Decoupling of respiration rates and abundance in marine prokaryoplankton

The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.

Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of four non-ribosomal peptides/polyketide (NRPs/PKS) antibiotics produced by Bacillus subtilis clade, we revealed that they acted synergistically to effectively eliminate phylogenetically distinct competitors. The production of these antibiotics came with a fitness cost manifested in growth inhibition, rendering their synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, antibiotic production was only induced by the presence of a peptidoglycan cue from a sensitive competitor, a response mediated by the global regulator of cellular competence, ComA. These results experimentally demonstrate a general ecological concept - closely related communities are favoured during competition, due to compatibility in attack and defence mechanisms.

The Effects of Photosensitizing Dyes Fagopyrin and Hypericin on Planktonic Growth and Multicellular Life in Budding Yeast

Naphthodianthrones such as fagopyrin and hypericin found mainly in buckwheat (Fagopyrum spp.) and St. John’s wort (SJW) (Hypericum perforatum L.) are natural photosensitizers inside the cell. The effect of photosensitizers was studied under dark conditions on growth, morphogenesis and induction of death in Saccharomyces cerevisiae. Fagopyrin and hypericin induced a biphasic and triphasic dose response in cellular growth, respectively, over a 10-fold concentration change. In fagopyrin-treated cells, disruptions in the normal cell cycle progression were evident by microscopy. DAPI staining revealed several cells that underwent premature mitosis without budding, a striking morphological abnormality. Flow Cytometric (FC) analysis using a concentration of 100 µM showed reduced cell viability by 41% in fagopyrin-treated cells and by 15% in hypericin-treated cells. FC revealed the development of a secondary population of G1 cells in photosensitizer-treated cultures characterized by small size and dense structures. Further, we show that fagopyrin and the closely related hypericin altered the shape and the associated fluorescence of biofilm-like structures. Colonies grown on solid medium containing photosensitizer had restricted growth, while cell-to-cell adherence within the colony was also affected. In conclusion, the photosensitizers under dark conditions affected culture growth, caused toxicity, and disrupted multicellular growth, albeit with different efficiencies.

Ecological status of a freshwater tectonic lake of the indo-burmese province: Implications for livelihood development

Tectonic lakes are among the most geologically fascinating and environmentally versatile hydrobiological systems found on the earth's surface. We conducted a study on the limnology of Tasek Lake, a tectonic lake located in the Indo-Burma Province of the South Asian region. Physico-chemical parameters of the lake's water along with its plankton were considered for the study. Their relationship was analysed by understanding their seasonal variations and through linear regression models. The water quality index (WQI), plankton diversity indices and canonical correspondence analysis (CCA) were computed. The ichthyofaunal diversity was also studied to get an insight into the lake's fishery potential. A preliminary assessment on the economic feasibility of converting Tasek Lake into a fishery was also completed. Results indicate moderate eutrophication in the lake and the plankton population is observed to be rich and abundant. The WQI value confirms the water to be of "very poor" quality. The CCA was done to analyze the relationships of physico-chemical parameters with months and seasons, and the relation between seasons and plankton assemblages. Results corroborate the results of WQI. Identified fish population suggest ample fishery potential of the lake. The economic assessment reveals that in order to maintain the ecological sustainability of the lake, it should be transformed into a recreational fishery, following a catch-and-release model. The study calls for urgent restoration of the lake so that not only its pristine ecology is survived but also its fishery potential is sustainably harnessed and local livelihood is improved.

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.

Biofilm dispersion

The formation of microbial biofilms enables single planktonic cells to assume a multicellular mode of growth. During dispersion, the final step of the biofilm life cycle, single cells egress from the biofilm to resume a planktonic lifestyle. As the planktonic state is considered to be more vulnerable to antimicrobial agents and immune responses, dispersion is being considered a promising avenue for biofilm control. In this Review, we discuss conditions that lead to dispersion and the mechanisms by which native and environmental cues contribute to dispersion. We also explore recent findings on the role of matrix degradation in the dispersion process, and the distinct phenotype of dispersed cells. Last, we discuss the translational and therapeutic potential of dispersing bacteria during infection.

Sensitivity of Planktonic Cells of Staphylococcus aureus to Elevated Hydrostatic Pressure as Affected by Mild Heat, Carvacrol, Nisin, and Caprylic Acid

Current study investigated effects of elevated hydrostatic pressure exposure in the presence of mild heat and natural antimicrobials against Staphylococcus aureus. Hydrostatic pressure of 350 to 550 MPa with nisin (5000 IU/mL), carvacrol, or caprylic acid (0.5% v/v) were applied for the reduction in four-strain mixture of S. aureus in HEPES buffer at 4 and 40 °C for up to 7 min. Results were statistically analyzed by ANOVA and D-values were additionally calculated using best-fitted linear model. Prior to exposure to treatments at 4 °C, counts of the pathogen were 7.95 ± 0.4 log CFU/mL and were reduced (p < 0.05) to 6.44 ± 0.3 log CFU/mL after 7 min of treatment at 450 MPa. D-value associated with this treatment was 5.34 min (R² = 0.72). At 40 °C, counts were 8.21 ± 0.7 and 5.77 ± 0.3 log CFU/mL before and after the 7-min treatments, respectively. D-value associated with 40 °C treatment was 3.30 min (R² = 0.62). Application of the antimicrobials provided additional pathogen reduction augmentation for treatments < 5 min. The results of the current study could be incorporated for meeting regulatory requirements such as Food Code, HACCP, and Preventive Control for Human Food of Food Safety Modernization Act for assuring microbiological safety of products against this prevalent pathogen of public health concern.

Periodic density as an endpoint of customized plankton community responses to petroleum hydrocarbons: A level of toxic effect should be matched with a suitable time scale

As an endpoint of community response to contaminants, average periodic density of populations (APDP) has been introduced to model species interactions in a community with 4 planktonic species. An ecological model for the community was developed by means of interspecific relationship including competition and predation to calculate the APDP. As a case study, we reported here the ecotoxicological effects of petroleum hydrocarbons (PHC) collected from Bohai oil field on densities of two algae, Platymonas subcordiformis and Isochrysis galbana, a rotifer, Brachionus plicatilis, and of a cladocera, Penilia avirostris, in single species and a microcosm experiment. Time scales expressing toxic effect increased with increasing levels of toxic effect from molecule to community. Remarkable periodic changes in densities were found during the tests in microcosm experiment, revealing a strong species reaction. The minimum time scale characterizing toxic effect at a community level should be the common cycle of population densities of the microcosm. In addition, the cycles of plankton densities shortened in general with increasing PHC, showing an evident toxic effect on the microcosm. Using APDP as the endpoint, a threshold concentration for the modeled microcosm was calculated to be 0.404 mg-PHC L^-1. The APDP was found to be more sensitive and reliable than the standing crops of populations as the endpoint. This indicated that the APDP, an endpoint at the community level, could be quantitatively related to the endpoints at the population level, and led to the quantitative concentration-toxic effect relationship at the community level.

