16S rRNA gene profiling of planktonic and biofilm microbial populations in the Gulf of Guinea using Illumina NGS

Biomineralization To Prevent Microbially Induced Corrosion on Concrete for Sustainable Marine Infrastructure

Microbially induced corrosion (MIC) on concrete represents a serious issue impairing the lifespan of coastal/marine infrastructure. However, currently developed concrete corrosion protection strategies have limitations in wide applications. Here, a biomineralization method was proposed to form a biomineralized film on concrete surfaces for corrosion inhibition. Laboratory seawater corrosion experiments were conducted under different conditions [e.g., chemical corrosion (CC), MIC, and biomineralization for corrosion inhibition]. A combination of chemical and mechanical property measurements of concrete (e.g., sulfate concentrations, permeability, mass, and strength) and a genotypic-based investigation of formed concrete biofilms was conducted to evaluate the effectiveness of the biomineralization approach on corrosion inhibition. The results show that MIC resulted in much higher corrosion rates than CC. However, the biomineralization treatment effectively inhibited corrosion because the biomineralized film decreased the total and relative abundance of sulfate-reducing bacteria (SRB) and acted as a protective layer to control the diffusion of sulfate and isolate the concrete from the corrosive SRB communities, which helps extend the lifespan of concrete structures. Moreover, this technique had no negative impact on the native marine microbial communities. Our study contributes to the potential application of biomineralization for corrosion inhibition to achieve long-term sustainability for major marine concrete structures.

Seasonal variation in the biological succession of marine diatoms over 316L stainless steel in a coastal environment of Chile

Characterizing seasonal changes in diatom community profiles in coastal environments is scarce worldwide. Despite diatoms being prevalent in microfouling, their role in microbially influenced corrosion of metallic materials remains poorly understood. This study reports the effect of seasonal variations on the settlement of marine diatoms and corrosion of 316 L stainless steel surfaces exposed to Chilean coastal seawater. Electron microscopy imaging revealed a diverse assembly of diatoms, exhibiting pronounced differences at genus level between summer and winter seasons, with a significant delay in diatom settlement during winter. Electrochemical measurements indicated an active role of diatoms in increasing corrosion current during biofilm development. While the final diatom composition was similar irrespective of the season, the analyses of diatom assemblages over time differed, showing faster colonization when silicate and nitrate were available. This study lays the foundation for future research on the dominant season-specific genera of diatoms to unveil the microbial interactions that could contribute to corrosion and to evaluate their potential as bioindicators for alternative surveillance strategies.

Characterization of the biofilm structure and microbial diversity of sulfate-reducing bacteria from petroleum produced water supplemented by different carbon sources

Colonization by sulfate-reducing bacteria (SRB) in environments associated with oil is mainly dependent on the availability of sulfate and carbon sources. The formation of biofilms by SRB increases the corrosion of pipelines and oil storage tanks, representing great occupational and operational risks and respective economic losses for the oil industry. The aim of this study was to evaluate the influence of the addition of acetate, butyrate, lactate, propionate and oil on the structure of biofilm formed in carbon steel coupons, as well as on the diversity of total bacteria and SRB in the planktonic and sessile communities from petroleum produced water. The biofilm morphology, chemical composition, average roughness and the microbial diversity was analyzed. In all carbon sources, formation of dense biofilm without morphological and/or microbial density differences was detected, with the most of cells observed in the form of individual rods. The diversity and richness indices of bacterial species in the planktonic community was greater than in the biofilm. Geotoga was the most abundant genus, and more than 85% of SRB species were common to all treatments. The functional predicted profile shown that the observed genres in planktonic communities were related to the reduction of sulfate, sulfite, elementary sulfur and other sulfur compounds, but the abundance varied between treatments. For the biofilm, the functions predicted profile for the oil treatment was the one that most varied in relation to the control, while for the planktonic community, the addition of all carbon sources interfered in the predicted functional profile. Thus, although it does not cause changes in the structure and morphology biofilm, the supplementation of produced water with different carbon sources is associated with changes in the SRB taxonomic composition and functional profiles of the biofilm and the planktonic bacterial communities.

High Taxonomic Diversity in Ship Bilges Presents Challenges for Monitoring Microbial Corrosion and Opportunity To Utilize Community Functional Profiling

