Biophysical controls on community succession in stream biofilms

Indole-3-acetic acid regulating the initial adhesion of microalgae in biofilm formation

Regulating the microalgal initial adhesion in biofilm formation is a key approach to address the challenges of attached microalgae cultivation. As a type of phytohormone, Indole-3-acetic acid (IAA) can promote the growth and metabolism of microalgae. However, limited knowledge has been acquired of how IAA can change the initial adhesion of microalgae in biofilm formation. This study focused on investigating the initial adhesion of microalgae under different IAA concentrations exposure in biofilm formation. The results showed that IAA showed obvious hormesis-like effects on the initial adhesion ability of microalgae biofilm. Under exposure to the low concentration (0.1 mg/L) of IAA, the initial adhesion quantity of microalgae on the surface of the carrier reached the highest value of 7.2 g/m2. However, exposure to the excessively high concentration (10 mg/L) of IAA led to a decrease in the initial adhesion capability of microalgal biofilms. The enhanced adhesion of microalgal biofilms due to IAA was attributed to the upregulation of genes related to the Calvin Cycle, which promoted the synthesis of hydrophobic amino acids, leading to increased protein secretion and altering the surface electron donor characteristics of microalgal biofilms. This, in turn, reduced the energy barrier between the carriers and microalgae. The research findings would provide crucial support for the application of IAA in regulating the operation of microalgal biofilm systems.

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.

Impact of hydrodynamics on community structure and metabolic production of marine biofouling formed in a highly energetic estuary

Biofouling is a specific lifestyle including both marine prokaryotic and eukaryotic communities. Hydrodynamics are poorly studied parameters affecting biofouling formation. This study aimed to investigate how water dynamics in the Etel Estuary (Northwest Atlantic coasts of France) influences the colonization of artificial substrates. Hydrodynamic conditions, mainly identified as shear stress, were characterized by measuring current velocity, turbulence intensity and energy using Acoustic Doppler Current Profiler (ADCP). One-month biofouling was analyzed by coupling metabarcoding (16S rRNA, 18S rRNA and COI genes), untargeted metabolomics (liquid chromatography coupled with high-resolution mass spectrometry, LC-HRMS) and characterization of the main biochemical components of the microbial exopolymeric matrix. A higher richness was observed for biofouling communities (prokaryotes and eukaryotes) exposed to the strongest currents. Ectopleura (Cnidaria) and its putative symbionts Endozoicomonas (Gammaproteobacteria) were dominant in the less dynamic conditions. Eukaryotes assemblages were specifically shaped by shear stress, leading to drastic changes in metabolite profiles. Under high hydrodynamic conditions, the exopolymeric matrix increased and was composed of 6 times more polysaccharides than proteins, these latter playing a crucial role in the adhesion and cohesion properties of biofilms. This original multidisciplinary approach demonstrated the importance of shear stress on both the structure of marine biofouling and the metabolic response of these complex communities.

Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America

A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.

The effects of flow field on the succession of the microbial community on artificial reefs

The flow field is one of the most important external conditions affecting the development of biofouling community on artificial reefs (ARs), especially the microbial community. In this article, we investigated the temporal dynamics of microbial communities between the stoss side and the lee side of ARs. The results showed that the composition and structure of microbial and macrobenthic communities between the stoss side and the lee side both presented obvious temporal variations. Microbial diversity and richness were higher on the stoss side than that on the lee side. There was a greater impact on bacterial and archaeal communities on temporal scale compared to that on micro-spatial scale, which was not suitable for the fungal community. The organism biomass, abundance and coverage of macrobenthic community on the lee side were higher than those on the stoss side, and the microbial diversity on the stoss side increased significantly with the organism coverage.