Scnn1b-Transgenic BALB/c Mice as a Model of Pseudomonas aeruginosa Infections of the Cystic Fibrosis Lung

The opportunistic pathogen Pseudomonas aeruginosa is responsible for much of the morbidity and mortality associated with cystic fibrosis (CF), a condition that predisposes patients to chronic lung infections. P. aeruginosa lung infections are difficult to treat because P. aeruginosa adapts to the CF lung, can develop multidrug resistance, and can form biofilms. Despite the clinical significance of P. aeruginosa, modeling P. aeruginosa infections in CF has been challenging. Here, we characterize Scnn1b-transgenic (Tg) BALB/c mice as P. aeruginosa lung infection models. Scnn1b-Tg mice overexpress the epithelial Na+ channel (ENaC) in their lungs, driving increased sodium absorption that causes lung pathology similar to CF. We intranasally infected Scnn1b-Tg mice and wild-type littermates with the laboratory P. aeruginosa strain PAO1 and CF clinical isolates and then assessed differences in bacterial clearance, cytokine responses, and histological features up to 12 days postinfection. Scnn1b-Tg mice carried higher bacterial burdens when infected with biofilm-grown rather than planktonic PAO1; Scnn1b-Tg mice also cleared infections more slowly than their wild-type littermates. Infection with PAO1 elicited significant increases in proinflammatory and Th17-linked cytokines on day 3. Scnn1b-Tg mice infected with nonmucoid early CF isolates maintained bacterial burdens and mounted immune responses similar to those of PAO1-infected Scnn1b-Tg mice. In contrast, Scnn1b-Tg mice infected with a mucoid CF isolate carried high bacterial burdens, produced significantly more interleukin 1β (IL-1β), IL-13, IL-17, IL-22, and KC, and showed severe immune cell infiltration into the bronchioles. Taken together, these results show the promise of Scnn1b-Tg mice as models of early P. aeruginosa colonization in the CF lung.

Potential Application of Protamine for Antimicrobial Biomaterials in Bone Tissue Engineering

Bacterial infection of biomaterials is a serious problem in the field of medical devices. It is urgently necessary to develop new biomaterials with bactericidal activity. Antimicrobial peptides and proteins (AMPs), alternative antibacterial agents, are expected to overcome the bacterial resistance. The aim of this study was to develop a new intelligent material in bone tissue engineering based on protamine-loaded hydroxyapatite (protamine/HAp) that uses AMPs rather than antibiotics. It was found that the adsorption of protamine to HAp followed the Langmuir adsorption model and was due to electrostatic and/or hydrophobic interactions. In vitro bacterial adhesion and growth on protamine/HAp was inhibited in a protamine dose-dependent manner. Adherent bacteria exhibited an aberrant morphology for high dosages of protamine/HAp, resulting in the formation of large aggregates and disintegration of the membrane. The released protamine from protamine/HAp also prevented the growth of planktonic bacteria in vitro. However, a high dosage of protamine from powders at loading concentrations over 1000 μg·mL-1 induced a cytotoxic effect in vitro, although those exhibited no apparent cytotoxicity in vivo. These data revealed that protamine/HAp (less than 1000 μg·mL-1) had both antimicrobial activity and biocompatibility and can be applied for bone substitutes in orthopedic fields.

Radioimmunotherapy of methicillin-resistant Staphylococcus aureus in planktonic state and biofilms

Background

Implant associated infections such as periprosthetic joint infections are difficult to treat as the bacteria form a biofilm on the prosthetic material. This biofilm complicates surgical and antibiotic treatment. With rising antibiotic resistance, alternative treatment options are needed to treat these infections in the future. The aim of this article is to provide proof-of-principle data required for further development of radioimmunotherapy for non-invasive treatment of implant associated infections.

Methods

Planktonic cells and biofilms of Methicillin-resistant staphylococcus aureus are grown and treated with radioimmunotherapy. The monoclonal antibodies used, target wall teichoic acids that are cell and biofilm specific. Three different radionuclides in different doses were used. Viability and metabolic activity of the bacterial cells and biofilms were measured by CFU dilution and XTT reduction.

Results

Alpha-RIT with Bismuth-213 showed significant and dose dependent killing in both planktonic MRSA and biofilm. When planktonic bacteria were treated with 370 kBq of ²¹³Bi-RIT 99% of the bacteria were killed. Complete killing of the bacteria in the biofilm was seen at 185 kBq. Beta-RIT with Lutetium-177 and Actinium-225 showed little to no significant killing.

Conclusion

Our results demonstrate the ability of specific antibodies loaded with an alpha-emitter Bismuth-213 to selectively kill staphylococcus aureus cells in vitro in both planktonic and biofilm state. RIT could therefore be a potentially alternative treatment modality against planktonic and biofilm-related microbial infections.

Genetic diversity and connectivity of Flaccisagitta enflata (Chaetognatha: Sagittidae) in the tropical Atlantic ocean (northeastern Brazil)

The phylogeography of the holoplanktonic chaetognath Flaccisagitta enflata was investigated in the Tropical Western Atlantic (TWA). Considering the cosmopolitan range of this species and the fact that its entire life cycle is planktonic, the central hypothesis of this study is that F. enflata exhibits connectivity due to its high dispersal capacity, forming a panmictic population among the study sites. The evaluated areas included neritic (Port of Recife–PR, and Tamandaré - TA) and oceanic (Fernando de Noronha Archipelago—FN, Rocas Atoll—RA, Guará seamount—GS and Saint Peter and Saint Paul’s Archipelago—SPSPA) locations of the Brazilian Blue Amazon. We used COI gene sequences as molecular marker. Partial sequences (425 bp) were obtained for 116 specimens and employed to reconstruct the phylogeny, build an haplotype network, evaluate gene flow through a migration model, and estimate diversity indices, population structuring and demographic history. High levels of haplotype diversity (mean: 0.98) and moderate to high levels of nucleotide diversity (mean: 0.023) were observed. The phylogeny and the haplotype network topologies showed some geographic clustering, indicating local structuring in GS and PR. This finding was supported by the AMOVA high global Φst (0.033, significant) and some pairwise Φst comparisons (7 out of 15 were significantly >0). Significant differences suggested lower levels of connectivity when GS population was compared to those of FN and SPSPA; as well as when TA was compared to FN. These results might be related to particularities of the oceanic dynamics which rules the TWA, sustaining such dissimilarities. Structuring was also observed between PR and all oceanic locations. We hypothesize that the topography of the port inlet, enclosured by a reef barrier, may constrain the water turnover ratio and thus migration rates of F. enflata in the TWA. Accordingly, Migrate-N yielded a four metapopulations model (PR ⇌ TA ⇌ SPSPA+FN ⇌ GS+RA) as the best (highest probability; ~0.90) to represent the structuring of F. enflata in the TWA. Therefore, the null hypothesis of one randomly mating population cannot be accepted. The demographic evaluation demonstrated that the neutral hypothesis of stable populations may not be rejected for most of the locations. This work is the start point to broaden the knowledge on the phylogeography and population genetic structure of a numerically dominant species in the Western Atlantic, with key role in the marine trophic web.

