Early bacterial biofilm colonizers in the coastal waters of Mauritius

Development and validation of a novel suspended particulate matter sampling device for analysis of particle-bound microbial communities

Biotic and abiotic materials attachment to suspended particulate matter in aquatic systems can increase their toxicity and health impacts and has led to an increased need for consistent sampling across various compartments. Sedimentation traps and continuous flow centrifuges are the traditional tools for sampling suspended particulate matter, while manta trawls have been widely used for surface water sampling of suspended or floating microplastics. Limitations, however, exist in the cost of sampling and infrastructure needed to deploy such devices. Here we report on the construction and usage of a novel suspended particulate matter sampling device, the microParticle Obtaining Trap (mPOT). Quality control testing of the mPOT showed suspended particle recovery rates of >90% for particles 100 µm and larger, while field sampling of groundwater, lake and river water shows consistent, size-fractionated recovery of particulate matter. The mPOT is well suited to sample systems not easily accessible by boat or for particles not commonly recovered by common suspended particulate matter sampling and for collection of particles smaller than 300 µm in size.

Chicken Juice Enhances C. jejuni NCTC 11168 Biofilm Formation with Distinct Morphological Features and Altered Protein Expression

Campylobacter jejuni is the foodborne pathogen causing most gastrointestinal infections. Understanding its ability to form biofilms is crucial for devising effective control strategies in food processing environments. In this study, we investigated the growth dynamics and biofilm formation of C. jejuni NCTC 11168 in various culture media, including chicken juice (CJ), brain heart infusion (BHI), and Mueller Hinton (MH) broth. Our results demonstrated that C. jejuni exhibited a higher growth rate and enhanced biofilm formation in CJ and in 1:1 mixtures of CJ with BHI or MH broth compared to these measures in BHI or MH broth alone. Electron microscopy unveiled distinct morphological attributes of late-stage biofilm cells in CJ, including the presence of elongated spiral-shaped cells, thinner stretched structures compared to regular cells, and extended thread-like structures within the biofilms. Proteomic analysis identified significant alterations in protein expression profiles in C. jejuni biofilms, with a predominance of downregulated proteins associated with vital functions like metabolism, energy production, and amino acid and protein biosynthesis. Additionally, a significant proportion of proteins linked to biofilm formation, virulence, and iron uptake were suppressed. This shift toward a predominantly coccoid morphology echoed the reduced energy demands of these biofilm communities. Our study unlocks valuable insights into C. jejuni's biofilm in CJ, demonstrating its adaptation and survival.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.

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.

Disturbance frequency directs microbial community succession in marine biofilms exposed to shear

IMPORTANCE

Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.

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.

Antifouling Potential of Ethyl Acetate Extract of Marine Bacteria Pseudomonas aeruginosa Strain RLimb

Biofouling is defined as the excessive colonization process of epibiotic organisms, ranging from microfoulers to macrofoulers, on any submerged surface in water. Previous research has attempted to explore the antifouling activity of bacterial isolates due to the biofouling problems occurring worldwide. One solution is to inhibit the early stage of fouling using secondary metabolites produced by marine bacteria. This study aims to determine the antifouling activities of the marine microorganism P. aeruginosa and to characterize the bacteria isolated as a potential anti-biofouling agent. The bacterial isolate was cultured and isolated on a media culture. The bacteria culture extract was extracted using ethyl acetate and concentrated prior to the bioassay method. It was screened for antibacterial activities against Gram-positive and Gram-negative bacteria, such as Bacillus cereus, Streptococcus uberis, Pseudomonas sp., and Vibrio parahaemolyticus, using the disk diffusion technique. The extract was investigated to verify its bioactivity in the prevention of biofilm formation following the crystal violet assay and aquarium test. The results indicated the inhibition of activity through biofilm formation, with the highest percentage at 83% of biofilm inhibition at a concentration of 0.1563 mg/mL. The bacterial isolate at a concentration of 5% showed the highest reduction in bacteria colonies in the aquarium test (161.8 × 103 CFU/mL compared to 722.5 × 103 CFU/mL for the blank sample). The bacterial isolate was characterized through phenotypic and genotypic tests for species identification. It was identified as a Gram-stain-negative, aerobic, and long-rod-shaped bacteria, designated as RLimb. Based on the 16S rDNA gene sequencing analysis, RLimb was identified as Pseudomonas aeruginosa (accession number: OP522351), exhibiting a similarity of 100% to the described neighbor P. aeruginosa strain DSM 50071. These results indicated that these isolated bacteria can potentially be used as a substitute for toxic antifoulants to prevent the formation of microfoulers.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