One of the key areas in which microbially influenced corrosion (MIC) has been found to be a problem is in the bilges of maritime vessels. To establish effective biological monitoring protocols, baseline knowledge of the temporal and spatial biological variation within bilges, as well as the effectiveness of different sampling methodologies, is critical. We used 16S rRNA gene metabarcoding of pelagic and sessile bacterial communities from ship bilges to assess the variation in bilge bacterial communities to determine how the inherent bilge diversity could guide or constrain biological monitoring. Bilge communities exhibited high levels of spatial and temporal variation, with >80% of the community able to be turned over in the space of 3 months, likely due to disturbance events such as cleaning and maintenance. Sessile and pelagic communities within a given bilge were also inherently distinct, with dominant exact sequence variants (ESVs) rarely shared between the two. Taxa containing KEGG orthologies (KOs) associated with dissimilatory sulfate reduction and biofilm production, functions typically associated with MIC, were generally more prevalent in sessile communities. Collectively, our findings indicate that neither bilge water nor an unaffected bilge from within the same vessel would constitute an appropriate reference community for MIC diagnosis. Optimal sampling locations and strategies that could be incorporated into a standardized method for monitoring bilge biology in relation to MIC were identified. Finally, taxonomic and functional comparisons of bilge diversity highlight the potential of functional approaches in future biological monitoring of MIC and MIC mitigation strategies in general. IMPORTANCE Microbially influenced corrosion (MIC) has been estimated to contribute 20 to 50% of the costs associated with corrosion globally. Diagnosis and monitoring of MIC are complex problems requiring knowledge of corrosion rates, corrosion morphology, and the associated microbiology to distinguish MIC from abiotic corrosion processes. Historically, biological monitoring of MIC utilized a priori knowledge to monitor sulfate-reducing bacteria; however, it is becoming widely accepted that a holistic or community-level understanding of corrosion-associated microbiology is needed for MIC diagnosis and monitoring. Before biology associated with MIC attack can be identified, standardized protocols for sampling and monitoring must be developed. The significance of our research is in contributing to the development of robust and repeatable sampling strategies of bilges, which are required for the development of standardized biological monitoring methods for MIC. We achieve this via a biodiversity survey of bilge communities and by comparing taxonomic and functional variation.

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.

Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study

Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.

Evaluation of microbial proliferation on cementitious materials exposed to biogas systems

Understanding the interactions between biofilm and cementitious materials in biogas production systems is an essential step toward the development of durable concrete for this expanding sector. Although the action of the liquid phase medium on the material has been the subject of several research studies, the possible impact of the material's properties on biofilm formation and composition has been little investigated, if at all. The aim of this paper is to evaluate the characteristics of the biofilm according to the surface properties of the materials. Four cementitious materials with different chemical and mineralogical compositions, and various topological surface characteristics (pastes of CEM I, CEM III/C and CAC, and CEM I paste treated with oxalic acid) were exposed to the liquid phase of a fermenting biowaste for 10 weeks. The steps of biofilm formation were observed using SEM. Even though all the cementitious material surfaces were intensely colonized at the end of the experiments, the establishment of the biofilm seems to have been delayed on the oxalate-treated CEM I and on CAC coupons. Roughness and surface pH effects were not of prime importance for the biofilm development. The analysis of bacterial population diversity using 16S rDNA sequencing showed a less diversified microbial flora in the biofilm than in the reaction medium.

The marine intertidal zone shapes oyster and clam digestive bacterial microbiota

Digestive microbiota provide a wide range of beneficial effects on host physiology and are therefore likely to play a key role in marine intertidal bivalve ability to acclimatize to the intertidal zone. This study investigated the effect of intertidal levels on the digestive bacterial microbiota of oysters (Crassostrea gigas) and clams (Ruditapes philippinarum), two bivalves with different ecological niches. Based on 16S rRNA region sequencing, digestive glands, seawater and sediments harbored specific bacterial communities, dominated by operational taxonomic units assigned to the Mycoplasmatales,Desulfobacterales and Rhodobacterales orders, respectively. Field implantation modified digestive bacterial microbiota of both bivalve species according to their intertidal position. Rhodospirillales and Legionellales abundances increased in oysters and clams from the low intertidal level, respectively. After a 14-day depuration process, these effects were still observed, especially for clams, while digestive bacterial microbiota of oysters were subjected to more short-term environmental changes. Nevertheless, 3.5 months stay on an intertidal zone was enough to leave an environmental footprint on the digestive bacterial microbiota, suggesting the existence of autochthonous bivalve bacteria. When comparing clams from the three intertidal levels, 20% of the bacterial assemblage was shared among the levels and it was dominated by an operational taxonomic unit affiliated to the Mycoplasmataceae and Spirochaetaceae families.