New findings on the effect of glyphosate on autotrophic and heterotrophic picoplankton structure: A microcosm approach

Massive use of glyphosate-based herbicides in agricultural activities has led to the appearance of this herbicide in freshwater systems, which represents a potential threat to these systems and their communities. These herbicides can affect autotrophic and heterotrophic picoplankton abundance. However, little is known about glyphosate impact on the whole structure of these assemblages. Herein, we used an 8-day long microcosm approach under indoor controlled conditions to analyze changes in the structure of picoplankton exposed to a single pulse of glyphosate. The analyzed picoplankton correspond to two outdoor ponds with contrasting states: "clear" (chlorophyll-a = 3.48 μg L-1± 1.15; nephelometric turbidity, NTU = 1) and "turbid" (chlorophyll-a = 105.96 μg L-1 ± 15.3; NTU = 48). We evaluated herbicide impact on different picoplankton cytometric populations and further explored changes in bacterial dominant operational taxonomic units (OTUs) fingerprinting. We observed that glyphosate induced a drastic decrease in the abundance of phycocyanin-rich picocyanobacteria. Particularly, in the turbid system this effect resulted in an 85 % decrease in the abundance of the whole autotrophic picoplankton. Glyphosate also changed the structure of the heterotrophic fraction by means of changing bacterial dominant OTUs fingerprinting patterns in both systems and by shifting the relative abundances of cytometric groups in the clear scenario. These results demonstrate that upon glyphosate exposure picoplanktonic fractions face not only the already reported changes in abundance, but also alterations in the composition of cytometric groups and of bacterial dominant operational taxonomic units. This research provides suitable and still little explored tools to analyze agrochemical effects on picoplanktonic communities.

Body Size, Light Intensity, and Nutrient Supply Determine Plankton Stoichiometry in Mixotrophic Plankton Food Webs

Trophic strategy determines stoichiometry of plankton. In general, heterotrophic zooplankton have lower and more stable C∶N and C∶P ratios than photoautotrophic phytoplankton, whereas mixotrophic protists, which consume prey and photosynthesize, have stoichiometry between zooplankton and phytoplankton. As trophic strategies change with cell size, body size may be a key trait influencing eukaryotic plankton stoichiometry. However, the relationship between body size and stoichiometry remains unclear. Here we measured plankton size-fractionated C∶N ratios under different intensities of light and nutrient supply in subtropical freshwater and marine systems. We found a unimodal body size-C∶N ratio pattern, with a maximum C∶N ratio at ∼50 μm diameter in marine and freshwater systems. Moreover, the variation in C∶N ratios is explained mainly by body size, followed by light intensity and nutrient concentration. To investigate the mechanisms behind this unimodal pattern, we constructed a size-based plankton food web model in which the trophic strategy and C∶N ratio are an emerging result. Our model simulations reproduce the unimodal pattern with a C∶N ratio of photoautotrophs ≤50 μm increasing with body size due to increase of photosynthetic carbon, whereas C∶N ratios of organisms >50 μm decrease with size due to decreasing photoautotrophic but increasing heterotrophic uptake. Based on our field observations and simulation, we extend the classic "light-nutrient" theory that determines plankton C∶N ratio to include body size and trophic strategy dependency. We conclude that body size and size-dependent uptake of resources (light, nutrients, and prey) determine plankton stoichiometry at various light and nutrient supplies.

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.

Variations in bacterioplankton communities in aquaculture ponds and the influencing factors during the peak period of culture

An increase in nutrient input may disturb the bacterioplankton communities in freshwater aquaculture ponds during the peak period of culture. Water samples were collected from ponds of three cultivated species. After the samples were filtered and total DNA was extracted, Illumina high-throughput sequencing was used to profile the spatiotemporal distributions in bacterioplankton communities, the belt diversity, and the influencing factors during this period of time. The results showed that Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla. Biological differences in cultivated species were the main influencing factors that shaped bacterioplankton communities. Monthly variations and thermal stratification provided little and no contribution to bacterioplankton communities, respectively. CODmn, Chla, and TN were the most appropriate parameters to describe the environmental interpretation of bacterial ordinations, and CODmn was the predominant factor. In addition, the higher similarity between CODmn and Chla, shown by clustering analysis, indicated that the algae-bacteria symbiotic system may have an important role in material circulation in freshwater aquaculture pond water during the peak period of culture. The present study has helped to elucidate the biological characteristics of aquaculture tail water, and enriched the basic data provided by bacterioplankton studies.

Upwelling Bays: How Coastal Upwelling Controls Circulation, Habitat, and Productivity in Bays

Bays in coastal upwelling regions are physically driven and biochemically fueled by their interaction with open coastal waters. Wind-driven flow over the shelf imposes a circulation in the bay, which is also influenced by local wind stress and thermal bay-ocean density differences. Three types of bays are recognized based on the degree of exposure to coastal currents and winds (wide-open bays, square bays, and elongated bays), and the characteristic circulation and stratification patterns of each type are described. Retention of upwelled waters in bays allows for dense phytoplankton blooms that support productive bay ecosystems. Retention is also important for the accumulation of larvae, which accounts for high recruitment in bays. In addition, bays are coupled to the shelf ecosystem through export of plankton-rich waters during relaxation events. Ocean acidification and deoxygenation are a concern in bays because local extrema can develop beneath strong stratification.

The North Atlantic Ecosystem, from Plankton to Whales

Compared with terrestrial ecosystems, marine ecosystems have a higher proportion of heterotrophic biomass. Building from this observation, we define the North Atlantic biome as the region where the large, lipid-rich copepod Calanus finmarchicus is the dominant mesozooplankton species. This species is superbly adapted to take advantage of the intense pulse of productivity associated with the North Atlantic spring bloom. Most of the characteristic North Atlantic species, including cod, herring, and right whales, rely on C. finmarchicus either directly or indirectly. The notion of a biome rests inherently on an assumption of stability, yet conditions in the North Atlantic are anything but stable. Humans have reduced the abundance of many fish and whales (though some recovery is underway). Humans are also introducing physical and chemical trends associated with global climate change. Thus, the future of the North Atlantic depends on the biome's newest species, Homo sapiens.