An appraisal of early stage biofilm-forming bacterial community assemblage and diversity in the Arabian Sea, India

The community composition and distribution of early-stage (24 h) biofilm-forming bacteria on two different surfaces (glass slide and polystyrene plastic slide) at three different locations (Diu, Alang and Sikka) were studied using a culture-dependent and next-generation sequencing (NGS) approach in the Arabian Sea, Gujarat, India. The most dominant phyla observed using the NGS approach were the Proteobacteria among the sampling sites. Gammaproteobacteria class dominated both the surfaces among the sites and accounted for 46.7% to 89.2% of total abundance. The culture-dependent analysis showed Proteobacteria and Firmicutes as the dominant phyla on the surfaces within the sampling sites. During the initial colonization, hydrocarbon-degrading bacterial strains have also attached to the surfaces. The outcome of this study would be of great importance for targeting the early stage biofilm-forming and hydrocarbon-degrading bacterial isolates may help to degrade plastic in the marine environment.

Metagenomic analysis of pioneer biofilm-forming marine bacteria with emphasis on Vibrio gigantis adhesion dynamics

Marine biofilms occur frequently and spontaneously in seawater, on almost any submerged solid surface. At the early stages of colonization, it consists of bacteria and evolves into a more complex community. Using 16S rRNA amplicon sequencing and comparative metagenomics, the composition and predicted functional potential of one- to three-day old bacterial communities in surface biofilms were investigated and compared to that of seawater. This confirmed the autochthonous marine bacterium Vibrio gigantis as an early and very abundant biofilm colonizer, also functionally linked to the genes associated with cell motility, surface attachment, and communication via signaling molecules (quorum sensing), all crucial for biofilm formation. The dynamics of adhesion on a solid surface of V. gigantis alone was also monitored in controlled laboratory conditions, using a newly designed and easily implementable protocol. Resulting in a calculated percentage of bacteria-covered surface, a convincing tendency of spontaneous adhering was confirmed. From the multiple results, its quantified and reproducible adhesion dynamics will be used as a basis for future experiments involving surface modifications and coatings, with the goal of preventing adhesion.

Microbial pioneers of plastic colonisation in coastal seawaters

Plastics, when entering the environment, are immediately colonised by microorganisms. This modifies their physico-chemical properties as well as their transport and fate in natural ecosystems, but whom pioneers this colonisation in marine ecosystems? Previous studies have focused on microbial communities that develop on plastics after relatively long incubation periods (i.e., days to months), but very little data is available regarding the earliest stages of colonisation on buoyant plastics in marine waters (i.e., minutes or hours). We conducted a preliminary study where the earliest hours of microbial colonisation on buoyant plastics in marine coastal waters were investigated by field incubations and amplicon sequencing of the prokaryotic and eukaryotic communities. Our results show that members of the Bacteroidetes group pioneer microbial attachment to plastics but, over time, their presence is masked by other groups - Gammaproteobacteria at first and later by Alphaproteobacteria. Interestingly, the eukaryotic community on plastics exposed to sunlight became dominated by phototrophic organisms from the phylum Ochrophyta, diatoms at the start and brown algae towards the end of the three-day incubations. This study defines the pioneering microbial community that colonises plastics immediately when entering coastal marine environments and that may set the seeding Plastisphere of plastics in the oceans.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Can Aggregate-Associated Organisms Influence the Fouling in a SWRO Desalination Plant?