Microbial Communities of Orange Tubercles in Accelerated Low-Water Corrosion

The rapid degradation of marine infrastructure at the low tide level due to accelerated low-water corrosion (ALWC) is a problem encountered worldwide. Despite this, there is limited understanding of the microbial communities involved in this process. We obtained samples of the orange-colored tubercles commonly associated with ALWC from two different types of steel sheet piling, located adjacent to each other but with different levels of localized corrosion, at a seaside harbor. The microbial communities from the outer and inner layers of the orange tubercles and from adjacent seawater were studied by pure culture isolation and metabarcoding of the 16S rRNA genes. A collection of 119 bacterial isolates was obtained from one orange tubercle sample, using a range of media in anaerobic and aerobic conditions. The metabarcoding results showed that sulfur and iron oxidizers were more abundant on the outer sections of the orange tubercles compared to the inner layers, where Deltaproteobacteria (which include many sulfate reducers) were more abundant. The microbial communities varied significantly between the inner and outer layers of the orange tubercles and also with the seawater but overall did not differ significantly between the two steel sheet types. Hence, we saw similar microbial communities in orange tubercles present, but different levels of localized corrosion, for two different types of colocated steel sheet piling. Metallurgical analysis found differences in composition, grain size, ferrite-pearlite ratio, and the extent of inclusions present between the two steel types investigated.IMPORTANCE The presence of orange tubercles on marine steel pilings is often used as an indication that accelerated low-water corrosion is taking place. We studied the microbial communities in attached orange tubercles on two closely located sheet pilings that were of different steel types. The attached orange tubercles were visually similar, but the extents of underlying corrosion on the different steel surfaces were substantially different. No clear difference was found between the microbial communities present on the two different types of sheet piling. However, there were clear differences in the microbial communities in the corrosion layers of tubercles, which were also different from the microbes present in adjacent seawater. The overall results suggest that the presence of orange tubercles, a single measurement of water quality, or the detection of certain general types of microbes (e.g., sulfate-reducing bacteria) should not be taken alone as definitive indications of accelerated corrosion.

Biodegradation of polyvinyl chloride plastic films by enriched anaerobic marine consortia

Plastics remarkably contribute to marine litter, which is raising serious concerns. Currently, little is known about the fate of most plastics entering the marine environment and their potential biodegradation rate and extent under anoxic conditions. In this work, biodegradation of polyvinyl chloride (PVC) films by consortia enriched from marine samples (litter and water) was evaluated in anaerobic microcosms. After 7 months, three microcosms showed dense biofilms on plastic surfaces, gravimetric weight losses up to 11.7 ± 0.6%, marked decreases in thermal stability and average molecular weight of the polymer, suggesting microbial attack towards polymer chains. After 24 months, further three consortia showed the same abilities. Microbial communities analyzed at month 24 included taxa closely related to those previously reported as halogenated organic compounds degraders. The study is the first report on PVC biodegradation by marine anaerobic microbes and provides insights on potential biodegradation of the plastic film introduced into the sea by native microbes.

Analysis of microbial contamination of household water purifiers

Household water purifiers are increasingly used to treat drinking water at the household level, but their influence on the microbiological safety of drinking water has rarely been assessed. In this study, representative purifiers, based on different filtering processes, were analyzed for their impact on effluent water quality. The results showed that purifiers reduced chemical qualities such as turbidity and free chlorine. However, a high level of bacteria (10²-10⁶ CFU/g) was detected at each stage of filtration using a traditional culture-dependent method, whereas quantitative PCR with propidium monoazide (PMA) treatment showed 10⁶-10⁸ copies/L of total viable bacteria in effluent water, indicating elevated microbial contaminants after purifiers. In addition, high-throughput sequencing revealed a diverse microbial community in effluents and membranes. Proteobacteria (22.06-97.42%) was the dominant phylum found in all samples, except for purifier B, in which Melainabacteria was most abundant (65.79%). For waterborne pathogens, Escherichia coli (10⁰-10⁶ copies/g) and Pseudomonas aeruginosa (10⁰-10⁵ copies/g) were frequently detected by qPCR. Sequencing also demonstrated the presence of E. coli (0-6.26%), Mycobacterium mucogenicum (0.01-3.46%), and P. aeruginosa (0-0.16%) in purifiers. These finding suggest that water from commonly used household purifiers still impose microbial risks to human health.

Effect of Tidal Cycles on Bacterial Biofilm Formation and Biocorrosion of Stainless Steel AISI 316L

The effects of tidal cycles associated with the water level on the biocorrosion of stainless steel AISI 316L were studied. Steel coupons were exposed to different conditions of immersion in mesocosms fed by fresh seawater either continuously or in accordance with the periodicity of natural tides. After 5 and 15 weeks, all coupons were found to have undergone ennoblement associated with the formation of a biofilm. Analysis of the composition of the bacterial community using denaturing gradient gel electrophoresis (DGGE) revealed differences in the biological succession. After 15 weeks, exposure to the simulated tidal conditions resulted in biofilms with lesser bacterial richness; the corresponding rate of corrosion, as determined by weight loss, was about 40 times lower compared to the case for the continuous exposure to seawater. Phylogenetic analysis of selected DGGE bands and the inspection of biofilm morphologies revealed that the faster rate of corrosion was associated with the presence of iron-oxidizing Zetaproteobacteria and eukaryotic photosynthetic microorganisms. On the other hand, intermittent exposure to seawater resulted in the succession of microorganisms resistant to the stress associated with sudden environmental changes, which was associated with a low rate of corrosion.