The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms

Cyclic AMP (cAMP) receptor protein (Crp) is an important transcriptional regulator of Yersinia pestis Expression of crp increases during pneumonic plague as the pathogen depletes glucose and forms large biofilms within lungs. To better understand control of Y. pestis Crp, we determined a 1.8-Å crystal structure of the protein-cAMP complex. We found that compared to Escherichia coli Crp, C helix amino acid substitutions in Y. pestis Crp did not impact the cAMP dependency of Crp to bind DNA promoters. To investigate Y. pestis Crp-regulated genes during plague pneumonia, we performed RNA sequencing on both wild-type and Δcrp mutant bacteria growing in planktonic and biofilm states in minimal media with glucose or glycerol. Y. pestis Crp was found to dramatically alter expression of hundreds of genes in a manner dependent upon carbon source and growth state. Gel shift assays confirmed direct regulation of the malT and ptsG promoters, and Crp was then linked to Y. pestis growth on maltose as a sole carbon source. Iron regulation genes ybtA and fyuA were found to be indirectly regulated by Crp. A new connection between carbon source and quorum sensing was revealed as Crp was found to regulate production of acyl-homoserine lactones (AHLs) through direct and indirect regulation of genes for AHL synthetases and receptors. AHLs were subsequently identified in the lungs of Y. pestis-infected mice when crp expression was highest in Y. pestis biofilms. Thus, in addition to the well-studied pla gene, other Crp-regulated genes likely have important functions during plague infection.IMPORTANCE Bacterial pathogens have evolved extensive signaling pathways to translate environmental signals into changes in gene expression. While Crp has long been appreciated for its role in regulating metabolism of carbon sources in many bacterial species, transcriptional profiling has revealed that this protein regulates many other aspects of bacterial physiology. The plague pathogen Y. pestis requires this global regulator to survive in blood, skin, and lungs. During disease progression, this organism adapts to changes within these niches. In addition to regulating genes for metabolism of nonglucose sugars, we found that Crp regulates genes for virulence, metal acquisition, and quorum sensing by direct or indirect mechanisms. Thus, this single transcriptional regulator, which responds to changes in available carbon sources, can regulate multiple critical behaviors for causing disease.

Microplastics in Tampa Bay, Florida: Abundance and variability in estuarine waters and sediments

This study provides the first measurement of microplastic abundance and distribution in surface waters and sediments in Tampa Bay, FL. Microplastic concentrations in discrete water samples ranged from 0.25 to 7.0 particles/L with an average of 0.94 (±0.52) particles/L. Samples taken with a 330 μm plankton net had 1.2-18.1 particles/m³ with an average of 4.5 (±2.3) particles/m³. Discrete samples were 200 times higher than net samples, suggesting substantial losses or undersampling with the net. For both discrete and plankton tow samples, there were no significant differences in concentrations between stations or regions. Intense rainfall events in the summer always preceded samples with substantially higher counts. Most (>75%) microplastics were fibers. Using an average value of 1 particle/L, Tampa Bay contains ~4 billion microplastic particles. Surface sediments had an average of 280 (±290) particles/kg, ranging from 30 to 790 particles/kg. Highest concentrations of microplastics were found in sediments close to industrial sources; lowest values in Middle and Lower Tampa Bay are consistent with shorter residence times.

Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm

BACKGROUND AND OBJECTIVE

Porphyromonas gingivalis, an oral microorganism residing in the subgingival biofilm, may exert diverse pathogenicity depending on the presence of specific virulence factors, but its gene expression has not been completely established. This investigation aims to compare the transcriptomic profile of this pathogen when growing within an in vitro multispecies biofilm or in a planktonic state.

MATERIALS AND METHODS

P. gingivalis ATCC 33277 was grown in anaerobiosis within multi-well culture plates at 37°C under two conditions: (a) planktonic samples (no hydroxyapatite discs) or (b) within a multispecies-biofilm containing Streptococcus oralis, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans deposited on hydroxyapatite discs. Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM) combined with Fluorescence In Situ Hybridization (FISH) were used to verify the formation of the biofilm and the presence of P. gingivalis. Total RNA was extracted from both the multispecies biofilm and planktonic samples, then purified and, with the use of a microarray, its differential gene expression was analyzed. A linear model was used for determining the differentially expressed genes using a filtering criterion of two-fold change (up or down) and a significance p-value of <0.05. Differential expression was confirmed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR).

RESULTS

SEM verified the development of the multispecies biofilm and FISH confirmed the incorporation of P. gingivalis. The microarray demonstrated that, when growing within the multispecies biofilm, 19.1% of P. gingivalis genes were significantly and differentially expressed (165 genes were up-regulated and 200 down-regulated), compared with planktonic growth. These genes were mainly involved in functions related to the oxidative stress, cell envelope, transposons and metabolism. The results of the microarray were confirmed by RT-qPCR.

CONCLUSION

Significant transcriptional changes occurred in P. gingivalis when growing in a multispecies biofilm compared to planktonic state.

Synergistic effects of LFchimera and antibiotic against planktonic and biofilm form of Aggregatibacter actinomycetemcomitans

Adjunctive use of antibiotics in periodontal treatment have limitations and disadvantages including bacterial resistance. Antimicrobial peptides (AMPs) are potential new agents that can combat bacterial infection. In this study, antimicrobial activity of different concentrations of conventional antibiotics minocycline (MH), doxycycline (DOX), and antimicrobial peptides LL-37, LL-31, Lactoferrin chimera (LFchimera) and Innate Defense Regulator Peptide 1018 (IDR-1018) against Aggregatibacter actinomycetemcomitans ATCC 43718 were determined using colony culturing assay. Subsequently, in vitro activity of the most effective drug and peptide combination was evaluated by checkerboard technique. Impact of the drug and peptide co-administration on biofilm at different stages, i.e., during adhesion and 1-day old biofilm was compared to each of the agents used alone. Results revealed that the killing effects of all AMPs range from 13–100%. In contrast, MH and DOX at 1 and 5 μM showed no killing activity and instead stimulated growth of bacteria. DOX has better killing activity than MH. LFchimera displayed the strongest killing amongst the peptides. Checkerboard technique revealed that combining DOX and LFchimera yielded synergism. Confocal laser scanning microscopy further showed that the combination of DOX and LFchimera caused significant reduction of bacterial adhesion and reduction of biomass, average biofilm thickness and substratum biofilm coverage of 1-day old biofilm compared to DOX and LFchimera alone. In conclusion, LFchimera alone and in combination with DOX exhibited strong antibacterial and anti-biofilm property against A. actinomycetemcomitans. The findings suggest that LFchimera should be considered for development as a new potential therapeutic agent that may be used as an adjunctive treatment for periodontitis.