This pilot study investigates the formation of aggregates within a desalination plant, before and after pre-treatment, as well as their potential impact on fouling. The objective is to provide an understanding of the biofouling potential of the feed water within a seawater reverse osmosis (SWRO) desalination plant, due to the limited removal of fouling precursors. The 16S and 18S rRNA was extracted from the water samples, and the aggregates and sequenced. Pre-treatment systems, within the plant remove < 5 µm precursors and organisms; however, smaller size particles progress through the plant, allowing for the formation of aggregates. These become hot spots for microbes, due to their nutrient gradients, facilitating the formation of niche environments, supporting the proliferation of those organisms. Aggregate-associated organisms are consistent with those identified on fouled SWRO membranes. This study examines, for the first time, the factors supporting the formation of aggregates within a desalination system, as well as their microbial communities and biofouling potential.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

Integration of Transcriptome and Metabolome Reveals the Genes and Metabolites Involved in Bifidobacterium bifidum Biofilm Formation

Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both B. bifidum biofilm and planktonic cells was performed to identify key genes and metabolites involved in biofilm formation. Two hundred thirty-five nonredundant differentially expressed genes (DEGs) (including vanY, pstS, degP, groS, infC, groL, yajC, tadB and sigA) and 219 nonredundant differentially expressed metabolites (including L-threonine, L-cystine, L-tyrosine, ascorbic acid, niacinamide, butyric acid and sphinganine) were identified. Thirteen pathways were identified during the integration of both transcriptomics and metabolomics data, including ABC transporters; quorum sensing; two-component system; oxidative phosphorylation; cysteine and methionine metabolism; glutathione metabolism; glycine, serine and threonine metabolism; and valine, leucine and isoleucine biosynthesis. The DEGs that relate to the integration pathways included asd, atpB, degP, folC, ilvE, metC, pheA, pstS, pyrE, serB, ulaE, yajC and zwf. The differentially accumulated metabolites included L-cystine, L-serine, L-threonine, L-tyrosine, methylmalonate, monodehydroascorbate, nicotinamide, orthophosphate, spermine and tocopherol. These results indicate that quorum sensing, two-component system and amino acid metabolism are essential during B. bifidum biofilm formation.

Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods

Advances in high-throughput sequencing technologies have enabled extensive studies of freshwater biofilms and significant breakthroughs in biofilm meta-omics. To date, however, no standardized protocols have been developed for the effective isolation of RNA from freshwater benthic biofilms. In this study, we compared column-based kit RNA extraction with five RNAzol-based extractions, differentiated by various protocol modifications. The RNA products were then evaluated to determine their integrity, purity and yield and were subjected to meta-transcriptomic sequencing and analysis. Significant discrepancies in the relative abundance of active communities and structures of eukaryotic, bacterial, archaebacterial, and viral communities were observed as direct outcomes of the tested RNA extraction methods. The column isolation-based group was characterized by the highest relative abundance of Archaea and Eukaryota, while the organic isolation-based groups commonly had the highest relative abundances of Prokaryota (bacteria). Kit extraction methods provided the best outcomes in terms of high-quality RNA yield and integrity. However, these methods were deemed questionable for studies of active bacterial communities and may contribute a significant degree of bias to the interpretation of downstream meta-transcriptomic analyses.

Transcriptome Analysis Reveals the Genes Involved in Bifidobacterium Longum FGSZY16M3 Biofilm Formation

