDact of Bird Colonies.]

Interactions of the main components of microbial planktonic food web (bacteria, heterotrophic nanoflagellates, and viruses) were studied in a protected overgrown littoral zone of the Rybinsk Reservoir (Upper Volga).. The effect of bird colonial, settlements (the Laridae family) on these processes was deter- mined. The following systems exhibited significant negative correlations: "heterotrophic nanoflagellates- large rod-shaped bacteria" ("predator-prey"), "viruses-bacteriophages-bacterial products" ("parasite-. host") and "heterotrophic nanoflagellates-viruses-bacteriophages." Relations between biotic factors con- trolling bacterial development were more pronounced outside the zone affected by colonial bird settlements. Near the bird colony the role of viruses in mortality of planktonic bacteria increased. Reproduction of bacte- rial cells accelerated in response to the increase in feeding activity of heterotrophic nanoflagellates. Viruses- bacteriophages and heterotrophic nanoflagellates probably eliminate different targets until medium-sized cells become predominant in the bacterial community. Then heterotrophic nanoflagellates consume bacterial cells infected with viruses.

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.

Spatial-temporal variations and diversity of the bacterioplankton communities in the coastal waters of Kuwait

The dynamics and composition of the bacterial community in the coastal waters of Kuwait are poorly understood. In this study, the spatial-temporal variations in the bacterial composition in the surface water along the Kuwaiti coast was examined by 16S rRNA denaturing gradient gel electrophoresis (DGGE) fingerprinting and phylogeny analyses. The sampling sites were Kuwait Bay, Al-Sabbiya (north of the bay) and Al-Khairan (to the south). The bacterial composition was more variable in the summer for all sites. A cluster analysis of the DGGE fingerprint revealed two main clusters, indicating a temporal similarity between sites. Kuwait Bay and Al-Khairan were more similar to each other than to Al-Sabbiya. The bacterial community composition exhibited distinctive spatial variations, with more diversity at Al-Khairan and less diversity at Al-Sabbiya. At all sites, the dominant bacteria were Alphaproteobacteria, in particular Rhodobacteraceae, followed by Alteromonadaceae (Gammaproteobacteria) and Bacteroidetes.

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography

Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico

Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific ‘microbial signature’ (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM.

[EFFECT OF TEMPERATURE ON THE VIABILITY OF PLANKTON CELLS AND MODEL LEGIONELLA PNEUMOPHILA BIOFILMS IN WATER]

AIM

Study the effect of water temperature from 40 to 70 degrees C on viability of plankton forms and model Legionella pneumophila under experimental conditions.

MATERIALS AND METHODS

Monospecies legionella biofilms, obtained in plates for enzyme immunoassay during 96 hours at 28 degrees C, and water suspension of BCYE agar cultivated cells of L. pneumophila at a concentration of 10(3) - 10(5) CFU per liter were used in the study for evaluation of bactericidal effect of temperature on various legionella forms.

RESULTS

Analysis of effects of various temperature regimens on plankton forms and model legionella biofilms has shown that at a temperature range from 50 to 60 degrees C a significant reduction of quantity of viable legionella cells occurs. Model legionella biofilms have partially conserved viability at a temperature of 60 degrees C and only exposition to a temperature of 70 degrees C resulted in death of legionella biofilms and plankton forms of bacteria. A dependence of viability conservation of legionella from the initial concentration of the causative agent in water and duration of exposition at varying temperature was shown.

CONCLUSION

Short-term heating at a temperature of at least 70 degrees C has the most pronounced bactericidal effect on plankton forms and model L. pneumophila biofilms under experimental conditions. Such temperature regimen could be used as one of the prophylaxis approaches during maintenance of especially dangerous water system and, fist of all, systems of hot water supply.