Photothermal-Induced Antibacterial Activity of Gold Nanorods Loaded into Polymeric Hydrogel against Pseudomonas aeruginosa Biofilm

In this study, the photothermal-induced bactericidal activity of phospholipid-decorated gold nanorods (DSPE-AuNR) suspension against Pseudomonas aeruginosa planktonic and biofilm cultures was investigated. We found that the treatment of planktonic culture of Pseudomonas aeruginosa with DSPE-AuNR suspension (0.25-0.03 nM) followed by a continuous laser beam exposure resulted in ~6 log cycle reduction of the bacterial viable count in comparison to the control. The percentage reduction of Pseudomonas aeruginosa biofilm viable count was ~2.5-6.0 log cycle upon laser excitation with different concentrations of DSPE-AuNR as compared to the control. The photothermal ablation activity of DSPE-AuNR (0.125 nM) loaded into poloxamer 407 hydrogel against Pseudomonas aeruginosa biofilm resulted in ~4.5-5 log cycle reduction in the biofilm viable count compared to the control. Moreover, transmission electron microscope (TEM) images of the photothermally-treated bacteria revealed a significant change in the bacterial shape and lysis of the bacterial cell membrane in comparison to the untreated bacteria. Furthermore, the results revealed that continuous and pulse laser beam modes effected a comparable photothermal-induced bactericidal activity. Therefore, it can be concluded that phospholipid-coated gold nanorods present a promising nanoplatform to eradicate Pseudomonas aeruginosa biofilm responsible for common skin diseases.

Efficacy of carvacrol against resistant rapidly growing mycobacteria in the planktonic and biofilm growth mode

Rapidly growing mycobacteria (RGM) are environmental bacteria found worldwide with a propensity to produce skin and soft-tissue infections. Among them, the most clinically relevant species is Mycobacterium abscessus. Multiple resistance to antibiotics and the ability to form biofilm contributes considerably to the treatment failure. The search of novel anti-mycobacterial agents for the control of biofilm growth mode is crucial. The aim of the present study was to evaluate the activity of carvacrol (CAR) against planktonic and biofilm cells of resistant RGM strains. The susceptibility of RGM strains (n = 11) to antibiotics and CAR was assessed by MIC/MBC evaluation. The CAR activity was estimated by also vapour contact assay. The effect on biofilm formation and preformed biofilm was measured by evaluation of bacterial growth, biofilm biomass and biofilm metabolic activity. MIC values were equal to 64 μg/mL for most of RGM isolates (32–512 μg/mL), MBCs were 2–4 times higher than MICs, and MICs of vapours were lower (16 μg/mL for most RGM isolates) than MICs in liquid phase. Regarding the biofilm, CAR at concentrations of 1/2 × MIC and 1/4 × MIC showed a strong inhibition of biofilm formation (61–77%) and at concentration above the MIC (2–8 × MIC) produced significant inhibition of 4- and 8-day preformed biofilms. In conclusion, CAR could have a potential use, also in vapour phase, for the control of RGM.

Effect of antimicrobial nanocomposites on Vibrio cholerae lifestyles: Pellicle biofilm, planktonic and surface-attached biofilm

Vibrio cholerae is an important human pathogen causing intestinal disease with a high incidence in developing countries. V. cholerae can switch between planktonic and biofilm lifestyles. Biofilm formation is determinant for transmission, virulence and antibiotic resistance. Due to the enhanced antibiotic resistance observed by bacterial pathogens, antimicrobial nanomaterials have been used to combat infections by stopping bacterial growth and preventing biofilm formation. In this study, the effect of the nanocomposites zeolite-embedded silver (Ag), copper (Cu), or zinc (Zn) nanoparticles (NPs) was evaluated in V. cholerae planktonic cells, and in two biofilm states: pellicle biofilm (PB), formed between air-liquid interphase, and surface-attached biofilm (SB), formed at solid-liquid interfaces. Each nanocomposite type had a distinctive antimicrobial effect altering each V. cholerae lifestyles differently. The ZEO-AgNPs nanocomposite inhibited PB formation at 4 μg/ml, and prevented SB formation and eliminated planktonic cells at 8 μg/ml. In contrast, the nanocomposites ZEO-CuNPs and ZEO-ZnNPs affect V. cholerae viability but did not completely avoid bacterial growth. At transcriptional level, depending on the nanoparticles and biofilm type, nanocomposites modified the relative expression of the vpsL, rbmA and bap1, genes involved in biofilm formation. Furthermore, the relative abundance of the outer membrane proteins OmpT, OmpU, OmpA and OmpW also differs among treatments in PB and SB. This work provides a basis for further study of the nanomaterials effect at structural, genetic and proteomic levels to understand the response mechanisms of V. cholerae against metallic nanoparticles.

Upwelling modulation of functional traits of a dominant planktonic grazer during "warm-acid" El Niño 2015 in a year-round upwelling area of Humboldt Current

Climate change is expected to exacerbate upwelling intensity and natural acidification in Eastern Boundaries Upwelling Systems (EBUS). Conducted between January-September 2015 in a nearshore site of the northern Humboldt Current System directly exposed to year-round upwelling episodes, this study was aimed at assessing the relationship between upwelling mediated pH-changes and functional traits of the numerically dominant planktonic copepod-grazer Acartia tonsa (Copepoda). Environmental temperature, salinity, oxygen, pH, alkalinity, chlorophyll-a (Chl), copepod adult size, egg production (EP), and egg size and growth were assessed through 28 random oceanographic surveys. Agglomerative clustering and multidimensional scaling identified three main di-similitude nodes within temporal variability of abiotic and biotic variables: A) “upwelling”, B) “non-upwelling”, and C) “warm-acid” conditions. Nodes A and B represented typical features within the upwelling phenology, characterized by the transition from low temperature, oxygen, pH and Chl during upwelling to higher levels during non-upwelling conditions. However, well-oxygenated, saline and “warm-acid” node C seemed to be atypical for local climatology, suggesting the occurrence of a low frequency oceanographic perturbation. Multivariate (LDA and ANCOVA) analyses revealed upwelling through temperature, oxygen and pH were the main factors affecting variations in adult size and EP, and highlighted growth rates were significantly lower under node C. Likely buffering upwelling pH-reductions, phytoplankton biomass maintained copepod reproduction despite prevailing low temperature, oxygen and pH levels in the upwelling setting. Helping to better explain why this species is among the most recurrent ones in these variable yet productive upwelling areas, current findings also provide opportune cues on plankton responses under warm-acid conditions, which are expected to occur in productive EBUS as a consequence of climate perturbations.