Biofilm formation has evolved as an adaptive strategy for bacteria to cope with harsh environmental conditions. Currently, little is known about the molecular mechanisms of biofilm formation in bifidobacteria. A time series transcriptome sequencing analysis of both biofilm and planktonic cells of Bifidobacterium longum FGSZY16M3 was performed to identify candidate genes involved in biofilm formation. Protein–protein interaction network analysis of 1296 differentially expressed genes during biofilm formation yielded 15 clusters of highly interconnected nodes, indicating that genes related to the SOS response (dnaK, groS, guaB, ruvA, recA, radA, recN, recF, pstA, and sufD) associated with the early stage of biofilm formation. Genes involved in extracellular polymeric substances were upregulated (epsH, epsK, efp, frr, pheT, rfbA, rfbJ, rfbP, rpmF, secY and yidC) in the stage of biofilm maturation. To further investigate the genes related to biofilm formation, weighted gene co-expression network analysis (WGCNA) was performed with 2032 transcript genes, leading to the identification of nine WGCNA modules and 133 genes associated with response to stress, regulation of gene expression, quorum sensing, and two-component system. These results indicate that biofilm formation in B. longum is a multifactorial process, involving stress response, structural development, and regulatory processes.

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

Background

Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services, particularly nutrient cycling in benthic habitats. The effects of climate change on host-associated microbiome composition are well-known, but functional changes and how they may impact host physiology and ecosystem functioning are poorly characterized. We investigated how environmental parameters affect oyster-associated microbial community structure and function along a trophic gradient in Narragansett Bay, Rhode Island, USA. Adult eastern oyster, Crassostrea virginica, gut and seawater samples were collected at 5 sites along this estuarine nutrient gradient in August 2017. Samples were analyzed by 16S rRNA gene sequencing to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbiome responses to local environments.

Results

There were significant differences in bacterial community structure between the eastern oyster gut and water samples, suggesting selection of certain taxa by the oyster host. Increasing salinity, pH, and dissolved oxygen, and decreasing nitrate, nitrite and phosphate concentrations were observed along the North to South gradient. Transcriptionally active bacterial taxa were similar for the different sites, but expression of oyster-associated microbial genes involved in nutrient (nitrogen and phosphorus) cycling varied throughout the Bay, reflecting the local nutrient regimes and prevailing environmental conditions.

Conclusions

The observed shifts in microbial community composition and function inform how estuarine conditions affect host-associated microbiomes and their ecosystem services. As the effects of estuarine acidification are expected to increase due to the combined effects of eutrophication, coastal pollution, and climate change, it is important to determine relationships between host health, microbial community structure, and environmental conditions in benthic communities.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-020-00066-0.

Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics

Microplastics are ubiquitous in aquatic ecosystems and provide a habitat for biofilm-forming bacteria. The genus Vibrio, which includes potential pathogens, was detected irregularly on microplastics. Since then, the potential of microplastics to enrich (and serve as a vector for) Vibrio has been widely discussed. We investigated Vibrio abundance and operational taxonomic unit (OTU) composition on polyethylene and polystyrene within the first 10 h of colonization during an in situ incubation experiment, along with those found on particles collected from the Baltic Sea. We used 16S rRNA gene amplicon sequencing and co-occurrence networks to elaborate the role of Vibrio within biofilms. Colonization of plastics with Vibrio was detectable after one hour of incubation; however, Vibrio numbers and composition were very dynamic, with a more stable population at the site with highest nutrients and lowest salinity. Likewise, Vibrio abundances on field-collected particles were variable but correlated with proximity to major cities. Vibrio was poorly connected within biofilm networks. Taken together, this indicates that Vibrio is an early colonizer of plastics, but that the process is undirected and independent of the specific surface. Still, higher nutrients could enhance a faster establishment of Vibrio populations. These parameters should be considered when planning studies investigating Vibrio on microplastics.

Biodegradation of Poly (Butylene Succinate) (PBS)/Stearate Modified Magnesium-Aluminium Layered Double Hydroxide Composites under Marine Conditions Prepared via Melt Compounding

In the present work, polybutylene succinate (PBS)/stearate modified magnesium-aluminium layered double hydroxide (St-Mg-Al LDH) composites were prepared via melt processing and the effect of different loadings of St-Mg-Al LDH on the degradation behaviour of PBS under marine conditions was investigated. The morphological, mechanical and thermal characteristics of the composites were studied using different characterisation techniques. Optical imaging and scanning electron microscopy revealed that the incorporation of St-Mg-Al LDH accelerates the degradation of PBS along with the activity of microorganisms adhered to the composite films. PBS/St-Mg-Al LDH composites are found to have lower thermal degradation temperatures than those of pure PBS. The decrease in thermal stability is correlated with the degradation of PBS due to the catalytic action Mg and Al present in LDH. Tensile and DMA analysis revealed that the addition of St-Mg-Al LDH did not have a significant impact on the mechanical properties of PBS.

