Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms?

The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the "species" and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore.

Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.

Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities

Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.

Enhanced effect and mechanism of nano Fe-Ca bimetallic oxide modified substrate on Cu(II) and Ni(II) removal in constructed wetland

In this study, Fe₂O₃ nanoparticles (Fe₂O₃ NPs) and CaO NPs were loaded on the zeolite sphere carrier to create nano Fe-Ca bimetallic oxide (Fe-Ca-NBMO) modified substrate, which was introduced into constructed wetland (CW) to remove Cu(II) and Ni(II) via constructing "substrate-microorganism" system. Adsorption experiments showed that the equilibrium adsorption capacities of Fe-Ca-NBMO modified substrate for Cu(II) and Ni(II) were respectively 706.48 and 410.59 mg/kg at an initial concentration of 20 mg/L, 2.45 and 2.39 times of gravel. The Cu(II) and Ni(II) removal efficiencies in CW with Fe-Ca-NBMO modified substrate respectively reached 99.7% and 99.9% at an influent concentration of 100 mg/L, significantly higher than those in gravel-based CW (47.0% and 34.3%). Fe-Ca-NBMO modified substrate could promote Cu(II) and Ni(II) removal by increasing electrostatic adsorption, chemical precipitation, as well as the abundances of resistant microorganisms (Geobacter, Desulfuromonas, Zoogloea, Dechloromonas, and Desulfobacter) and functional genes (copA, cusABC, ABC.CD.P, gshB, and exbB). This study provided an effective method to enhance Cu(II) and Ni(II) removal of electroplating wastewater by CW with Fe-Ca-NBMO modified substrate.

Ecological insights into the resilience of marine plastisphere throughout a storm disturbance

Among numerous research about marine plastisphere, the community living on the surface of plastic debris, little attention was given to the ecological mechanisms governing prokaryotes compared to eukaryotes, and even less focused on their resilience in a changing climate with more storm prevalence. Our current research recruited an integrated approach involving community succession across temporal dimension, ecological mechanisms that govern the assembly, and resilience to environmental perturbations to highlight the ecology of different kingdoms in the plastisphere. Towards this goal, we examined the succession of the prokaryotic and eukaryotic communities on artificial plastic nets in a sidestream of seawater from the Gulf of Aqaba over 35 days. A robust local storm enabled investigation of the alterations before, during, and after this disturbance, aiming at the community's potential to recover. Data from 16S and 18S rRNA sequencing and microscopic analyses decrypted the plastisphere diversity, community assembly, and stochasticity, followed by further analyses of functional and co-occurrence networks for the prokaryotic group. Prokaryotic and eukaryotic communities underwent exact opposite ecological mechanisms. While determinism driven by a robust environmental selection dictated the prokaryotic community assembly, stochasticity prevailed when this condition was relaxed. Interestingly, resilience against disturbance was observed in prokaryotes but not in eukaryotes. The decrease in compositional, functional diversity and network complexity in the prokaryotic community was reversed, presumably due to the niche specification process and high dispersal. Niche specification following perturbation was evident in some bacteria by selected functions associated with plastic degradation, stress response, and antibiotic resistance. On the contrary, eukaryotes decreased in diversity and were dominated by the commonly found Chlorophyta towards the later successional period. Novel findings on the ecology of marine plastisphere during perturbation encourage the integration of this aspect into prediction research.

Structure and Dynamics of Periphyton in a Neotropical Freshwater Lake, with Emphasis on Ciliates and Their Relationships with Bacterial Taxa

Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.