Relative effect of hydraulics, physico-chemistry and other biofilm algae on benthic cyanobacteria assemblages in a regulated river

The development of benthic cyanobacteria currently raises concern worldwide because of their potential to produce toxins. As a result, understanding which measures of biotic and abiotic parameters influence the development of cyanobacterial assemblages is of great importance to guide management actions. In this study, we investigate the relative contributions of abiotic and biotic parameters that may drive the development of cyanobacterial assemblages in river biofilms. First, a 2D hydrodynamic model allowed us to retrace changes in depths and velocities according to discharge at a 4 m² resolution. From this model, we set up three hydraulic zones in each of the 4 reaches investigated along a 50-km-long river stretch. We further used univariate, multivariate and variance partitioning analyses to assess the contribution of past and present hydraulics, present physical and chemical parameters and algae to the temporal variability of cyanobacterial assemblage composition. The cyanobacterial assemblages were generally dominated by Phormidium sp., Lyngbya sp., Planktolyngbya sp. and Oscillatoria sp., four genera known to contain potentially toxic species. The highest biovolumes of cyanobacteria were present in low velocity zones in early summer and shifted to high velocity zones in late summer, highlighting the major influence of hydraulic parameters on benthic cyanobacteria settlement and development in rivers. Considering the identified genera, biofilms present a potentially high risk of toxin production. Relations between cyanobacterial development, toxin production and environmental parameters need to be further assessed to better estimate this risk.

Advances in bioleaching of waste lithium batteries under metal ion stress

In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.

Effect of hydrodynamics on the transformation of nitrogen in river water by regulating the mass transfer performance of dissolved oxygen in biofilm

Biofilms drive crucial ecosystem processes in rivers. This study provided the basis for overall quantitative calculations about the contribution of biofilms to the nitrogen cycle. At the early stage of biofilm formation, dissolved oxygen (DO) could penetrate the biofilms. As the biofilm grew and the thickness increased, then the mass transfer of DO was restricted. The microaerobic layer firstly appeared in biofilm under the turbulent flow conditions, with the appearance of the microaerobic and anaerobic layer, the nitrification and denitrification reaction could proceed smoothly in biofilm. And the removal efficiency of total nitrogen (TN) increased as the biofilm matured. Under the turbulent flow conditions, mature biofilms had the smallest thickness, but the highest proportion the anaerobic layer to the biofilm thickness, the highest density, and the highest nitrogen removal efficiency. However, the nitrogen removal efficiency of biofilm was the lowest under laminar flow conditions. The difference of layered structure of biofilm and the DO flux in biofilm explained the difference of nitrogen migration and transformation in river water under different hydrodynamic conditions. This study would help control the growth of biofilm and improve the nitrogen removal capacity of biofilm by regulating hydrodynamic conditions.

Effects of hydrodynamic conditions on the composition, spatiotemporal distribution of different extracellular polymeric substances and the architecture of biofilms

Microbial biofilms are common on abiotic and biotic surfaces, especially in rivers, which drive crucial ecosystem processes. The microorganisms of biofilms are surrounded by a self-produced extracellular polymeric substance (EPS). In this study, we investigated the effects of different hydrodynamic conditions on the composition, spatiotemporal distribution of different extracellular polymeric substances, and the architecture of biofilms. Multidisciplinary methods offer complementary insights into complex architecture correlations in biofilms. The biofilms formed in turbulent flow with high shear force were thin but dense. However, the biofilms formed under laminar flow conditions were thick but relatively loose. The thickness and compactness of the biofilms formed in the transitional flow were different from those of the other biofilms. The compact structure of the biofilm helped to resist shear forces to minimize detachment. Under the turbulent flow condition, bacteria, exopolysaccharides, and extracellular proteins permeated through the biofilm, and more extracellular polysaccharides enveloped bacteria and extracellular proteins. However, under the transitional flow condition, the extracellular polysaccharides and proteins were fewer than those under the turbulent flow condition; bacteria and algae were seen more prominently in the upper layer of the biofilm. Under the laminar flow condition, the distribution of extracellular polysaccharides, extracellular proteins, and bacteria was relatively uniform throughout the biofilm. The number of extracellular polysaccharides was greater than that of extracellular proteins. The total number of EPS in the biofilm was the largest under turbulent flow condition, followed by that under transitional flow condition and then under laminar flow condition. This study also observed that soluble EPS (S-EPS) were secreted first, followed by loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS). In particular, the adhesion of LB-EPS and flocculation capability of TB-EPS play some role in regulating biofilm formation. This study would help to perfect the five-stages theory of biofilm formation.