Enhancing robustness of aerobic granule sludge under low C/N ratios with addition of kitchen wastewater

Aerobic granular sludge (AGS) is one of the most promising biotechnologies for wastewater treatment. However, the instability of AGS at low carbon to nitrogen (C/N) ratios limited its application. In this study, kitchen wastewater addition in the influent was found to improve the morphology, characteristics, and treatment performance of AGS at low C/N ratios of 10, 5 and 2, which strongly reduced the negative impact of low C/N ratios on the biomass concentration, settleability, EPS secretion, stability and performance of AGS. At C/N ratio of 2, sludge disintegration was observed in RA with synthetic wastewater as influent, while the sludge in RB was able to keep a compact microbial structure with particle size of 1.0-1.5 mm. When C/N ratio decreased from 20 to 2 (phase 1 to 4), the MLSS, SVI and EPS secretion in RB were negatively affected at the beginning of each phase, but recovered to 4800 mg L^-1, 60 mL g^-1, and 86 mg/g SS at the end of phase 4 (C/N ratio of 2), which were 1.3, 0.6 and 1.3 times of those in RA, respectively. Meanwhile, the removal efficiencies of COD, TN, TP and NH₄⁺-N in RB were 90%, 73%, 53%, and 99% at the end of phase 4, which were 1.1, 1.2, 2.2 and 2.4 times of those in RA, respectively. Thus, high-performance AGS with enhanced robustness and high abundance of HN-AD functional bacteria Paracoccus was obtained. These findings provided a promising and cost-effective method to improve the long-term stability and performance of AGS dealing with wastewater of low C/N ratio.

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.

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides

Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.

Degradability and biofouling of oxo-biodegradable polyethylene in the planktonic and benthic zones of the Arabian Gulf

Little is known about the degradability of oxo-biodegradable polyethylene (OXO-PE) and its surface fouling bacterial communities in the marine environment. The degradation of OXO-PE, PE and polyethylene terephthalate (PET) was compared at two depths (2 m and 6 m) in the Arabian Gulf. Scanning electron microcopy (SEM) revealed more fissure formation on OXO-PE and PE than on PET, indicating physical degradation. The formation of hydroxyl groups and carbonyl bonds, by Fourier-transform infrared spectroscopy (FTIR), suggests chemical degradation of OXO-PE. Plastisphere bacterial communities on OXO-PE and PE were different than on PET. Proteobacteria, Bacteriodetes and Planctomycetes were detected on all plastics, however, sequences of Alteromonas and Zoogloea were OXO-PE-specific suggesting a possible involvement of these bacterial genera in OXO-PE degradation. We conclude that OXO-PE shows increased signs of degradation with time owing to the combination of abiotic and biotic processes, and its degradation is higher in the benthic than in the planktonic zone.

Marine biofilm bacterial community response and carbon steel loss following Deepwater Horizon spill contaminant exposure

Steel marine structures provide foci of biodiversity when they develop into artificial reefs. Development begins with deposition of a biofilm. The effects of contaminants from oil spills on biofilm microbiomes, microbially-induced corrosion (MIC) and metal loss may impact preservation of marine metal structures. A microcosm experiment exposed biofilms on carbon steel disks (CSDs) to crude oil, dispersant, and dispersed oil to address their impacts on bacterial composition and metal loss and pitting. Biofilm diversity increased over time in all exposures. Community composition in dispersant and dispersed oil treatments deviated from the controls for the duration of a 12-week experiment. As biofilms matured, Pseudomonadaceae increased while Rhodobacteraceae decreased in abundance in dispersed oil treatments compared to the controls and dispersant treatments. Greatest mass loss and deepest pitting on CSDs were observed in dispersed oil treatments, suggesting impacts manifest as a consequence of increased MIC potential on carbon steel.