Impacts of UV-C irradiation on marine biofilm community succession

Marine biofilms are diverse microbial communities and important ecological habitats forming on surfaces submerged in the ocean. Biofilm communities resist environmental disturbance, making them a nuisance to some human activities ('biofouling'). Anti-fouling solutions rarely address the underlying stability or compositional responses of these biofilms. Using bulk measurements and molecular analyses, we examined temporal and UV-C antifouling-based shifts in marine biofilms in the coastal Western North Atlantic Ocean during early fall. Over a 24-d period, bacterial communities shifted from early dominance of Gammaproteobacteria to increased proportions of Alphaproteobacteria, Bacteroidia and Acidimicrobiia. In a network analysis based on temporal covariance, Rhodobacteraceae (Alphaproteobacteria) nodes were abundant and densely connected with generally positive correlations. In the eukaryotic community, persistent algal, protistan, and invertebrate groups were observed, although consistent temporal succession was not detected. Biofilm UV-C treatment at 13 and 20 days resulted in losses of chlorophyll a and transparent exopolymer particles, indicating biomass disruption. Bacterial community shifts suggested that UV-C treatment decreased biofilm maturation rate and was associated with proportional shifts among diverse bacterial taxa. UV-C treatment was also associated with increased proportions of protists potentially involved in detritivory and parasitism. Older biofilm communities had increased resistance to UV-C, suggesting that early biofilms are more susceptible to UV-C based antifouling. The results suggest that UV-C irradiation is potentially an effective antifouling method in marine environments in terms of biomass removal and in slowing maturation. However, as they mature, biofilm communities may accumulate microbial members that are tolerant or resilient under UV-treatment. Importance Marine biofilms regulate processes from organic matter and pollutant turnover to eukaryotic settlement and growth. Biofilm growth and eukaryotic settlement interfering with human activities via growth on ship hulls, aquaculture operations, or other marine infrastructure are called 'biofouling'. There is a need to develop sustainable anti-fouling techniques by minimizing impacts to surrounding biota. We use the biofouling-antifouling framework to test hypotheses about marine biofilm succession and stability in response to disturbance, using a novel UV-C LED device. We demonstrate strong bacterial biofilm successional patterns and detect taxa potentially contributing to stability under UV-C stress. Despite UV-C-associated biomass losses and varying UV susceptibility of microbial taxa, we detected high compositional resistance among biofilm bacterial communities, suggesting decoupling of disruption in biomass and community composition following UV-C irradiation. We also report microbial covariance patterns over 24 days of biofilm growth, pointing to areas for study of microbial interactions and targeted antifouling.

Fishmeal replacement by periphyton reduces the fish in fish out ratio and alimentation cost in gilthead sea bream Sparus aurata

Aquaculture threatens natural resources by fishing down the sea to supply fishmeal. Alternative protein sources in aquafeeds can provide a solution, particularly those that are waste from other operations and thereby reduce feed production costs. Toward this goal, we examined the waste biomass of marine periphyton from biofilters of an integrated multi-trophic aquaculture (IMTA) system as a replacement for fishmeal in diets of gilthead seabream (Sparus aurata). Four isoproteic (41%) and isolipidic (16.7%) aquafeeds were formulated with increased content of periphyton and a corresponding decrease in fishmeal from 20 to 15, 10, or 0%. The growth and biochemical content of seabream fingerlings (initial body weight 10 g) were examined over 132 days. Replacing 50% of fishmeal by waste periphyton improved feed conversion ratio (1.2 vs. 1.35 in the control diet) without harming fish growth. The complete replacement of fishmeal with periphyton resulted in 15% slower growth but significantly higher protein content in the fish flesh (59 vs. 52% in the control diet). Halving fishmeal content reduced feed cost by US$ 0.13 kg⁻¹ feed and saved 30% in the cost of conversion of feed to fish biomass (US$ 0.58 kg⁻¹ produced fish vs. $0.83 in the control diet). Finally, the total replacement of fishmeal by waste periphyton in the diet reduced the fish in—fish out ratio to below 1 (0.5–0.9) as compared to 1.36 in the control diet. Replacing fishmeal with on-farm produced periphyton minimizes aquaculture footprint through the removal of excess nutrients in effluents and the use of waste biomass to reduce the ‘fish in’ content in aquafeeds and fish production costs. The present study demonstrates the great practical potential of this dual use of marine periphyton in enhancing the circular economy concept in sustainable fish production.

Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

Periphyton as an important source of methylmercury in Everglades water and food web

Periphyton is ubiquitous in Florida Everglades and has a profound effect on mercury (Hg) cycling. Enhanced methylmercury (MeHg) production in periphyton has been well documented, but the re-distribution of MeHg from periphyton remains unknown. In this study, periphyton, sediments, surface water, periphyton overlying water, and periphyton porewater were collected from Everglades for analyzing the distribution of MeHg and total Hg (THg). Results showed that there were no significant differences in THg and MeHg in different types of periphyton, but they all displayed higher MeHg levels than sediments. MeHg distribution coefficients (logk_d) in periphyton were lower than in sediments, suggesting that periphyton MeHg could be more labile entering aquatic cycling and bioaccumulation. In water, the more the distance of water samples taken from periphyton, the lower the MeHg and dissolved organic carbon concentrations were detected. In extracellular polymeric substances of periphyton, MeHg in colloidal fractions was significantly higher than that in capsular fractions. It was estimated that approximately 10% (or 1.35 kg) of periphyton MeHg were passed on to mosquitofish entering the food web during wet season, contributing 73% of total Hg stocked in mosquitofish. These results revealed the importance of periphyton on water MeHg distribution and MeHg bioaccumulation in Everglades.

Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences

With the advent of next-generation sequencing technology, it has become convenient and cost efficient to thoroughly characterize the microbial diversity and taxonomic composition in various environmental samples. Millions of sequencing data can be generated, and how to utilize this enormous sequence resource has become a critical concern for microbial ecologists. One particular challenge is the OTUs (operational taxonomic units) picking in 16S rRNA sequence analysis. Lucky, this challenge can be directly addressed by sequence clustering that attempts to group similar sequences. Therefore, numerous clustering methods have been proposed to help to cluster 16S rRNA sequences into OTUs. However, each method has its clustering mechanism, and different methods produce diverse outputs. Even a slight parameter change for the same method can also generate distinct results, and how to choose an appropriate method has become a challenge for inexperienced users. A lot of time and resources can be wasted in selecting clustering tools and analyzing the clustering results. In this study, we introduced the recent advance of clustering methods for OTUs picking, which mainly focus on three aspects: (i) the principles of existing clustering algorithms, (ii) benchmark dataset construction for OTU picking and evaluation metrics, and (iii) the performance of different methods with various distance thresholds on benchmark datasets. This paper aims to assist biological researchers to select the reasonable clustering methods for analyzing their collected sequences and help algorithm developers to design more efficient sequences clustering methods.

Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations

The antibacterial agent Triclosan (TCS) is a ubiquitous environmental contaminant due to its widespread use. Sensitivity to TCS varies substantially among eu- and pro-karyotic species and its risk for the marine environment remains to be better elucidated. In particular, the effects that TCS causes on marine microbial communities are largely unknown. In this study we therefore used 16S amplicon rDNA sequencing to investigate TCS effects on the bacterial composition in marine periphyton communities that developed under long-term exposure to different TCS concentrations. Exposure to TCS resulted in clear changes in bacterial composition already at concentrations of 1 to 3.16 nM. We conclude that TCS affects the structure of the bacterial part of periphyton communities at concentrations that actually occur in the marine environment. Sensitive taxa, whose abundance decreased significantly with increasing TCS concentrations, include the Rhodobiaceae and Rhodobacteraceae families of Alphaproteobacteria, and unidentified members of the Candidate division Parcubacteria. Tolerant taxa, whose abundance increased significantly with higher TCS concentrations, include the families Erythrobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteroidetes), Bdellovibrionaceae (Deltaproteobacteria), several families of Gammaproteobacteria, and members of the Candidate phylum Gracilibacteria. Our results demonstrate the variability of TCS sensitivity among bacteria, and that TCS can change marine bacterial composition at concentrations that have been detected in the marine environment.

Distinct Temporal Succession of Bacterial Communities in Early Marine Biofilms in a Portuguese Atlantic Port

Marine biofilms are known to influence the corrosion of metal surfaces in the marine environment. Despite some recent research, the succession of bacterial communities colonizing artificial surfaces remains uncharacterized in some temporal settings. More specifically, it is not fully known if bacterial colonizers of artificial surfaces are similar or distinct in the different seasons of the year. In particular the study of early biofilms, in which the bacterial cells communities first adhere to artificial surfaces, are crucial for the development of the subsequent biofilm communities. In this work, we used amplicon-based NGS (next-generation sequencing) and universal 16S rRNA bacterial primers to characterize the early biofilm bacterial communities growing on 316 L stainless steel surfaces in a Northern Portugal port. Sampling spanned 30-day periods in two distinct seasons (spring and winter). Biofilm communities growing in steel surfaces covered with an anti-corrosion paint and planktonic communities from the same location were also characterized. Our results demonstrated that distinct temporal patterns were observed in the sampled seasons. Specifically, a significantly higher abundance of Gammaproteobacteria and Mollicutes was found on the first days of biofilm growth in spring (day 1 to day 4) and a higher abundance of Alphaproteobacteria during the same days of biofilm growth in winter. In the last sampled day (day 30), the spring biofilms significantly shifted toward a dominance of photoautotrophic groups (mostly diatoms) and were also colonized by some macrofouling communities, something not observed during the winter sampling. Our results revealed that bacterial composition in the biofilms was particularly affected by the sampled day of the specific season, more so than the overall effect of the season or overall sampling day of both seasons. Additionally, the application of a non-fouling-release anti-corrosion paint in the steel plates resulted in a significantly lower diversity compared with plates without paint, but this was only observed during spring. We suggest that temporal succession of marine biofilm communities should be taken in consideration for future antifouling/anti-biofilm applications.

