Site-specific variation in Antarctic marine biofilms established on artificial surfaces

Structural properties and microbial diversity of the biofilm colonizing plastic substrates in Terra Nova Bay (Antarctica)

Microbial colonization on plastic polymers has been extensively explored, however the temporal dynamics of biofilm community in Antarctic environments are almost unknown. As a contribute to fill this knowledge gap, the structural characteristics and microbial diversity of the biofilm associated with polyvinyl chloride (PVC) and polyethylene (PE) panels submerged at 5 m of depth and collected after 3, 9 and 12 months were investigated in four coastal sites of the Ross Sea. Additional panels placed at 5 and 20 m were retrieved after 12 months. Chemical characterization was performed by FTIR-ATR and Raman (through Surface-Enhanced Raman Scattering, SERS) spectroscopy. Bacterial community composition was quantified at a single cell level by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and Confocal Laser Scanning Microscopy (CLSM); microbial diversity was assessed by 16S rRNA gene sequencing. This multidisciplinary approach has provided new insights into microbial community dynamics during biofouling process, shedding light on the biofilm diversity and temporal succession on plastic substrates in the Ross Sea. Significant differences between free-living and microbial biofilm communities were found, with a more consolidated and structured community composition on PVC compared to PE. Spectral features ascribable to tyrosine, polysaccharides, nucleic acids and lipids characterized the PVC-associated biofilms. Pseudomonadota (among Gamma-proteobacteria) and Alpha-proteobacteria dominated the microbial biofilm community. Interestingly, in Road Bay, close to the Italian "Mario Zucchelli" research station, the biofilm growth - already observed during summer season, after 3 months of submersion - continued afterwards leading to a massive microbial abundance at the end of winter (after 12 months). After 3 months, higher percentages of Gamma-proteobacteria in Road Bay than in the not-impacted site were found. These observations lead us to hypothesize that in this site microbial fouling developed during the first 3 months could serve as a starter pioneering community stimulating the successive growth during winter.

Substrate Specificity of Biofilms Proximate to Historic Shipwrecks

The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.

Gut microbiota, behavior, and nutrition after type 1 diabetes diagnosis: A longitudinal study for supporting data in the metabolic control

Introduction

Type 1 diabetes (T1D) risk involves genetic susceptibility but also epigenetics, environment, and behaviors. Appropriate metabolic control, especially quickly after the diagnosis, is crucial for the patient quality of life.

Methods

This study aimed to produce a quantitative comparison of the behavior, nutrition habits, and gut microbiota composition between the onset and the 1-year follow-up in 35 children with T1D.

Results and discussion

At follow-up, with the metabolic control, many parameters improved significantly, with respect to the onset, such as glycated hemoglobin (-19%), body mass index (BMI), and also nutritional behaviors, such as normal calorie intake (+6%), carbohydrate intake (-12%), extra portion request (-4%), and meals distribution during the day. Moreover, glycated hemoglobin decrement correlated with both total and rapid absorption carbohydrate intake (Spearman's rho = 0.288, 95% CI 0.066-0.510, p = 0.013), showing as the nutritional behavior supported the insulin therapy efficiency. The next-generation sequencing (NGS) analysis of microbiota revealed abundance differences for Ruminococcus bromii and Prevotella copri (higher at onset, p < 0.001) and the genera Succinivibrio and Faecalibacterium (lower at onset, p < 0.001), as a consequence of nutritional behavior, but it was not the only changing driver. The qRT-PCR analysis showed significant variations, in particular for Bacteroidetes and Bifidobacterium spp. (+1.56 log gene copies/g stool at follow-up, p < 0.001). During the year, in 11% of the patients, severe clinical episodes occurred (hypoglycemic or ketoacidosis). The likelihood of a severe hypoglycemic episode was modulated when the Methanobrevibacter smithii amount increased (odds ratio 3.7, 95% CI 1.2-11.4, p = 0.026). Integrated evaluation, including nutritional behavior and microbiota composition, could be considered predictive of the metabolic control management for children cohort with a recent diagnosis of T1D.