Convergence of biofilm successional trajectories initiated during contrasting seasons

Biofilm communities play a major role in explaining the temporal variation of biogeochemical conditions in freshwater ecosystems, and yet we know little about how these complex microbial communities change over time (aka succession), and from different initial conditions, in comparison to other stream communities. This has resulted in limited knowledge on how biofilm community structure and microbial colonization vary over relevant time scales to become mature biofilms capable of significant alteration of the freshwater environment in which they live. Here, we monitored successional trajectories of biofilm communities from summer and winter in a headwater stream and evaluated their structural state over time by DNA high-throughput sequencing. Significant differences in biofilm composition were observed when microbial colonization started in the summer vs. winter seasons, with higher percentage of algae (Bacillariophyta) and Bacteroidetes in winter-initiated samples but higher abundance of Proteobacteria (e.g., Rhizobiales, Rhodobacterales, Sphingomonadales, and Burkholderiales), Actinobacteria, and Chloroflexi in summer-initiated samples. Interestingly, results showed that despite seasonal effects on early biofilm succession, biofilm community structures converged after 70 days, suggesting the existence of a stable, mature community in the stream that is independent of the environmental conditions during biofilm colonization. Overall, our results show that algae are important in the early development of biofilm communities during winter, while heterotrophic bacteria play a more critical role during summer colonization and development of biofilms.

Biofilm assemblage and activity on plastic in urban streams at a continental scale: Site characteristics are more important than substrate type

The fate of plastics in rivers is a key component of the global plastic cycle. Plastics entering freshwater ecosystems are colonized by microbial biofilms, and microbe-plastic interactions can influence ecosystem processes and plastic fate. While literature examining the role of geographic region on plastic biofilms is quickly expanding, research which covers large (i.e., continental) spatial scales and includes freshwater ecosystems is warranted. In addition, most research focuses on bacterial communities, while biofilm eukaryotes are less commonly studied. We assessed biofilm metabolism and community structure on plastic (foamed polystyrene and polyvinyl chloride; PVC) and natural substrates (unglazed ceramic tile) in urban streams spanning a nested geographic gradient in the continental United States. We measured biofilm biomass, community respiration, and chlorophyll a, in addition to assessing marker gene-based community diversity of bacterial, fungal, and algal assemblages. Results demonstrated some substrate-specific trends in biofilm characteristics, including higher biofilm biomass on polystyrene across sites, and lower diversity of bacterial assemblages on both types of plastic litter versus tile. However, there were no differences among substrates for chlorophyll, respiration, and the abundance and diversity of algal and fungal assemblages. Thus, we concluded that the primary driver of biofilm metabolism and community composition were site characteristics, rather than substrate type. Additional studies are needed to quantify which site-specific characteristics drive biofilm dynamics on plastic litter in streams (e.g., water chemistry, light, seasonality, hydrology). These results add to the growing literature on the biofilm 'plastisphere' in aquatic ecosystems, demonstrating that the factors which control the assembly and activity of biofilm communities on plastic substrates (including bacteria, algal, and fungal assemblages together) in urban streams are similar to those driving biofilm dynamics on natural substrates.

Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes' ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes' existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes' ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.

Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network

During transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale.

A Review of Microalgal Biofilm Technologies: Definition, Applications, Settings and Analysis

Biofilm-based algal cultivation has many advantages over the conventional suspended growth methods and has received increased attention as a potential platform for algal production, wastewater treatment (nutrient removal), and a potential pathway to supply feedstock for microalgae-based biorefinery attempts. However, the attached cultivation by definition and application is a result of a complex interaction between the biotic and abiotic components involved. Therefore, the entire understanding of the biofilm nature is still a research challenge due to the need for real-time analysis of the system. In this review, the state of the art of biofilm definition, its life cycle, the proposed designs of bioreactors, screening of carrier materials, and non-destructive techniques for the study of biofilm formation and performance are summarized. Perspectives for future research needs are also discussed to provide a primary reference for the further development of microalgal biofilm systems.

Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review

Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm^-2y^-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.

Bacterial streamers as colloidal systems: Five grand challenges

Bacteria can thrive in biofilms, which are intricately organized communities with cells encased in a self-secreted matrix of extracellular polymeric substances (EPS). Imposed hydrodynamic stresses can transform this active colloidal dispersion of bacteria and EPS into slender thread-like entities called streamers. In this perspective article, the reader is introduced to the world of such deformable 'bacteria-EPS' composites that are a subclass of the generic flow-induced colloidal structures. While bacterial streamers have been shown to form in a variety of hydrodynamic conditions (turbulent and creeping flows), its abiotic analogues have only been demonstrated in low Reynolds number (Re < 1) particle-laden polymeric flows. Streamers are relevant to a variety of situations ranging from natural formations in caves and river beds to clogging of biomedical devices and filtration membranes. A critical review of the relevant biophysical aspects of streamer formation phenomena and unique attributes of its material behavior are distilled to unveil five grand scientific challenges. The coupling between colloidal hydrodynamics, device geometry and streamer formation are highlighted.

Both Pseudomonas aeruginosa and Candida albicans Accumulate Greater Biomass in Dual-Species Biofilms under Flow

Microbe-microbe interactions can strongly influence growth and biofilm formation kinetics. For Pseudomonas aeruginosa and Candida albicans, which are found together in diverse clinical sites, including urinary and intravenous catheters and the lungs of individuals with cystic fibrosis (CF), we compared the kinetics of biofilm formation by each species in dual-species and single-species biofilms. We engineered fluorescent protein constructs for P. aeruginosa (producing mKO-κ) and C. albicans (producing mKate2) that did not alter growth and enabled single-cell resolution imaging by live-sample microscopy. Using these strains in an optically clear derivative of synthetic CF sputum medium, we found that both P. aeruginosa and C. albicans displayed increased biovolume accumulation—by three- and sixfold, respectively—in dual-species biofilms relative to single-species biofilms. This result was specific to the biofilm environment, as enhanced growth was not observed in planktonic cocultures. Stimulation of C. albicans biofilm formation occurred regardless of whether P. aeruginosa was added at the time of fungal inoculation or 24 h after the initiation of biofilm development. P. aeruginosa biofilm increases in cocultures did not require the Pel extracellular polysaccharide, phenazines, and siderophores known to influence C. albicans. P. aeruginosa mutants lacking Anr, LasR, and BapA were not significantly stimulated by C. albicans, but they still promoted a significant enhancement of biofilm development of the fungus, suggesting a fungal response to the presence of bacteria. Last, we showed that a set of P. aeruginosa clinical isolates also prompted an increase of biovolume by C. albicans in coculture.

IMPORTANCE There is an abundance of work on both P. aeruginosa and C. albicans in isolation, and quite some work as well on the way these two microbes interact. These studies do not, however, consider biofilm environments under flow, and our results here show that the expected outcome of interaction between these two pathogens can actually be reversed under flow, from pure antagonism to an increase in biomass on the part of both. Our work also highlights the importance of cellular-scale spatial structure in biofilms for understanding multispecies population dynamics.

Diversity and structure of microbial biofilms on microplastics in riverine waters of the Pearl River Delta, China