A Brief Recap of Microbial Adhesion and Biofilms

Food and beverage industries operate their production units under stringent hygiene standards to verify high-quality products. However, the presence of biofilms can cause hygienic problems in the industries in the case of pathogenic organisms. Microorganisms can form biofilms, which are resistant to cleaning and disinfection. Microorganisms in biofilms are closely packed in a matrix that acts as a barrier to cleaning and disinfection. Biofilms are observed in processing equipment and open surfaces, resulting in food safety problems or weakening of production efficiency. This review provides a recap of the biofouling process, including the production mechanisms and control techniques of microbial adhesion. Microbial adhesion and colonization are the sine qua non of the establishment of bacterial pathogenesis and this report focuses on their prevention.

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.

Short-term succession of marine microbial fouling communities and the identification of primary and secondary colonizers

Microbial succession during the initial stages of marine biofouling has been rarely studied, especially in the Arabian Gulf. This study was undertaken to follow temporal shifts in biofouling communities in order to identify primary and secondary colonizers. Quantitative analysis revealed a significant increase in total biomass, coverage of macrofoulers, chlorophyll a concentrations, and bacterial counts with time. The relative abundance of the adnate diatoms increased with time, whereas it decreased in the case of the plocon diatoms. Non-metric multidimensional scaling (NMDS) ordination based on MiSeq data placed the bacterial communities in three distinct clusters, depending on the time of sampling. While the relative abundance of Alphaproteobacteria and Flavobacteriia decreased with time, suggesting their role as primary colonizers, the relative abundance of Actinobacteria and Planctomycetia increased with time, suggesting their role as secondary colonizers. Biofouling is a dynamic process that involves temporal quantitative and qualitative shifts in the micro- and macrofouling communities.

Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment

Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.

Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities

Extreme habitats are not only limited to natural environments, but also exist in manmade systems, for instance, household appliances such as dishwashers. Limiting factors, such as high temperatures, high and low pHs, high NaCl concentrations, presence of detergents, and shear force from water during washing cycles, define microbial survival in this extreme system. Fungal and bacterial diversity in biofilms isolated from rubber seals of 24 different household dishwashers was investigated using next-generation sequencing. Bacterial genera such as Pseudomonas, Escherichia, and Acinetobacter, known to include opportunistic pathogens, were represented in most samples. The most frequently encountered fungal genera in these samples belonged to Candida, Cryptococcus, and Rhodotorula, also known to include opportunistic pathogenic representatives. This study showed how specific conditions of the dishwashers impact the abundance of microbial groups and investigated the interkingdom and intrakingdom interactions that shape these biofilms. The age, usage frequency, and hardness of incoming tap water of dishwashers had significant impact on bacterial and fungal community compositions. Representatives of Candida spp. were found at the highest prevalence (100%) in all dishwashers and are assumed to be one of the first colonizers in recently purchased dishwashers. Pairwise correlations in tested microbiomes showed that certain bacterial groups cooccur, as did the fungal groups. In mixed bacterial-fungal biofilms, early adhesion, contact, and interactions were vital in the process of biofilm formation, where mixed complexes of bacteria and fungi could provide a preliminary biogenic structure for the establishment of these biofilms.

IMPORTANCE Worldwide demand for household appliances, such as dishwashers and washing machines, is increasing, as is the number of immunocompromised individuals. The harsh conditions in household dishwashers should prevent the growth of most microorganisms. However, our research shows that persisting polyextremotolerant groups of microorganisms in household appliances are well established under these unfavorable conditions and supported by the biofilm mode of growth. The significance of our research is in identifying the microbial composition of biofilms formed on dishwasher rubber seals, how diverse abiotic conditions affect microbiota, and which key microbial members were represented in early colonization and contamination of dishwashers, as these appliances can present a source of domestic cross-contamination that leads to broader medical impacts.