Marine biofilms: diversity, interactions and biofouling

Marine biofilms are ubiquitous in the marine environment. These complex microbial communities rapidly respond to environmental changes and encompass hugely diverse microbial structures, functions and metabolisms. Nevertheless, knowledge is limited on the microbial community structures and functions of natural marine biofilms and their influence on global geochemical cycles. Microbial cues, including secondary metabolites and microbial structures, regulate interactions between microorganisms, with their environment and with other benthic organisms, which affects their community succession and metamorphosis. Furthermore, marine biofilms are key mediators of marine biofouling, which greatly affect marine industries. In this Review, we discuss marine biofilm dynamics, including their diversity, abundance and functions. We also highlight knowledge gaps, areas for future research and potential biotechnological applications of marine biofilms.

New insights into the structure and function of the prokaryotic communities colonizing plastic debris collected in King George Island (Antarctica): Preliminary observations from two plastic fragments

In Antarctic regions, the composition and metabolic activity of microbial assemblages associated with plastic debris ("plastisphere") are almost unknown. A macroplastic item from land (MaL, 30 cm) and a mesoplastic from the sea (MeS, 4 mm) were collected in Maxwell Bay (King George Island, South Shetland) and analyzed by Fourier transform infrared spectroscopy in attenuated total reflectance geometry (FTIR-ATR), which confirmed a polystyrene foam and a composite high-density polyethylene composition for MaL and MeS, respectively. The structure and function of the two plastic-associated prokaryotic communities were studied by complementary 16S ribosomal RNA gene clone libraries, total bacterioplankton and culturable heterotrophic bacterial counts, enzymatic activities of the whole community and enzymatic profiles of bacterial isolates. Results showed that Gamma- and Betaproteobacteria (31% and 28%, respectively) dominated in MeS, while Beta- and Alphaproteobacteria (21% and 13%, respectively) in MaL. Sequences related to oil degrading bacteria (Alcanivorax,Marinobacter) confirmed the known anthropogenic pressure in King George Island. This investigation on plastic-associated prokaryotic structure and function represents the first attempt to characterize the ecological role of plastisphere in this Antarctic region and provides the necessary background for future research on the significance of polymer type, surface characteristics and environmental conditions in shaping the plastisphere.

Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area

Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.

Metal resistance genes enrichment in marine biofilm communities selected by biocide-containing surfaces in temperate and tropical coastal environments

Microorganisms able to form biofilms in marine ecosystems are selected depending on immersed surfaces and environmental conditions. Cell attachment directly on toxic surfaces like antifouling coatings suggests a selection of tolerant (or resistant) organisms with characteristics conferring adaptive advantages. We investigated if environment would drive metal resistance gene abundance in biofilms on artificial surfaces. Biofilms were sampled from three surfaces (a PVC reference and two antifouling coatings) deployed in three coastal waters with dissimilar characteristics: The Mediterranean Sea (Toulon) and Atlantic (Lorient) and Indian (Reunion) Oceans. The two coatings differed in metals composition, either Cu thiocyanate and Zn pyrithione (A3) or Cu2O (Hy). Metal resistance genes (MRG) specific to copper (cusA, copA, cueO) or other metals (czcA and pbrT) were monitored with qPCR in parallel to the microbial community using 16S rRNA gene metabarcoding. A lower α-diversity on A3 or Hy than on PVC was observed independent on the site. Weighted Unifrac suggested segregation of communities primarily by surface, with lower site effect. Metacoder log2 fold change ratio and LeFSe discrimination suggested Marinobacter to be specific of Hy and Altererythrobacter, Erythrobacter and Sphingorhabdus of A3. Likewise, the relative abundance of MRG (MRG/bacterial 16S rRNA) varied between surfaces and sites. A3 presented the greatest relative abundances for cusA, cueO and czcA. The latter could only be amplified from A3 communities, except at Toulon. Hy surface presented the highest relative abundance for copA, specifically at Lorient. These relative abundances were correlated with LeFSe discriminant taxa. Dasania correlated positively with all MRG except cueO. Marinobacter found in greater abundance in Hy biofilm communities correlated with the highest abundances of copA and Roseovarius with czcA. These results prove the selection of specific communities with abilities to tolerate metallic biocides forming biofilms over antifouling surfaces, and the secondary but significant influence of local environmental factors.