A comprehensive survey of integron-associated genes present in metagenomes

Background

Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.

Results

Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.

Conclusions

Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.

Influence of epiphytic bacteria on arsenic metabolism in Hydrilla verticillata

Microbial assemblages such as biofilms around aquatic plants play a major role in arsenic (As) cycling, which has often been overlooked in previous studies. In this study, arsenite (As(III))-oxidizing, arsenate (As(V))-reducing and As(III)-methylating bacteria were found to coexist in the phyllosphere of Hydrilla verticillata, and their relative activities were shown to determine As speciation, accumulation and efflux. When exposed to As(III), As(III) oxidation was not observed in treatment H(III)-B, whereas treatment H(III)+B showed a significant As(III) oxidation ability, thereby indicating that epiphytic bacteria displayed a substantial As(III) oxidation ability. When exposed to As(V), the medium only contained 5.89% As(III) after 48 h of treatment H(V)-B, while an As(III) content of 86.72% was observed after treatment H(V)+B, thereby indicating that the elevated As(III) in the medium probably originated from As(V) reduction by epiphytic bacteria. Our data also indicated that oxidizing bacteria decreased the As accumulation (by approximately 64.44% compared with that of treatment H(III)-B) in plants, while reducing bacteria played a critical role in increasing As accumulation (by approximately 3.31-fold compared with that of treatment H(V)-B) in plants. Regardless of whether As(III) or As(V) was supplied, As(III) was dominant in the plant tissue (over 75%). Furthermore, the presence of epiphytic bacteria enhanced As efflux by approximately 9-fold. Metagenomic analysis revealed highly diverse As metabolism genes in epiphytic bacterial community, particularly those related to energetic metabolism (aioAB), and As resistance (arsABCR, acr3, arsM). Phylogenetic analysis of As metabolism genes revealed evidence of both vertical inheritance and horizontal gene transfer, which might have contributed to the evolution of the As metabolism genes. Taken together, our research suggested that the diversity of As metabolism genes in epiphytic bacterial community is associated with aquatic submerged macrophytes which may play an important role in As biogeochemistry in aquatic environments.

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes

Microbes in epiphytic biofilms and surface sediments play crucial roles in the biogeochemical cycles in wetlands. However, little is known about the compositions of microbial community in wetlands dominated with submersed macrophytes. In this study, bacterial and eukaryotic community in epiphytic biofilms and surface sediments were investigated in wetlands with artificial plants and Myriophyllum verticillatum from September (~27 °C) to January (~9 °C). A total of 30 (including 13 bacterial and 17 eukaryotic) and 34 (including 14 bacterial and 20 eukaryotic) phyla were detected in epiphytic biofilms and sediments, respectively. Microbial community in epiphytic biofilms shifted with decreasing temperature, and biofilms on M. verticillatum were generally similar to those on artificial plants. Though the OTUs and Shannon values were significantly higher in sediments than epiphytic biofilms (p < 0.05), numbers of strongly correlated edges detected in biofilms (64 nodes with 182 edges) were at least three times of those in sediments (40 nodes with 57 edges) as revealed by co-occurrence networks analysis (|r| > 0.7, p < 0.05). These data suggest that there were complex interactions among microbes in epiphytic biofilms than sediments. Positive relationships among microbes revealed the predation, symbiosis, parasitism relationships and the collective degradation of organic matter, while negative ones may be ascribed to their different lifestyles. These results highlight that artificial plants play a similar role as submersed macrophytes as microbial carriers and can be potentially used an alternative substitutes to submersed macrophytes in wetlands.