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations

Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L^-1), medium (10 μg L^-1) and high (20 μg L^-1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Growth impacts of Saharan dust, mineral nutrients, and CO2 on a planktonic herbivore in southern Mediterranean lakes

Rising levels of CO₂ can boost plant biomass but reduce its quality as a food source for herbivores. However, significant uncertainties remain as to the degree to which the effect is modulated by other environmental factors and the underlying processes causing these responses in nature. To address these questions, we carried out CO₂-manipulation experiments using natural seston from three lakes under nutrient-enriched conditions (mimicking eutrophication and atmospheric dust-input processes) as a food source for the planktonic Daphnia pulicaria. Contrary to expectations, there were no single effects of rising CO₂ on herbivorous growth. Instead, synergistic CO₂ × nutrient interactions indicated that CO₂ did not support higher zooplankton growth rates unless supplemented with dust or inorganic nutrients (nitrogen, N; phosphorus, P) in two of three studied lakes. The overall positive correlation between zooplankton growth and seston carbon (C), but not seston C:P, suggested that this was a food quantity-mediated response. In addition, we found that this correlation improved when the data were grouped according to the nutrient treatments, and that the response was largest for dust. The synergistic CO₂ × nutrient effects reported here imply that the effects of rising CO₂ levels on herbivorous growth may be strongly influenced by eutrophication processes and the increase in dust deposition predicted for the Mediterranean region.

Profiling physicochemical and planktonic features from discretely/continuously sampled surface water

There is an increasing need for assessing aquatic ecosystems that are globally endangered. Since aquatic ecosystems are complex, integrated consideration of multiple factors utilizing omics technologies can help us better understand aquatic ecosystems. An integrated strategy linking three analytical (machine learning, factor mapping, and forecast-error-variance decomposition) approaches for extracting the features of surface water from datasets comprising ions, metabolites, and microorganisms is proposed herein. The three developed approaches can be employed for diverse datasets of sample sizes and experimentally analyzed factors. The three approaches are applied to explore the features of bay water surrounding Odaiba, Tokyo, Japan, as a case study. Firstly, the machine learning approach separated 681 surface water samples within Japan into three clusters, categorizing Odaiba water into seawater with relatively low inorganic ions, including Mg, Ba, and B. Secondly, the factor mapping approach illustrated Odaiba water samples from the summer as rich in multiple amino acids and some other metabolites and poor in inorganic ions relative to other seasons based on their seasonal dynamics. Finally, forecast-error-variance decomposition using vector autoregressive models indicated that a type of microalgae (Raphidophyceae) grows in close correlation with alanine, succinic acid, and valine on filters and with isobutyric acid and 4-hydroxybenzoic acid in filtrate, Ba, and average wind speed. Our integrated strategy can be used to examine many biological, chemical, and environmental physical factors to analyze surface water.

The effects of a mixture of copper, nickel, and zinc on the structure and function of a freshwater planktonic community

It is generally assumed that as long as the majority of species experiences no direct adverse effects attributable to a single substance (i.e., potentially affected fraction [PAF] <5%), no significant structural or functional effects at the community level are expected to occur. Whether this assumption holds for mixed metal contamination is not known. In the present study, we tested this by performing a microcosm experiment in which a naturally occurring freshwater planktonic community was exposed to a copper-nickel-zinc (Cu-Ni-Zn) mixture for 8 wk and various structural and functional community-level traits were assessed. In the low mixture concentration treatments (i.e., Ni-Zn mixtures, because there was no difference in Cu concentrations in these treatments with the control), community-level effects were relatively simple, only involving phytoplankton species groups. In the high mixture concentration treatments (Cu-Ni-Zn mixtures), community-level effects were more complex, involving several phytoplankton and zooplankton species groups. Multisubstance PAF (msPAF) values for all mixture treatments were calculated by applying the concentration addition model to bioavailability-normalized single-metal species sensitivity distributions (SSDs). Consistent effects on the structural traits community composition, abundance of zooplankton species groups, species diversity, and species richness and on the functional trait dissolved organic carbon (DOC) concentration (as a proxy for the microbial loop and pelagic food web interactions) were only observed at msPAF values >0.05 (i.e., in the Cu-Ni-Zn mixture). However, consistent effects on the abundance of various phytoplankton species groups (structural traits) and on 2 measures of community respiration, overnight Δ dissolved oxygen (ΔDO) and ΔpH (functional traits), were already observed at msPAF values of ≤0.05 (i.e., in the Ni-Zn mixture). This indicates that the threshold msPAF value of 0.05 was not protective against metal mixture exposure for all community-level structural and functional endpoints in the present study. A possible explanation for this result is the mismatch between the species in the SSD and those in our microcosm community. Indeed, our data suggest that the presence of one single dominant and very Zn- and/or Ni-sensitive species in the investigated community (i.e., a cyanobacteria of the genus Oscillatoria), which is not represented in the SSD of these metals, was probably the driver of all observed effects at or below an msPAF of 0.05. Overall, the present results show that SSDs are not necessarily a good predictor of community-level effects for all types of communities and that the presence of dominant sensitive species may result in significant, consistent effects on certain structural and functional community-level endpoints at msPAF values ≤0.05, which is generally considered protective in many regulatory frameworks. Environ Toxicol Chem 2018;37:2380-2400. © 2018 SETAC.

Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

BACKGROUND

Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized.

RESULTS

The genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions.

CONCLUSIONS

Because of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability

Intensive shrimp farming is generally accompanied by nutrient enrichment and gradual eutrophication, which impose major threats to shrimp culture ecosystems. However, little is known about how the bacterioplankton community in a rearing environment responds to increased eutrophication during shrimp culture processes. In this study, we used the MiSeq sequencing technique to explore the impacts of nutrient enrichment on the assembly and stability of the bacterioplankton community. Our results showed that magnitudes of the changes in the bacterioplankton community compositions (BCCs) and diversity were closely associated with eutrophication level. Moreover, a phylogenetic-based mean nearest taxon distance (MNTD) analysis revealed that increased eutrophication significantly (P < 0.01) changed the bacterioplankton ecological processes from deterministic to stochastic. A structural equation model showed that eutrophication indicators affected the BCCs either directly by controlling resources or indirectly by modifying other environmental variables of the shrimp ponds in complex pathways. Furthermore, association network comparisons revealed that nutrient enrichment increased the complexity of interspecies interactions and the proportion of cooperative interactions and decreased the proportion of generalists, which suggest that nutrient enrichment destroyed the community stability. These findings suggest that minimizing nutrient pollution, especially at the end of cultivation, could be an important management tool for establishing a microbially mature water system.

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river

Although the influence of microbial community assembly processes on aquatic ecosystem function and biodiversity is well known, the processes that govern planktonic communities in human-impacted rivers remain largely unstudied. Here, we used multivariate statistics and a null model approach to test the hypothesis that environmental conditions and obstructed dispersal opportunities, dictate a deterministic community assembly for phytoplankton and bacterioplankton across contrasting hydrographic conditions in a subtropical mid-sized river (Jiulong River, southeast China). Variation partitioning analysis showed that the explanatory power of local environmental variables was larger than that of the spatial variables for both plankton communities during the dry season. During the wet season, phytoplankton community variation was mainly explained by local environmental variables, whereas the variance in bacterioplankton was explained by both environmental and spatial predictors. The null model based on Raup-Crick coefficients for both planktonic groups suggested little evidences of the stochastic processes involving dispersal and random distribution. Our results showed that hydrological change and landscape structure act together to cause divergence in communities along the river channel, thereby dictating a deterministic assembly and that selection exceeds dispersal limitation during the dry season. Therefore, to protect the ecological integrity of human-impacted rivers, watershed managers should not only consider local environmental conditions but also dispersal routes to account for the effect of regional species pool on local communities.