Microbiota, epidemiological and nutritional factors related to ketoacidosis at the onset of type 1 diabetes

AIMS

The incidence of type 1 diabetes has increased over the last decades. The pathological pathway is not yet clear, even if genetic and environmental risk factors are known. An early diagnosis can avoid ketoacidosis and its complications. This work aims to discuss the determinants of both ketoacidosis at the onset and access by hospital emergency departments without a suspected diagnosis.

METHODS

An observational bi-centric prospective study was conducted in Northern Italy, on a paediatric population including Italian and migrant patients at the diabetes onset. Seventy-four type 1 diabetes patients, both Italian and migrant, were included in the study. Anthropometric, socio-economic, behavioural, clinical data were collected, and microbiota analyses were performed using stool samples.

RESULTS

Regular physical activity is associated with lower ketoacidosis incidence at onset (OR 0.33 95% CI 0.12-0.95 p < 0.05), as is higher blood vitamin D level (OR 0.92 95% CI 0.85-0.99 p < 0.05). Moreover, a higher weaning age (OR 0.49 95% CI 0.27-0.89 p < 0.05), higher vitamin D level (OR 0.90 95% CI 0.83-0.98 p < 0.05) and a higher level of Akkermansia muciniphila (OR 0.46 95% CI 0.25-0.87 p < 0.05) are associated factors to lower frequency of type 1 diabetes onset without a suspected diagnosis. Diabetes migrant status is not a risk factor for severe type 1 diabetes onset; on the other hand, some protective factors are significantly more diffused among Italians, such as regular sport activity and non-critical vitamin D levels.

CONCLUSION

Behavioural and nutritional data, such as microbiota bio-indicators, seem to be useful to identify an at-risk population to prevent ketoacidosis and its severe complications.

Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study

Type 1 diabetes (T1D) is a common autoimmune disease that is characterized by insufficient insulin production. The onset of T1D is the result of gene-environment interactions. Sociodemographic and behavioural factors may contribute to T1D, and the gut microbiota is proposed to be a driving factor of T1D. An integrated preventive strategy for T1D is not available at present. This case-control study attempted to estimate the exposure linked to T1D to identify significant risk factors for healthy children. Forty children with T1D and 56 healthy controls were included in this study. Anthropometric, socio-economic, nutritional, behavioural, and clinical data were collected. Faecal bacteria were investigated by molecular methods. The findings showed, in multivariable model, that the risk factors for T1D include higher Firmicutes levels (OR 7.30; IC 2.26-23.54) and higher carbohydrate intake (OR 1.03; IC 1.01-1.05), whereas having a greater amount of Bifidobacterium in the gut (OR 0.13; IC 0.05 - 0.34) was a protective factor for T1D. These findings may facilitate the development of preventive strategies for T1D, such as performing genetic screening, characterizing the gut microbiota, and managing nutritional and social factors.

The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts

Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. The haloarchaeal stress response protects cells against abiotic stressors through the synthesis of stress proteins. This includes other heat shock stress proteins (Hsp), thermoprotectants, survival proteins, universal stress proteins, and multicellular structures. Gene and family stress proteins are highly conserved among members of the halophilic archaea and their study should continue in order to develop means to improve for biotechnological purposes. In this review, all the mechanisms to cope with stress response by haloarchaea are discussed from a global perspective, specifically focusing on the role played by universal stress proteins.

The Role of Biofilms Developed under Different Anthropogenic Pressure on Recruitment of Macro-Invertebrates

Microbial biofilms can be key mediators for settlement of macrofoulers. The present study examines the coupled effects of microbial biofilms and local environmental conditions on the composition, structure and functioning of macrofouling assemblages. Settlement of invertebrates over a gradient of human-impacted sites was investigated on local biofilms and on biofilms developed in marine protected areas (MPAs). Special attention was given to the presence of non-indigenous species (NIS), a global problem that can cause important impacts on local assemblages. In general, the formation of macrofouling assemblages was influenced by the identity of the biofilm. However, these relationships varied across levels of anthropogenic pressure, possibly influenced by environmental conditions and the propagule pressure locally available. While the NIS Watersipora subatra seemed to be inhibited by the biofilm developed in the MPA, Diplosoma cf. listerianum seemed to be attracted by biofilm developed in the MPA only under mid anthropogenic pressure. The obtained information is critical for marine environmental management, urgently needed for the establishment of prevention and control mechanisms to minimize the settlement of NIS and mitigate their threats.