Extracellular Electron Transfer Is a Bottleneck in the Microbiologically Influenced Corrosion of C1018 Carbon Steel by the Biofilm of Sulfate-Reducing Bacterium Desulfovibrio vulgaris

Carbon steels are widely used in the oil and gas industry from downhole tubing to transport trunk lines. Microbes form biofilms, some of which cause the so-called microbiologically influenced corrosion (MIC) of carbon steels. MIC by sulfate reducing bacteria (SRB) is often a leading cause in MIC failures. Electrogenic SRB sessile cells harvest extracellular electrons from elemental iron oxidation for energy production in their metabolism. A previous study suggested that electron mediators riboflavin and flavin adenine dinucleotide (FAD) both accelerated the MIC of 304 stainless steel by the Desulfovibrio vulgaris biofilm that is a corrosive SRB biofilm. Compared with stainless steels, carbon steels are usually far more prone to SRB attacks because SRB biofilms form much denser biofilms on carbon steel surfaces with a sessile cell density that is two orders of magnitude higher. In this work, C1018 carbon steel coupons were used in tests of MIC by D. vulgaris with and without an electron mediator. Experimental weight loss and pit depth data conclusively confirmed that both riboflavin and FAD were able to accelerate D. vulgaris attack against the carbon steel considerably. It has important implications in MIC failure analysis and MIC mitigation in the oil and gas industry.

Planktonic and biofilm-grown nitrogen-cycling bacteria exhibit different susceptibilities to copper nanoparticles

Proper characterization of nanoparticle (NP) interactions with environmentally relevant bacteria under representative conditions is necessary to enable their sustainable manufacture, use, and disposal. Previous nanotoxicology research based on planktonic growth has not adequately explored biofilms, which serve as the predominant mode of bacterial growth in natural and engineered environments. Copper nanoparticle (Cu-NP) impacts on biofilms were compared with respective planktonic cultures of the ammonium-oxidizing Nitrosomonas europaea, nitrogen-fixing Azotobacter vinelandii, and denitrifying Paracoccus denitrificans using a suite of independent toxicity diagnostics. Median inhibitory concentration (IC50) values derived from adenosine triphosphate (ATP) for Cu-NPs were lower in N. europaea biofilms (19.6 ± 15.3 mg/L) than in planktonic cells (49.0 ± 8.0 mg/L). However, in absorbance-based growth assays, compared with unexposed controls, N. europaea growth rates in biofilms were twice as resilient to inhibition than those in planktonic cultures. Similarly, relative to unexposed controls, growth rates and yields of P. denitrificans in biofilms exposed to Cu-NPs were 40-fold to 50-fold less inhibited than those in planktonic cells. Physiological evaluation of ammonium oxidation and nitrate reduction suggested that biofilms were also less inhibited by Cu-NPs than planktonic cells. Furthermore, functional gene expression for ammonium oxidation (amoA) and nitrite reduction (nirK) showed lower inhibition by NPs in biofilms relative to planktonic-grown cells. These results suggest that biofilms mitigate NP impacts, and that nitrogen-cycling bacteria in wastewater, wetlands, and soils might be more resilient to NPs than planktonic-based assessments suggest.

Distribution and diversity of bacterioplankton communities in subtropical seawater around Xiamen Island, China

Marine bacterioplankton communities have profound impact on global biogeochemical cycles and ecological balances. However, relatively little is known about the bacterioplankton communities and the factors shaping their spatial distribution in subtropical island. Here, the bacterioplankton communities around a typical subtropical island, Xiamen Island, were revealed by analyzing bacterial 16S rRNA gene through quantitative PCR (qPCR) and 454 pyrosequencing methods. The qPCR results indicated that the abundance of 16S rRNA gene ranged from 2.07 × 10(7) to 2.13 × 10(8)copies mL(-1) in surface seawater among eight sampling sites (S1-S8) around Xiamen Island, and the nitrogen and phosphorus-rich sites (S5 and S8) were detected with higher 16S rRNA gene abundance. Pyrosequencing evidenced that a total of 267 genera of 47 classes in 26 different phyla (or candidate phyla) and some unclassified bacteria were obtained from seawater around Xiamen Island. The most dominant phylum was Proteobacteria (49.62-76.84% among sites), followed by Bacteroidetes (6.64-20.88%), Actinobacteria (2.58-9.20%), Firmicutes (0.03-13.30%), Verrucomicrobia (0.23-2.67%) and Planctomycetes (0.14-2.20%). Among eight sites, the nitrogen and phosphorus-rich sites (S5 and S8) exhibited higher proportions of Gammaproteobacteria, Epsilonproteobacteria, Firmicutes and lower proportions of Alphaproteobacteria and Planctomycetes than other sites. S5 and S8 also had more similar β-diversity, and sampling site near the estuary (S8) showed the highest bacterial diversity. Redundancy analysis (RDA) confirmed that total nitrogen and total phosphorus significantly (P<0.05 and P<0.01, respectively) influenced the bacterioplankton communities around Xiamen Island. These results will provide insights into bacterial abundance, diversity and distribution patterns, as well as their controlling factors, in subtropical marine ecosystems.