Microbial Composition and Variability of Natural Marine Planktonic and Biofouling Communities From the Bay of Bengal

The Bay of Bengal (BoB) is the largest bay in the world and presents a unique marine environment that is subjected to severe weather, a distinct hydrographic regime and a large anthropogenic footprint. Despite these features and the BoB’s overall economic significance, this ecosystem and its microbiome remain among the most underexplored in the world. In this study, amplicon-based microbial profiling was used to assess the bacterial, archaeal, and micro-eukaryotic content of unperturbed planktonic and biofilm/biofouling communities within the BoB. Planktonic microbial communities were collected during the Southwest monsoon season from surface (2 m), subsurface (75 m), and deep-sea (1000 m) waters from six south-central BoB locations and were compared to concomitant mature biofouling communities from photic-zone subsurface moorings (∼75 m). The results demonstrated vertical stratification of all planktonic communities with geographic variations disappearing in the deep-sea environment. Planktonic microbial diversity was found to be driven by different members of the community, with the most dominant phylotypes driving the diversity of the photic zone and rarer species playing a more influential role within the deep-sea. Geographic variability was not observed in the co-located biofouling microbiomes, but community composition and variability was found to be driven by depth and the presence of macro-fouling and photosynthetic organisms. Overall, these results provide much needed baselines for longitudinal assessments that can be used to monitor the health and evolution of this dynamic and critically important marine environment.

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.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.

Microbial Diversity of Chronic Wound and Successful Management of Traditional Chinese Medicine

Chronic ulcer, including diabetic ulcer, varicose ulcer, and pressure ulcer, negatively affects patients' quality of life. As microbiology plays an important role in the mechanism of pathology for chronic wound healing, this study concentrates on microecology environment of the wound and how Traditional Chinese Medicine (TCM) regulates wound bacteria. Method. The study took wound samples from 35 patients and analyzed bacteria variation before and after TCM treatment by 16s rRNA sequencing. All samples were evaluated from aspects of α-diversity, β-diversity, and Simpson's Diversity index. Result. After total DNA extraction, PCR, and 16S rRNA sequencing of wound bacteria from 35 individuals, it was discovered that younger patients with shorter course of disease have a higher microbial diversity and were easier to recover from ulcers. Additionally, gender also played a vital role in wound healing, and a significant microbial diversity existed between male and female patients. Conclusion. Patients with chronic ulcers achieved a positive effect after TCM treatment (skin-producing ointment). Mechanistically, TCM helped promote wound healing by regulating the wound microbiota.

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species

Strongylid nematodes in large terrestrial herbivores such as great apes, equids, elephants, and humans tend to occur in complex communities. However, identification of all species within strongylid communities using traditional methods based on coproscopy or single nematode amplification and sequencing is virtually impossible. High-throughput sequencing (HTS) technologies provide opportunities to generate large amounts of sequence data and enable analyses of samples containing a mixture of DNA from multiple species/genotypes. We designed and tested an HTS approach for strain-level identification of gastrointestinal strongylids using ITS-2 metabarcoding at the MiSeq Illumina platform in samples from two free-ranging non-human primate species inhabiting the same environment, but differing significantly in their host traits and ecology. Although we observed overlapping of particular haplotypes, overall the studied primate species differed in their strongylid nematode community composition. Using HTS, we revealed hidden diversity in the strongylid nematode communities in non-human primates, more than one haplotype was found in more than 90% of samples and coinfections of more than one putative species occurred in 80% of samples. In conclusion, the HTS approach on strongylid nematodes, preferably using fecal samples, represents a time and cost-efficient way of studying strongylid communities and provides a resolution superior to traditional approaches.

Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing

Next Generation Sequencing (NGS), using the Illumina^® metabarcoding system, showed differences between biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro. Two church biofilms (on granite and augen gneiss) were dominated by Actinobacteria; the third (granite), surrounded by trees and further from intense vehicular traffic, by Gammaproteobacteria. Yeast-like forms of Basidiomycetes and Ascomycetes were major fungi on all facades, but 22.8% of Operational Taxonomic Units could not be assigned to any fungal taxon after DNA amplification with ITS primers and analysis with the UNITE database, indicating the need for more fungal NGS studies. The pipeline used in analysis of the V4 region of rRNA bacterial gene sequences influenced the taxa detected, with two major classes and many genera identified only by the pipeline using the Greengenes, and not the Silva, database. Principal Components Analysis separated façade biofilms into the appropriate three groups and indicated greater dissimilarity of the tree-surrounded church biofilm from the others, confirmed by Jaccard Similarity coefficients, suggesting that local environment influences community composition more than stone type. NGS allows rapid and detailed analysis of microbiomes, but results must be carefully assessed and must not be used as the sole indication of community composition.