Microbial Colonization in Marine Environments: Overview of Current Knowledge and Emerging Research Topics

Microbial biofilms are biological structures composed of surface-attached microbial communities embedded in an extracellular polymeric matrix. In aquatic environments, the microbial colonization of submerged surfaces is a complex process involving several factors, related to both environmental conditions and to the physical-chemical nature of the substrates. Several studies have addressed this issue; however, more research is still needed on microbial biofilms in marine ecosystems. After a brief report on environmental drivers of biofilm formation, this study reviews current knowledge of microbial community attached to artificial substrates, as obtained by experiments performed on several material types deployed in temperate and extreme polar marine ecosystems. Depending on the substrate, different microbial communities were found, sometimes highlighting the occurrence of species-specificity. Future research challenges and concluding remarks are also considered. Emphasis is given to future perspectives in biofilm studies and their potential applications, related to biofouling prevention (such as cell-to-cell communication by quorum sensing or improved knowledge of drivers/signals affecting biological settlement) as well as to the potential use of microbial biofilms as sentinels of environmental changes and new candidates for bioremediation purposes.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.

Shear Stress as a Major Driver of Marine Biofilm Communities in the NW Mediterranean Sea

While marine biofilms depend on environmental conditions and substrate, little is known about the influence of hydrodynamic forces. We tested different immersion modes (dynamic, cyclic and static) in Toulon Bay (north-western Mediterranean Sea; NWMS). The static mode was also compared between Toulon and Banyuls Bays. In addition, different artificial surfaces designed to hamper cell attachment (self-polishing coating: SPC; and fouling-release coating: FRC) were compared to inert plastic. Prokaryotic community composition was affected by immersion mode, surface characteristics and site. Rhodobacteriaceae and Flavobacteriaceae dominated the biofilm community structure, with distinct genera according to surface type or immersion mode. Cell density increased with time, greatly limited by hydrodynamic forces, and supposed to delay biofilm maturation. After 1 year, a significant impact of shear stress on the taxonomic structure of the prokaryotic community developed on each surface type was observed. When surfaces contained no biocides, roughness and wettability shaped prokaryotic community structure, which was not enhanced by shear stress. Conversely, the biocidal effect of SPC surfaces, already major in static immersion mode, was amplified by the 15 knots speed. The biofilm community on SPC was 60% dissimilar to the biofilm on the other surfaces and was distinctly colonized by Sphingomonadaceae ((Alter)Erythrobacter). At Banyuls, prokaryotic community structures were more similar between the four surfaces tested than at Toulon, due possibly to a masking effect of environmental constraints, especially hydrodynamic, which was greater than in Toulon. Finally, predicted functions such as cell adhesion confirmed some of the hypotheses drawn regarding biofilm formation over the artificial surfaces tested here.

Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming

Marine encrusting communities play vital roles in benthic ecosystems and have major economic implications with regards to biofouling. However, their ability to persist under projected warming scenarios remains poorly understood and is difficult to study under realistic conditions. Here, using heated settlement panel technologies, we show that after 18 months Antarctic encrusting communities do not acclimate to either +1 °C or +2 °C above ambient temperatures. There is significant up-regulation of the cellular stress response in warmed animals, their upper lethal temperatures decline with increasing ambient temperature and population genetic analyses show little evidence of differential survival of genotypes with treatment. By contrast, biofilm bacterial communities show no significant differences in community structure with temperature. Thus, metazoan and bacterial responses differ dramatically, suggesting that ecosystem responses to future climate change are likely to be far more complex than previously anticipated.

Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

Marine biofilms: diversity of communities and of chemical cues

Surfaces immersed in seawater are rapidly colonized by various microorganisms, resulting in the formation of heterogenic marine biofilms. These communities are known to influence the settlement of algae spores and invertebrate larvae, triggering a succession of fouling events, with significant environmental and economic impacts. This review covers recent research regarding the differences in composition of biofilms isolated from different artificial surface types and the influence of environmental factors on their formation. One particular phenomenon - bacterial quorum sensing (QS) - allows bacteria to coordinate swarming, biofilm formation among other phenomena. Some other marine biofilm chemical cues are believed to modulate the settlement and the succession of macrofouling organisms, and they are also reviewed here. Finally, since the formation of a marine biofilm is considered to be an initial, QS-dependent step in the development of marine fouling events, QS inhibition is discussed on its potential as a tool for antibiofouling control in marine settings.

Analysis of marine microbial communities colonizing various metallic materials and rust layers

High-throughput sequencing was used to visualize microbial biocoenoses on different metallic surfaces and rust layers of highly corroded steels after immersion in coastal marine water for 30 months at Sanya, China. Distinct microbial community compositions were observed on these metallic surfaces. The dominant genus was the copper-tolerant, acid-producing Lactobacillus on copper alloys, the common aerobic surface colonizers Bacillus and Ruegeria on aluminum alloys, and aerobic biofilm-forming Pseudomonas on carbon steel. Most of these are copiotrophic microbes compared to planktonic microbes, which are oligotrophic. Additionally, sulfate-reducing prokaryotes (SRP) were detected in the rust layer, but the dominant genera changed from the outer layer to the inner part. The dominant genera detected in the outer, middle and inner rusts layers were Desulfotomaculum, Desulfonatronum (obligate anaerobe) and Desulfovibiro (electroactive), respectively. Further, the coexistence of methanogens with SRP suggests interspecies interactions.

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.

The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis

Vessel hulls and underwater infrastructure can be severely impacted by marine biofouling. Knowledge on which abiotic conditions of artificial structures influence bacterial and eukaryotic community composition is limited. In this study, settlement plates with differing surface texture, orientation and copper-based anti-fouling coatings were deployed in a marina. After three months, biofouling samples were collected and bacterial and eukaryotic communities characterised using DNA metabarcoding. The copper anti-fouling coating treatments incurred the most significant compositional changes (p ≤ 0.001) within both domains. Bacterial diversity decreased, with Gammaproteobacteria becoming the dominant phylum. In contrast, protist diversity increased as well as opportunist nematodes and bryozoans; urochordates and molluscs became less abundant. Network analyses displayed complex relationships on untreated plates, while revealing a simpler, but disturbed and unstable community composition on the anti-fouling coated plates. These networks of copper treatments displayed opportunist taxa that appeared as key organisms in structuring the bacterial and eukaryotic communities.

Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea

Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L^-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.

Effects of organic pollution on biological communities of marine biofilm on hard substrata

We examined the effect of organic enrichment on diatom and bacterial assemblages of marine epilithic biofilms on two locations in the Mediterranean, one situated in Spain and the other in Greece. Total organic carbon, total organic nitrogen, stable isotopes (δ(13)C and δ(15)N) and chlorophyll a indicated significant incorporation of organic wastes, increased primary production and trophic niche modifications on the biofilms close to the organic enrichment source. In Spain, where the organic load was higher than in Greece, diatom and, to some extent, bacterial assemblages varied following the organic enrichment gradient. The taxonomic richness of diatom and bacterial communities was not influenced by organic enrichment. Classical community parameters showed consistent patterns to organic pollution in both locations, whereas community assemblages were only influenced when organic pollution was greatest. The successional patterns of these communities were similar to other epilithic communities. The modification of community assemblages induced by organic pollution may affect ecological functions.

Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm

Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.

Identification of bacterial strains isolated from the Mediterranean Sea exhibiting different abilities of biofilm formation

The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.