Riverine runoff is a significant transport pathway for microplastics (MPs) discharged from land-based sources to marine environments where MPs accumulate. Knowledge of riverine MP-associated biofilms will improve the understanding of the fate and potential effects of MPs in marine environments. This study aimed to characterize the microbial biofilms colonizing MPs in the riverine water of the Pearl River Delta, China, and identify the seasonal, geographical and environmental influences on MP-associated communities. We sampled MPs and the surrounding surface water from eight outlets in three seasons and analyzed their microbial communities by Illumina sequencing of the 16S rRNA gene libraries. Across all sampling seasons and locations, abundant MP-colonizing taxa belonged to the phylum Proteobacteria, which suggested initial biofilm development on those MPs. The structure and composition of MP-attached microbial communities varied with respect to season and location, and the microbial diversity of the MP-associated biofilm communities decreased in June compared with that in the April and November sampling events. Opportunistic pathogens of the genus Acinetobacter were significantly enriched on the MP surfaces for all sampling events. Among the 15 environmental variables examined, the main drivers of MP-associated biofilm community composition included IC, alkalinity, TOC, TDS, Cl^-, NO₃^-, NO₂^- and pH. This study provides an insight into the environmental factors that shape microbial biofilm colonization on MPs in estuary environments and a further understanding of the structure, diversity and ecological roles of MP-associated communities.

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer

Biodegradation is responsible for most contaminant removal in plumes of organic compounds and is fastest at the plume fringe where microbial cell numbers and activity are highest. As the plume migrates from the source, groundwater containing the contaminants and planktonic microbial community encounters uncontaminated substrata on which an attached community subsequently develops. While attached microbial communities are important for biodegradation, the time needed for their establishment, their relationship with the planktonic community and the processes controlling their development are not well understood. We compare the dynamics of development of attached microbial communities on sterile substrata in the field and laboratory microcosms, sampled simultaneously at intervals over two years. We show that attached microbial cell numbers increased rapidly and stabilised after similar periods of incubation (∼100 days) in both field and microcosm experiments. These timescales were similar even though variation in the contaminant source evident in the field was absent in microcosm studies, implying that this period was an emergent property of the attached microbial community. 16S rRNA gene sequencing showed that attached and planktonic communities differed markedly, with many attached organisms strongly preferring attachment. Successional processes were evident, both in community diversity indices and from community network analysis. Community development was governed by both deterministic and stochastic processes and was related to the predilection of community members for different lifestyles and the geochemical environment.

Responses of periphyton communities to abrupt changes in water temperature and velocity, and the relevance of morphology: A mesocosm approach

Sudden instream releases of water from hydropower plants (hydropeaking [HP]) can cause abrupt temperature variations (thermopeaking [TP]), typically on a daily/sub-daily basis. In alpine rivers, hydropeaking and thermopeaking waves usually overlap, which leads to a multiple stressor of flow velocity pulses and temperature alteration. Periphytic communities could give important insights into the effects of combined thermo- and hydropeaking (THP) in stream ecosystems. Thus, the study's first aim was to assess the combined effects of thermo-hydropeaking on structural (composition, biomass) and functional (photosynthesis, enzyme activity) properties of periphyton. The second aim was to assess the interaction between periphytic algae and the heterotrophic communities (bacteria) and determine how biotic and abiotic factors explain the variability of bacterial enzymatic activities in the periphyton. We assessed the effects of repeated cold and warm thermo-hydropeaking for 24 days on periphyton, by manipulating discharge and temperature in six experimental flumes directly fed by an Alpine stream. Our study revealed that THP had structural and functional effects on periphyton in oligotrophic streams, where the effects depending on the direction of the temperature change (cold/warm) and on the morphological setting (pool/riffle). The results showed that even a short-term increase in flow velocity and temperature decrease could induce better growth conditions for diatoms. Additionally, an increase in the interaction between periphytic algae and bacteria during thermo-hydropeaking was also shown, this coupling being more pronounced in pool than in riffle sections. Our results clearly showed that riffle sections develop less periphytic algal biomass and activity and therefore, THP can reduce biomass availability for primary consumers in large areas of impacted streams. These findings highlight the importance of mitigation measures, focusing on establishing heterogeneous stream bed areas, with frequent pool and riffle sequences.