Transient changes in bacterioplankton communities induced by the submarine volcanic eruption of El Hierro (Canary Islands)

The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1–V3 regions for Bacteria and V3–V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70–200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed.

Electron acceptor-dependent respiratory and physiological stratifications in biofilms

Bacterial respiration is an essential driving force in biogeochemical cycling and bioremediation processes. Electron acceptors respired by bacteria often have solid and soluble forms that typically coexist in the environment. It is important to understand how sessile bacteria attached to solid electron acceptors respond to ambient soluble alternative electron acceptors. Microbial fuel cells (MFCs) provide a useful tool to investigate this interaction. In MFCs with Shewanella decolorationis, azo dye was used as an alternative electron acceptor in the anode chamber. Different respiration patterns were observed for biofilm and planktonic cells, with planktonic cells preferred to respire with azo dye while biofilm cells respired with both the anode and azo dye. The additional azo respiration dissipated the proton accumulation within the anode biofilm. There was a large redox potential gap between the biofilms and anode surface. Changing cathodic conditions caused immediate effects on the anode potential but not on the biofilm potential. Biofilm viability showed an inverse and respiration-dependent profile when respiring with only the anode or azo dye and was enhanced when respiring with both simultaneously. These results provide new insights into the bacterial respiration strategies in environments containing multiple electron acceptors and support an electron-hopping mechanism within Shewanella electrode-respiring biofilms.

Comparative studies of the immunogenicity and protective potential of biofilm vs planktonic Staphylococcus aureus vaccine against bovine mastitis using non-invasive mouse mastitis as a model system

This study was undertaken to compare the immunogenicity and protective potential of biofilm vs planktonic Staphylococcus aureus vaccine for the prevention of mastitis using the mouse as a model system. Mice immunized with formalin-killed whole cell vaccine of S. aureus residing in a biofilm when delivered via an intramammary route produced a cell mediated immune response. Mice immunized with this biofilm vaccine showed significant reductions in colonization by S. aureus in mammary glands, severity of clinical symptoms and tissue damage in mammary glands in comparison with the mice immunized with formalin-killed whole cells of planktonic S. aureus. The planktonic vaccine administered by a subcutaneous route produced a significantly higher humoral immune response (IgG1 and IgG) than the biofilm vaccine. However, considering the host response, tissue damage, the clinical severity and colonization of S. aureus in mammary glands, the biofilm vaccine performed better in immunogenicity and protective potential when administered by the intramammary route.

Investigation of the effectiveness of disinfectants against planktonic and biofilm forms of P. aeruginosa and E. faecalis cells using a compilation of cultivation, microscopic and flow cytometric techniques

This study evaluated the effectiveness of selected disinfectants against bacterial cells within a biofilm using flow cytometry, the conventional total viable count test and scanning electron microscopy (SEM). A flow cytometric procedure based on measurement of the cellular redox potential (CRP) was demonstrated to have potential for the rapid evaluation of activity against biofilm and planktonic forms of microbes. Quaternary ammonium compound-based disinfectant (QACB) demonstrated a higher level of anti-microbial activity than a performic acid preparation (PAP), with mean CRP values against P. aeruginosa cells of 2 and 1.33 relative fluorescence units (RFU) vs 63.33 and 61.33 RFU for 8 and 24 h cultures respectively. Flow cytometric evaluation of the anti-biofilm activity demonstrated a higher efficacy of QACB compared to PAP for P. aeruginosa cells of 1 and 0.66 RFU vs 18.33 and 22.66 RFU for 8 and 24 h cultures respectively. SEM images of treated P. aeruginosa cells demonstrated disinfectant-specific effects on cell morphology.