Antifouling coatings influence both abundance and community structure of colonizing biofilms: a case study in the Northwestern Mediterranean Sea

When immersed in seawater, substrates are rapidly colonized by both micro- and macroorganisms. This process is responsible for important economic and ecological prejudices, particularly when related to ship hulls or aquaculture nets. Commercial antifouling coatings are supposed to reduce biofouling, i.e., micro- and macrofoulers. In this study, biofilms that primarily settled on seven different coatings (polyvinyl chloride [PVC], a fouling release coating [FRC], and five self-polishing copolymer coatings [SPC], including four commercial ones) were quantitatively studied, after 1 month of immersion in summer in the Toulon Bay (Northwestern Mediterranean Sea, France), by using flow cytometry (FCM), microscopy, and denaturing gradient gel electrophoresis. FCM was used after a pretreatment to separate cells from the biofilm matrix, in order to determine densities of heterotrophic bacteria, picocyanobacteria, and pico- and nanoeukaryotes on these coatings. Among diatoms, the only microphytobenthic class identified by microscopy, Licmophora, Navicula, and Nitzschia were determined to be the dominant taxa. Overall, biocide-free coatings showed higher densities than all other coatings, except for one biocidal coating, whatever the group of microorganisms. Heterotrophic bacteria always showed the highest densities, and diatoms showed the lowest, but the relative abundances of these groups varied depending on the coating. In particular, the copper-free SPC failed to prevent diatom settlement, whereas the pyrithione-free SPC exhibited high picocyanobacterial density. These results highlight the interest in FCM for antifouling coating assessment as well as specific selection among microbial communities by antifouling coatings.

Sponge larval settlement cues: the role of microbial biofilms in a warming ocean

Microbial biofilms play important roles in initiating settlement of marine invertebrate larvae. Given the importance of habitat selection by the motile larval phase, understanding settlement choices is critical if we are to successfully predict the population dynamics of sessile adults. Marine microbial biofilms show remarkable variability in community composition, often mediated by environmental conditions and biofilm age. To determine if biofilm communities were influenced by the time allowed to establish (age) and/or seawater temperature, we manipulated experimental surfaces to firstly determine biofilm community composition and secondly test larval settlement responses for the abundant coral reef sponge Rhopaloeides odorabile. Microbial profiling of biofilms revealed different communities according to both age and temperature. Biofilm community composition, as a result of both elevated seawater temperature and biofilm age, contributed to settlement for sponge larvae with markedly higher numbers of larvae settling to biofilms developed over longer periods (10 d) and at temperatures 2–6°C above ambient.

Marine biofilms on artificial surfaces: structure and dynamics

The search for new antifouling (AF) coatings that are environmentally benign has led to renewed interest in the ways that micro-organisms colonize substrates in the marine environment. This review covers recently published research on the global species composition and dynamics of marine biofilms, consisting mainly of bacteria and diatoms found on man-made surfaces including AF coatings. Marine biofilms directly interact with larger organisms (macrofoulers) during colonization processes; hence, recent literature on understanding the basis of the biofilm/macrofouling interactions is essential and will also be reviewed here. Overall, differences have been identified in species composition between biofilm and planktonic forms for both diatoms and bacteria at various exposure sites. In most studies, the underlying biofilm was found to induce larval and spore settlement of macrofoulers; however, issues such as reproducibility, differences in exposure sites and biofilm composition (natural multispecies vs. monospecific species) may influence the outcomes.

Archaeal biofilms: the great unexplored

Biofilms are currently viewed as the most common form in which microorganisms exist in nature. Bacterial biofilms play important roles in disease and industrial applications, and they have been studied in great detail. Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. Therefore, we aim to highlight the available information and indicate open questions in this field.

The effect of surface colour on the formation of marine micro and macrofouling communities

The effect of substratum colour on the formation of micro- and macro fouling communities was investigated. Acrylic tiles, painted either black or white were covered with transparent sheets in order to ensure similar surface properties. All substrata were exposed to biofouling at 1 m depth for 40 d in the Marina Bandar al Rowdha (Muscat, Sea of Oman). Studies were conducted in 2010 over a time course of 5, 10 and 20 d, and in 2012 samples were collected at 7, 14 and 21 d. The densities of bacteria on the black and white substrata were similar with the exception of day 10, when the black substrata had a higher abundance than white ones. Pyrosequencing via 454 of 16S rRNA genes of bacteria from white and black substrata revealed that Alphaproteobacteria and Firmicutes were the dominant groups. SIMPER analysis demonstrated that bacterial phylotypes (uncultured Gammaproteobacteria, Actibacter, Gaetbulicola, Thalassobius and Silicibacter) and the diatoms (Navicula directa, Navicula sp. and Nitzschia sp.) contributed to the dissimilarities between communities developed on white and black substrata. At day 20, the highest amount of chlorophyll a was recorded in biofilms developed on black substrata. SIMPER analysis showed that Folliculina sp., Ulva sp. and Balanus amphitrite were the major macro fouling species that contributed to the dissimilarities between the communities formed on white and black substrata. Higher densities of these species were observed on black tiles. The results emphasise the effect of substratum colour on the formation of micro and macro fouling communities; substratum colour should to be taken into account in future studies.