Microbial diversity accumulates in a downstream direction in the Three Gorges Reservoir

Organic and inorganic materials migrate downstream and have important roles in regulating environmental health in the river networks. However, it remains unclear whether and how a mixture of materials (i.e., microbial species) from various upstream habitats contribute to microbial community coalescence upstream of a dam. Here we track the spatial variation in microbial abundance and diversity in the Three Gorges Reservoir based on quantitative PCR and 16S rRNA gene high-throughput sequencing data. We further quantitatively assess the relative contributions of microbial species from mainstem, its tributaries, and the surrounding riverbank soils to the area immediately upstream of the Three Gorges Dam (TGD). We found an increase of microbial diversity and the convergent microbial distribution pattern in areas immediately upstream of TGD, suggesting this area become a new confluence for microbial diversity immigrating from upstream. Indeed, the number of shared species increased from upstream to TGD but unique species decreased, indicating immigration of various sources of microbial species overwhelms local environmental conditions in structuring microbial community close to TGD. By quantifying the sources of microbial species close to TGD, we found little contribution from soils as compared to tributaries, especially for sites closer to TGD, suggesting tributary microbes have greater influence on microbial diversity and environmental health in the Three Gorges Reservoir. Collectively, our results suggest that tracking microbial geographic origin and evaluating accumulating effects of microbial diversity shed light on the ecological processes in microbial communities and provide information for regulating aquatic ecological health.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms

Microbial community composition and stability affect pollutant removal for biological/granular activated carbon (BAC/GAC) processes. Here, we pre-loaded the organic carbon substrates sucrose, lactose, and Lysogeny Broth (LB) medium onto new GAC prior to use and then tested whether this substrate pre-loading promoted development of biofilms with high coverage that remained stable for prolonged operational periods. Temporal dynamics of the biomass and microbial community on the GAC were monitored via flow cytometry (FCM) and sequencing, respectively, in both batch and continuous-flow experiments. In comparison with the non-loaded GAC (control), the initial biofilm biomass on substrate-loaded GAC was 3–114 times higher, but the initial richness was considerably lower (only accounting for 13–28% of the control). The initial community compositions were significantly different between batch and continuous-flow column experiments, even when loaded with the same substrates. In the continuous-flow column experiments, both biomass and microbial community composition became remarkably similar to the control filters after 64 days of operation. From these findings, we conclude that substrate-loaded GAC could enhance initial colonization, affecting both biomass and microbial community composition. However, the biomass and composition did not remain stable during long-term operation due to continuous dispersal and competition from influent bacteria.

Treated wastewater reuse in micro-irrigation: effect of shear stress on biofilm development kinetics and chemical precipitation

Treated wastewater in micro-irrigation is a promising approach that could be used to decrease the pressure on good quality water resources. However, the clogging of such systems due to biofilm development and chemical precipitation constitute a constraint with the use of treated wastewater (TWW) and lead to lower irrigation system performance. The objective of this work is to study the development of biofilm and composition of fouling due to TWW under shear stresses of 0.7, 2.2 and 4.4 Pa detected along micro-irrigation systems. For this purpose, a Taylor-Couette reactor (TCR) was specifically calibrated for the cultivation of biofilm. The analysis of fouling composition samples (organic and inorganic) shows that biofilm tends to develop under the highest shear stress value (4.4 Pa). Precipitation of calcium carbonate in the form of calcite was observed in conjunction with biofilm growth using X-ray diffractometry (XRD) and thermogravimetric analysis (TGA). These results can be used to ascertain the origins of chemical and biological clogging of drippers and fouling of pipes related to reclaimed water- irrigation.

Seasonal variations in arsenic mobility and bacterial diversity: The case study of Huangshui Creek, Shimen Realgar Mine, Hunan Province, China