Bacterioplankton Responses to Increased Organic Carbon and Nutrient Loading in a Boreal Estuary-Separate and Interactive Effects on Growth and Respiration

Increases in the terrestrial export of dissolved organic carbon (C) to rivers may be associated with additional loading of organic nitrogen (N) and phosphorus (P) to the coastal zone. However, little is known about how these resources interact in the regulation of heterotrophic bacterioplankton metabolism in boreal coastal ecosystems. Here, we measured changes in bacterioplankton production (BP) and respiration (BR) in response to full-factorial (C, N, and P) enrichment experiments at two sites within the Öre estuary, northern Sweden. The BR was stimulated by single C additions and further enhanced by combined additions of C and other nutrients. Single addition of N or P had no effect on BR rates. In contrast, BP was primarily limited by P at the site close to the river mouth and did not respond to C or N additions. However, at the site further away from the near the river mouth, BP was slightly stimulated by single additions of C. Possibly, the natural inflow of riverine bioavailable dissolved organic carbon induced local P limitation of BP near the river mouth, which was then exhausted and resulted in C-limited BP further away from the river mouth. We observed positive interactions between all elements on all responses except for BP at the site close to the river mouth, where P showed an independent effect. In light of predicted increases in terrestrial P and C deliveries, we expect future increases in BP and increases of BR of terrestrially delivered C substrates at the Öre estuary and similar areas.

Growth of a common planktonic diatom quantified using solid medium culturing

The ability to grow on solid culture medium is a pre-requisite for a successful microbial genetic model organism. Skeletonema marinoi, a bloom-forming, planktonic marine microalga, is widely used in ecological, evolutionary and population genetics studies. We have tested and confirmed the ability of this common organism to grow on solid culture medium (agar) under experimentally manipulated conditions. We established a protocol for quantifying growth characteristics - length of lag phase, growth rate, maximum biomass yield - on agar medium. The procedure was tested under experimental treatments and the resulting growth changes correlated with those observed in standard liquid culture. The ability to grow on solid medium broadens the use of S. marinoi as a molecular model, where agar is routinely used for various purposes (growth, selection, storage); and the possibility to quantify colony growth opens the way for high throughput, automated, or semi-automated phenotyping solutions.

Chronic biofilm-based infections: skewing of the immune response

Many of the deadliest bacterial diseases that plague humanity in the modern age are caused by bacterial biofilms that produce chronic infections. However, most of our knowledge of the host immune response comes from the study of planktonic pathogens. While there are similarities in the host response to planktonic and biofilm bacteria, specific immune responses toward biofilms have not been well studied; the only apparent difference is the inability to clear the bacteria allowing the biofilm infection to become chronic. In some cases, the biofilms skew T-cell response toward a balance that allows a stalemate between the host and the pathogen, in which the infection can become persistent. In this minireview, we will summarize well-known examples of this phenomena as well as some emerging studies that may indicate that this situation is much more common than initially thought.

A regional algorithm to model mesozooplankton biomass along the southwestern Bay of Bengal

A three-dimensional regression analysis attempted to model mesozooplankton (MSP) biomass using sea surface temperature (SST) and chlorophyll-a (Chl-a). The study was carried out from January 2014 to July 2015 in the southwestern Bay of Bengal (BoB) and sampling was carried out on board Sagar Manjusha and Sagar Purvi. SST ranged from 26.2 to 33.1 °C while Chl-a varied from 0.04 to 6.09 μg L^-1. During the course of the study period, there was a weak correlation (r = 0.32) between SST and Chl-a statistically. MSP biomass varied from 0.42 to 9.63 mg C m^-3 and inversely related with SST. Two kinds of approaches were adopted to develop the model by grouping seasonal datasets (four seasonal algorithms) and comprising all datasets (one annual algorithm). Among the four functions used (linear, paraboloid, the Lorentzian and the Gaussian functions), paraboloid model was best suited. The best seasonal and annual algorithms were applied in the synchronous MODIS-derived SST and Chl-a data to estimate the MSP biomass in the southwestern BoB. The modelled MSP biomass was validated with field MSP biomass and the result was statistically significant, showing maximum regression coefficient for the seasonal algorithms (R² = 0.60; p = 0.627; α = 0.05), than the annual algorithm (R² = 0.52; p = 0.015, α = 0.05).

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.

Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8

A number of bacteria adopt various lifestyles such as planktonic free-living or sessile biofilm stages. This enables their survival and development in a wide range of contrasting environments. With the aim of highlighting specific metabolic shifts between these phenotypes and to improve the overall understanding of marine bacterial adhesion, a dual metabolomics/proteomics approach was applied to planktonic and biofilm cultures of the marine bacterium Pseudoalteromonas lipolytica TC8. The liquid chromatography mass spectrometry (LC-MS) based metabolomics study indicated that membrane lipid composition was highly affected by the culture mode: phosphatidylethanolamine (PEs) derivatives were over-produced in sessile cultures while ornithine lipids (OLs) were more specifically synthesized in planktonic samples. In parallel, differences between proteomes revealed that peptidases, oxidases, transcription factors, membrane proteins and the enzymes involved in histidine biosynthesis were over-expressed in biofilms while proteins involved in heme production, nutrient assimilation, cell division and arginine/ornithine biosynthesis were specifically up-regulated in free-living cells.

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons

Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m^-1), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 μg L^-1). Virus abundance varied from 0.37 × 10⁸ to 117 × 10⁸ virus-like-particle (VLP) mL^-1, with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 10⁷ to 56.5 × 10⁷ VLP mL^-1 h^-1 and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.