Archaeal biofilms: widespread and complex

Biofilms or multicellular structures become accepted as the dominant microbial lifestyle in Nature, but in the past they were only studied extensively in bacteria. Investigations on archaeal monospecies cultures have shown that many archaeal species are able to adhere on biotic and abiotic surfaces and form complex biofilm structures. Biofilm-forming archaea were identified in a broad range of extreme and moderate environments. Natural biofilms observed are mostly mixed communities composed of archaeal and bacterial species of various abundances. The physiological functions of the archaea identified in such mixed communities suggest a significant impact on the biochemical cycles maintaining the flow and recycling of the nutrients on earth. Therefore it is of high interest to investigate the characteristics and mechanisms underlying the archaeal biofilm formation. In the present review, I summarize and discuss the present investigations of biofilm-forming archaeal species, i.e. their diverse biofilm architectures in monospecies or mixed communities, the identified EPSs (extracellular polymeric substances), archaeal structures mediating surface adhesion or cell–cell connections, and the response to physical and chemical stressors implying that archaeal biofilm formation is an adaptive reaction to changing environmental conditions. A first insight into the molecular differentiation of cells within archaeal biofilms is given.

Terrestrial runoff controls the bacterial community composition of biofilms along a water quality gradient in the Great Barrier Reef

16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyll a concentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.

Effects of eutrophication, seasonality and macrofouling on the diversity of bacterial biofilms in equatorial coral reefs

Biofilms play an important role as a settlement cue for invertebrate larvae and significantly contribute to the nutrient turnover in aquatic ecosystems. Nevertheless, little is known about how biofilm community structure generally responds to environmental changes. This study aimed to identify patterns of bacterial dynamics in coral reef biofilms in response to associated macrofouling community structure, microhabitat (exposed vs. sheltered), seasonality, and eutrophication. Settlement tiles were deployed at four reefs along a cross-shelf eutrophication gradient and were exchanged every 4 months over 20 months. The fouling community composition on the tiles was recorded and the bacterial community structure was assessed with the community fingerprinting technique Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial operational taxonomic unit (OTU) number was higher on exposed tiles, where the fouling community was homogenous and algae-dominated, than in sheltered habitats, which were occupied by a variety of filter feeders. Furthermore, OTU number was also highest in eutrophied near-shore reefs, while seasonal variations in community structure were most pronounced in the oligotrophic mid-shelf reef. In contrast, the macrofouling community structure did not change significantly with seasons. Changes in bacterial community patterns were mostly affected by microhabitat, seasonal and anthropogenically derived changes in nutrient availability, and to a lesser extent by changes in the macrofouling community structure. Path analysis revealed a complex interplay of various environmental and biological factors explaining the spatial and temporal variations in bacterial biofilm communities under natural conditions.

Effects of ocean acidification on microbial community composition of, and oxygen fluxes through, biofilms from the Great Barrier Reef