Proteome profile of a pandemic Vibrio parahaemolyticus SC192 strain in the planktonic and biofilm condition

Vibrio parahaemolyticus is one of the leading causative agents of foodborne diseases in humans. In this study, the proteome profiles of the pandemic strain V. parahaemolyticus SC192 belonging to the O3:K6 serovar during the planktonic and biofilm stages were analyzed by two-dimensional liquid chromatography coupled to tandem mass spectrometry. This non-gel-based multidimensional protein identification technology approach identified 45.5% of the proteome in the reference genome V. parahaemolyticus RIMD 2210633. This is the largest proteome coverage obtained so far in V. parahaemolyticus and provides evidence for expression of 27% of the hypothetical proteins. Comparison of the planktonic and biofilm proteomes based on their cluster of orthologous groups, gene ontologies and KEGG pathways provides basic information on biofilm specific functions and pathways. To the authors' knowledge, this is the first study to generate a global proteome profile of the pandemic strain of V. parahaemolyticus and the method reported here could be used to rapidly obtain a snapshot of the proteome of any microorganism at a given condition.

Influence of calcium in extracellular DNA mediated bacterial aggregation and biofilm formation

Calcium (Ca²⁺) has an important structural role in guaranteeing the integrity of the outer lipopolysaccharide layer and cell walls of bacterial cells. Extracellular DNA (eDNA) being part of the slimy matrix produced by bacteria promotes biofilm formation through enhanced structural integrity of the matrix. Here, the concurrent role of Ca²⁺ and eDNA in mediating bacterial aggregation and biofilm formation was studied for the first time using a variety of bacterial strains and the thermodynamics of DNA to Ca²⁺ binding. It was found that the eDNA concentrations under both planktonic and biofilm growth conditions were different among bacterial strains. Whilst Ca²⁺ had no influence on eDNA release, presence of eDNA by itself favours bacterial aggregation via attractive acid-base interactions in addition, its binding with Ca²⁺ at biologically relevant concentrations was shown further increase in bacterial aggregation via cationic bridging. Negative Gibbs free energy (ΔG) values in iTC data confirmed that the interaction between DNA and Ca²⁺ is thermodynamically favourable and that the binding process is spontaneous and exothermic owing to its highly negative enthalpy. Removal of eDNA through DNase I treatment revealed that Ca²⁺ alone did not enhance cell aggregation and biofilm formation. This discovery signifies the importance of eDNA and concludes that existence of eDNA on bacterial cell surfaces is a key facilitator in binding of Ca²⁺ to eDNA thereby mediating bacterial aggregation and biofilm formation.

Antagonistic coevolution of marine planktonic viruses and their hosts

The potential for antagonistic coevolution between marine viruses and their (primarily bacterial) hosts is well documented, but our understanding of the consequences of this rapid evolution is in its infancy. Acquisition of resistance against co-occurring viruses and the subsequent evolution of virus host range in response have implications for bacterial mortality rates as well as for community composition and diversity. Drawing on examples from a range of environments, we consider the potential dynamics, underlying genetic mechanisms and fitness costs, and ecological impacts of virus-host coevolution in marine waters. Given that much of our knowledge is derived from laboratory experiments, we also discuss potential challenges and approaches in scaling up to diverse, complex networks of virus-host interactions. Finally, we note that a variety of novel approaches for characterizing virus-host interactions offer new hope for a mechanistic understanding of antagonistic coevolution in marine plankton.