Growth and antibiotic resistance acquisition of Escherichia coli in a river that receives treated sewage effluent

Wastewater treatment plants could discharge Escherichia coli and antibiotic resistant bacteria to the environment adjacent to, or downstream of their discharge point. However, their discharge also contains nutrients which could promote growth of E. coli in water environments. This study was done to clarify the potential of growth and antibiotic resistance acquisition of E. coli in a river environment. Levels of E. coli were monitored in a river that receives treated sewage effluent for over four years. River water, periphyton and sediment samples were collected at sites upstream and downstream of treated sewage inflow. Concentrations of E. coli increased in river water and periphyton at the sites downstream of the treated sewage inflow, although levels of E. coli were very low or below detection limit in the treated sewage samples. Concentrations of Chlorophyll a increased at the downstream sites, likely due to nutrient input from the treated sewage. Based on pulsed field gel electrophoresis, identical genotype occurred at multiple sites both upstream and downstream of the treated sewage inflow. However, strains resistant to antibiotics such as ampicillin, cefazolin, ciprofloxacin, and chloramphenicol were more frequently obtained from the downstream sites than the upstream sites. Multidrug resistant E. coli strains were detected in periphyton and sediment samples collected at the downstream sites. Non-resistant strains with PDGE genotype identical to the multi-drug strains were also detected, indicating that E. coli might have become resistant to antibiotics by acquiring resistance genes via horizontal gene transfer. Laboratory incubation experiment showed the growth of E. coli in periphyton or sediment-fed river water samples. These results suggest that the wastewater treatment inflow did not directly provide E. coli to the river water, but could promote the growth of periphyton, which could lead to the elevated levels of E. coli and the emergence of antibiotic resistant E. coli.

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations

Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.e., photosynthesis and community tolerance to Cu). Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and photosynthetic activity. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9,504 and 1,242 OTUs for 16S and 18S, respectively, reflecting the high biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 0.01 μM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (0.06 μM), which is still in the range of the Cu concentrations observed in the area (0.08 μM). The current environmental quality standard for Cu of 0.07 μM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of photosynthetic activity. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including taxa within Proteobacteria, Bacteroidetes, Stramenopiles, and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic taxa, and therefore to identify particularly sensitive, non-cultivable taxa.

A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms

BACKGROUND

Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.

RESULTS

We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.

CONCLUSIONS

The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.

Metabarcoding and metabolomics offer complementarity in deciphering marine eukaryotic biofouling community shifts

Metabarcoding and metabolomics were used to explore the taxonomic composition and functional diversity of eukaryotic biofouling communities on plates with antifouling paints at two French coastal sites: Lorient (North Eastern Atlantic Ocean; temperate and eutrophic) and Toulon (North-Western Mediterranean Sea; mesotrophic but highly contaminated). Four distinct coatings were tested at each site and season for one month. Metabarcoding showed biocidal coatings had less impact on eukaryotic assemblages compared to spatial and temporal effects. Ciliophora, Chlorophyceae or Cnidaria (mainly hydrozoans) were abundant at Lorient, whereas Arthropoda (especially crustaceans), Nematoda, and Ochrophyta dominated less diversified assemblages at Toulon. Seasonal shifts were observed at Lorient, but not Toulon. Metabolomics also showed clear site discrimination, but these were associated with a coating and not season dependent clustering. The meta-omics analysis enabled identifications of some associative patterns between metabolomic profiles and specific taxa, in particular those colonizing the plates with biocidal coatings at Lorient.

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.

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments

Surface colonization in seawater first corresponds to the selection of specific microbial biofilm communities. By coupling flow cytometry, microscopy and high throughput sequencing (HTS, 454 pyrosequencing) with artificial surfaces and environmental analyses, we intend to identify the contribution of biofilm community drivers at two contrasted French sites, one temperate and eutrophic (Lorient, Atlantic coast) and the other at a mesotrophic but highly contaminated bay (Toulon, North-Western Mediterranean Sea). Microbial communities were shaped by high temperatures, salinity and lead at Toulon by but nutrients and DOC at Lorient. Coatings including pyrithione exhibited a significant decrease of their microbial densities except for nanoeukaryotes. Clustering of communities was mainly based on the surface type and secondly the site, whereas seasons appeared of less importance. The in-depth HTS revealed that γ- and α-proteobacteria, but also Bacteroidetes, dominated highly diversified bacterial communities with a relative low β-diversity. Sensitivity to biocides released by the tested antifouling coatings could be noticed at different taxonomic levels: the percentage of Bacteroidetes overall decreased with the presence of pyrithione, whereas the α/γ-proteobacteria ratio decreased at Toulon when increased at Lorient. Small diatom cells (Amphora and Navicula spp.) dominated on all surfaces, whereas site-specific sub-dominant taxa appeared clearly more sensitive to biocides. This overall approach exhibited the critical significance of surface characteristics in biofilm community shaping.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.