Rising anthropogenic CO(2) emissions acidify the oceans, and cause changes to seawater carbon chemistry. Bacterial biofilm communities reflect environmental disturbances and may rapidly respond to ocean acidification. This study investigates community composition and activity responses to experimental ocean acidification in biofilms from the Australian Great Barrier Reef. Natural biofilms grown on glass slides were exposed for 11 d to four controlled pCO(2) concentrations representing the following scenarios: A) pre-industrial (∼300 ppm), B) present-day (∼400 ppm), C) mid century (∼560 ppm) and D) late century (∼1140 ppm). Terminal restriction fragment length polymorphism and clone library analyses of 16S rRNA genes revealed CO(2) -correlated bacterial community shifts between treatments A, B and D. Observed bacterial community shifts were driven by decreases in the relative abundance of Alphaproteobacteria and increases of Flavobacteriales (Bacteroidetes) at increased CO(2) concentrations, indicating pH sensitivity of specific bacterial groups. Elevated pCO(2) (C + D) shifted biofilm algal communities and significantly increased C and N contents, yet O(2) fluxes, measured using in light and dark incubations, remained unchanged. Our findings suggest that bacterial biofilm communities rapidly adapt and reorganize in response to high pCO(2) to maintain activity such as oxygen production.

Effect of substrate type on bacterial community composition in biofilms from the Great Barrier Reef

Natural and anthropogenic impacts such as terrestrial runoff, influence the water quality along the coast of the Great Barrier Reef (GBR) and may in turn affect coral reef communities. Associated bacterial biofilms respond rapidly to environmental conditions and are potential bioindicators for changes in water quality. As a prerequisite to study the effects of water quality on biofilm communities, appropriate biofilm substrates for deployment in the field must be developed and evaluated. This study investigates the effect of different settlement substrates (i.e. glass slides, ceramic tiles, coral skeletons and reef sediments) on bacterial biofilm communities grown in situ for 48 days at two locations in the Whitsunday Island Group (Central GBR) during two sampling times. Bacterial communities associated with the biofilms were analysed using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of 16S rRNA genes. Findings revealed that substrate type had little influence on bacterial community composition. Of particular relevance, glass slides and coral skeletons exhibited very similar communities during both sampling times, suggesting the suitability of standardized glass slides for long-term biofilm indicator studies in tropical coral reef ecosystems.

Biofilm responses to marine fish farm wastes

The changes in the biofilm community due to organic matter enrichment, eutrophication and metal contamination derived from fish farming were studied. The biofilm biomass, polysaccharide content, trophic niche and element accumulation were quantified along an environmental gradient of fish farm wastes in two seasons. Biofilm structure and trophic diversity was influenced by seasonality as well as by the fish farm waste load. Fish farming enhanced the accumulation of organic carbon, nutrients, selenium and metals by the biofilm community. The accumulation pattern of these elements was similar regardless of the structure and trophic niche of the community. This suggests that the biofilm communities can be considered a reliable tool for assessing dissolved aquaculture wastes. Due to the ubiquity of biofilms and its wide range of consumers, its role as a sink of dissolved wastes may have important implications for the transfer of aquaculture wastes to higher trophic levels in coastal systems.

TBT contamination of remote marine environments: ship groundings and ice-breakers as sources of organotins in the Great Barrier Reef and Antarctica

Remote marine environments such as many parts of the Great Barrier Reef (GBR) and the Antarctic are often assumed to be among the most pristine natural habitats. While distance protects them from many sources of pollution, recent studies have revealed extremely high concentrations of organotins in areas associated with shipping activities. Sediments at sites of ship groundings on the GBR have been found to contain up to 340,000 microg Sn kg(-1). Very high concentrations (up to 2290 microg Sn kg(-1)) have been detected in nearshore Antarctic sediments adjacent to channels cut through sea ice by ice-breaking vessels. In both cases, the bulk of the contamination is associated with flakes of antifouling paint abraded from vessel hulls, resulting in patchy but locally intense contamination of sediments. These particulates are likely to continue releasing organotins, rendering grounding sites and ice-breaking routes point-sources of contamination of surrounding environments. While the areas exposed to biologically-harmful concentrations of leached chemicals are likely to be limited in extent (1000-10,000 m(2)), deposition of antifouling paints constitutes a persistent ecological risk in otherwise pristine marine environments of high conservation value. The risk of contamination of GBR and Antarctic sediments by organotins needs to be considered against an important alternative risk: that less effective antifouling of ships hulls may increase the frequency of successful invasions by non-indigenous species. Additional options to minimise ecological risk include accident prevention and reducing organotin contamination from grounding sites through removal or treatment of contaminated sediments, as has been done at some sites in the GBR.