In situ interactions between photosynthetic picoeukaryotes and bacterioplankton in the Atlantic Ocean: evidence for mixotrophy

Heterotrophic bacterioplankton, cyanobacteria and phototrophic picoeukaryotes (< 5 μm in size) numerically dominate planktonic oceanic communities. While feeding on bacterioplankton is often attributed to aplastidic protists, recent evidence suggests that phototrophic picoeukaryotes could be important bacterivores. Here, we present direct visual evidence from the surface mixed layer of the Atlantic Ocean that bacterioplankton are internalized by phototrophic picoeukaryotes. In situ interactions of phototrophic picoeukaryotes and bacterioplankton (specifically Prochlorococcus cyanobacteria and the SAR11 clade) were investigated using a combination of flow cytometric cell sorting and dual tyramide signal amplification fluorescence in situ hybridization. Using this method, we observed plastidic Prymnesiophyceae and Chrysophyceae cells containing Prochlorococcus, and to a lesser extent SAR11 cells. These microscopic observations of in situ microbial trophic interactions demonstrate the frequency and likely selectivity of phototrophic picoeukaryote bacterivory in the surface mixed layer of both the North and South Atlantic subtropical gyres and adjacent equatorial region, broadening our views on the ecological role of the smallest oceanic plastidic protists.

Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling

There is increasing recognition that stochasticity involved in gene regulatory processes may help cells enhance the signal or synchronize expression for a group of genes. Thus the validity of the traditional deterministic approach to modeling the foregoing processes cannot be without exception. In this study, we identify a frequently encountered situation, i.e., the biofilm, which has in the past been persistently investigated with intracellular deterministic models in the literature. We show in this paper circumstances in which use of the intracellular deterministic model appears distinctly inappropriate. In Enterococcus faecalis, the horizontal gene transfer of plasmid spreads drug resistance. The induction of conjugation in planktonic and biofilm circumstances is examined here with stochastic as well as deterministic models. The stochastic model is formulated with the Chemical Master Equation (CME) for planktonic cells and Reaction-Diffusion Master Equation (RDME) for biofilm. The results show that although the deterministic model works well for the perfectly-mixed planktonic circumstance, it fails to predict the averaged behavior in the biofilm, a behavior that has come to be known as stochastic focusing. A notable finding from this work is that the interception of antagonistic feedback loops to signaling, accentuates stochastic focusing. Moreover, interestingly, increasing particle number of a control variable could lead to an even larger deviation. Intracellular stochasticity plays an important role in biofilm and we surmise by implications from the model, that cell populations may use it to minimize the influence from environmental fluctuation.

[Dimensional structure of bacterial communities of the winter plankton Pechora sea and its formation]

For the Pechora sea, according to microbiological shootings during winter seasons 2002-2005, the analysis of conditions forming of an abundance winter bacterial communities a plankton is carried out. For the outlined varieties of waters, regularities of distribution of segregate groups bacterial communities are discussed. The natural modification of microbiologic indicators ona gradient of parametres a physical and chemical complex is shown. In subglacial conditions average number bacterioplankton 234 thousand in cell/ml, cellular volume - 0.58 μm3, at square of 550 mm2/L. A biomass store a stratum of probed harbour area Pechora sea of 0-25 m to 187 x 10(90 G.

Probing electron transfer with Escherichia coli: a method to examine exoelectronics in microbial fuel cell type systems

Escherichia coli require mediators or composite anodes for substantial outward electron transfer, >8A/m(2). To what extent non-mediated direct electron transfer from the outer cell envelope to the anode occurs with E. coli is a debated issue. To this end, the redox behaviour of non-exoelectrogenic E. coli K12 was investigated using a bi-cathodic microbial fuel cell. The electromotive force caused by E. coli biofilms mounted 0.2-0.3 V above the value with the surrounding medium. Surprisingly, biofilms that started forming at different times synchronised their EMF even when physically separated. Non-mediated electron transfer from E. coli biofilms increased above background currents passing through the cultivation medium. In some instances, currents were rather high because of a sudden discharge of the medium constituents. Mediated conditions provided similar but more pronounced effects. The combined step-by-step method used allowed a systematic analysis of exoelectronics as encountered in microbial fuel cells.