Variability of ultraplankton composition and distribution in an oligotrophic coastal ecosystem of the NW Mediterranean Sea derived from a two-year survey at the single cell level

Ultraplankton [heterotrophic prokaryotes and ultraphytoplankton (<10 μm)] were monitored weekly over two years (2009 & 2010) in a coastal area of the NW Mediterranean Sea. Six clusters were differentiated by flow cytometry on the basis of their optical properties, two heterotrophic prokaryote (HP) subgroups labelled LNA and HNA (low and high nucleic acid content respectively), Prochlorococcus, Synechococcus, autotrophic picoeukaryotes and nanoeukaryotes. HP represented an important component of the microbial assemblage over the survey with relatively small abundance variation through seasons. The carbon biomass ratio HP/ultraphytoplankton averaged 0.45, however this ratio exceeded 1 during spring. Ultraphytoplankton biomass made about 50% of the total autotrophic carbon estimates but this contribution increased up to 97% and 67% during the 2009 and 2010 spring periods respectively. Within ultraphytoplankton, nanoeukaryote represent the most important ultraphytoplankton group in terms of autotrophic carbon biomass (up to 70%). Picoeukaryote maximum abundance occurred in winter. Synechococcus was the most abundant population (maximum 1.2 x 10 5 cells cm-3) particularly in spring where it represented up to 54% of ultraphytoplankton carbon biomass. The warmer winter-spring temperatures and the lengthening of the stratification period created a favorable situation for the earlier appearance of Synechococcus and its persistence throughout summer, paralleling Prochlorococcus development. Prochlorococcus was dominant over summer and autumn with concentrations up to 1.0 × 10 5 cells cm-3. While the abundance of Synechococcus throughout survey was of the same order as that reported in western Mediterranean Sea, Prochlorococcus was more abundant and similar to the more typical oligotrophic and warm waters. The abundance variation of the ultraplankton components through the survey was relatable to variations in the hydrological and nutrient conditions.

The Major Outer Membrane Protein MopB Is Required for Twitching Movement and Affects Biofilm Formation and Virulence in Two Xylella fastidiosa strains

MopB is a major outer membrane protein (OMP) in Xylella fastidiosa, a bacterial plant pathogen that causes losses on many economically important crops. Based on in silico analysis, the uncharacterized MopB protein of X. fastidiosa contains a β-barrel structure with an OmpA-like domain and a predicted calcium-binding motif. Here, MopB function was studied by mutational analysis taking advantage of the natural competence of X. fastidiosa. Mutants of mopB were constructed in two different X. fastidiosa strains, the type strain Temecula and the more virulent WM1-1. Deletion of the mopB gene impaired cell-to-cell aggregation, surface attachment, and biofilm formation in both strains. Interestingly, mopB deletion completely abolished twitching motility. Electron microscopy of the bacterial cell surface revealed that mopB deletion eliminated type IV and type I pili formation, potentially caused by destabilization of the outer membrane. Both mopB mutants showed reduced virulence using tobacco (Nicotiana tabacum) as a host under greenhouse conditions. These results suggest that MopB has pleiotropic functions in biofilm formation and twitching motility and is important for virulence of X. fastidiosa.

The HIV aspartyl protease inhibitor ritonavir impairs planktonic growth, biofilm formation and proteolytic activity in Trichosporon spp

This study evaluated the effect of the protease inhibitor ritonavir (RIT) on Trichosporon asahii and Trichosporon inkin. Susceptibility to RIT was assessed by the broth microdilution assay and the effect of RIT on protease activity was evaluated using azoalbumin as substrate. RIT was tested for its anti-biofilm properties and RIT-treated biofilms were assessed regarding protease activity, ultrastructure and matrix composition. In addition, antifungal susceptibility, surface hydrophobicity and biofilm formation were evaluated after pre-incubation of planktonic cells with RIT for 15 days. RIT (200 μg ml^-1) inhibited Trichosporon growth. RIT (100 μg ml^-1) also reduced protease activity of planktonic and biofilm cells, decreased cell adhesion and biofilm formation, and altered the structure of the biofilm and the protein composition of the biofilm matrix. Pre-incubation with RIT (100 μg ml^-1) increased the susceptibility to amphotericin B, and reduced surface hydrophobicity and cell adhesion. These results highlight the importance of proteases as promising therapeutic targets and reinforce the antifungal potential of protease inhibitors.

Unusual cohabitation and competition between Planktothrix rubescens and Microcystis sp. (cyanobacteria) in a subtropical reservoir (Hammam Debagh) located in Algeria

Succession in bloom-forming cyanobacteria belonging to distant functional groups in freshwater ecosystems is currently an undescribed phenomenon. However in the Hammam Debagh reservoir (Algeria), P. rubescens and Microcystis sp. co-occur and sometimes proliferate. With the aim of identifying the main factors and processes involved in this unusual cohabitation, water samples were collected monthly from February 2013 to June 2015 at the subsurface at four sampling stations and along the entire water column at one sampling station. In addition, the composition of the cyanobacterial communities was estimated by Illumina sequencing of a 16S rRNA gene fragment from samples collected over one year (October 2013-November 2014). This molecular approach showed that the Hammam Debagh reservoir displays high species richness (89 species) but very low diversity due to the high dominance of Microcystis in this community. Furthermore, it appears that Planktothrix rubescens and Microcystis sp. coexisted (from September to January) but proliferated alternately (Spring 2015 for P. rubescens and Spring 2014 and Autumn 2014/2015 for Microcystis). The main factors and processes explaining these changes in bloom-forming species seem to be related to the variation in the depth of the lake during the mixing period and to the water temperatures during the winter prior to the bloom season in spring.

The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA)

Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems.

Effects of adaptation to carvacrol on Staphylococcus aureus in the planktonic and biofilm phases

The effect of exposure to sub-minimum inhibitory concentrations of carvacrol, for either 3-10 days, on direct (carvacrol) or cross-protection (cinnamaldehyde, eugenol, antibiotics) and the influence on planktonic and biofilm growth of four Staphylococcus aureus strains were reported. The sequential exposure to carvacrol resulted in a direct protection that was more evident in two of the four strains after 10 days. No significant cross-protection against cinnamaldehyde, eugenol and antibiotics was detected. An adaptive response was associated with a prolonged lag phase, a lower yield of bacteria, a colony phenotype likely to be associated to small colony variants and an increase in biofilm production. Generally, the biofilm of the adapted strains was less susceptible to subMICs of carvacrol compared to the biofilms of non-adapted strains. In contrast, it was demonstrated that in the case of mature biofilms the susceptibility was similar. The exposure of S. aureus to carvacrol at concentrations above the MIC resulted in a very low mutation frequency.

Silver oxynitrate - an efficacious compound for the prevention and eradication of dual-species biofilms

Preventing and eradicating biofilms remains a challenge in clinical and industrial settings. Recently, the present authors demonstrated that silver oxynitrate (Ag₇NO₁₁) prevented and eradicated single-species planktonic and biofilm populations of numerous microbes at lower concentrations than other silver (Ag) compounds. Here, the antimicrobial and anti-biofilm efficacy of Ag₇NO₁₁ is elaborated by testing its in vitro activity against combinations of dual-species, planktonic and biofilm populations of Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa. As further evidence emerges that multispecies bacterial communities are more common in the environment than their single-species counterparts, this study reinforces the diverse applicability of the minimal biofilm eradication concentration (MBEC™) assay for testing antimicrobial compounds against biofilms. Furthermore, this study demonstrated that Ag₇NO₁₁ had enhanced antimicrobial and anti-biofilm activity compared to copper sulfate (CuSO₄) and silver nitrate (AgNO₃) against the tested bacterial species.

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.