Rivers throughout the world have been contaminated by arsenic dispersed from mining activities. The biogeochemical cycling of this arsenic has been shown to be due to factors such as pH, Eh, ionic strength and microbial activity, but few studies have examined the effects of both seasonal changes and microbial community structure on arsenic speciation and flux in mining-affected river systems. To address this research gap, a study was carried out in Huangshui Creek, Hunan province, China, which has been severely impacted by long-term historic realgar (α-As₄S₄) mining. Water and sediment sampling, and batch experiments at different temperatures using creek sediment, were used to determine the form, source and mobility of arsenic. Pentavalent (AsO₄³) and trivalent arsenic (AsO₃^3-) were the dominant aqueous species (70-89% and 30-11%, respectively) in the creek, and the maximum concentration of inorganic arsenic in surface water was 10,400 μg/L. Dry season aqueous arsenic concentrations were lower than those in the wet season samples. The sediments contained both arsenate and arsenite, and relative proportions of these varied with season. 8.3 tons arsenic per annum were estimated to be exported from Huangshui Creek. Arsenic release from sediment increased by 3 to 5 times in high water temperature batch experiments (25 and 37 °C) compared to those carried out at low temperature (8 °C). Our data suggest that the arsenic-containing sediments were the main source of arsenic contamination in Huangshui Creek. Microbial community structured varied at the different sample sites along the creek. Redundancy analysis (RDA) showed that both temperature and arsenic concentrations were the main controlling factors on the structure of the microbial community. Protecbacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, and Planctomycetes were the stable dominant phyla in both dry and wet seasons. The genera Flavobacterium, Hydrogenophaga and Sphingomonas occurred in the most highly arsenic contaminated sites, which removed arsenic by related metabolism.Our findings indicate that seasonal variations profoundly control arsenic flux and species, microbial community structure and ultimately, the biogeochemical fate of arsenic.

Biofilm mechanics: Implications in infection and survival

It has long been recognized that biofilms are viscoelastic materials, however the importance of this attribute to the survival and persistence of these microbial communities is yet to be fully realized. Here we review work, which focuses on understanding biofilm mechanics and put this knowledge in the context of biofilm survival, particularly for biofilm-associated infections. We note that biofilm viscoelasticity may be an evolved property of these communities, and that the production of multiple extracellular polymeric slime components may be a way to ensure the development of biofilms with complex viscoelastic properties. We discuss viscoelasticity facilitating biofilm survival in the context of promoting the formation of larger and stronger biofilms when exposed to shear forces, promoting fluid-like behavior of the biofilm and subsequent biofilm expansion by viscous flow, and enabling resistance to both mechanical and chemical methods of clearance. We conclude that biofilm viscoelasticity contributes to the virulence of chronic biofilm infections.

Relationship between aquifer biofilms and unattached microbial indicators of urban groundwater contamination

Aquifers, springs and other groundwater-dependent ecosystems are threatened by urban land use, which causes water quality deterioration through nutrient loading, sewage infiltration, groundwater extraction and, along coasts, seawater intrusion. The presence of certain microbes in groundwater can indicate that an aquifer is anthropogenically contaminated. Interpretations made from observations of indicator microbes in groundwater are limited because the relationship between the presumably allochthonous indicator microbes and relevant autochthonous microbial communities has not been characterized. This study addressed whether autochthonous aquifer biofilms can influence the presence of presumed microbial indicators in groundwater, and simultaneously used microbial indicators to trace sources of urban contamination at a karst spring of conservation concern. These questions were approached using a 17-month time series analysis of attached biofilm and adjacent unattached bacteria in the submerged karst aquifer conduit associated with this spring. Environmental 16S rRNA gene sequencing was performed to characterize these communities, and community structure data were contextualized with groundwater geochemical and hydrogeological measurements. Linear regression models were developed to explain the relative abundance patterns of indicator microbes and other unattached microbes at this site. The results of this study suggest that dominant aquifer biofilms do not influence the presence of unattached microbial taxa that are presumed to be indicators of groundwater contamination, and generated new information about the origin of coliform bacteria at the study site. These results build confidence in the use of microbial indicators in groundwater-dependent ecosystem conservation strategies and inform future management plans for urban aquifers and springs worldwide.

Taxonomic dependency of beta diversity components in benthic communities of bacteria, diatoms and chironomids along a water-depth gradient

Community variation (i.e., beta diversity) along geographical gradients is a well-known ecological pattern, but the corresponding variation in beta diversity components (e.g., species turnover and nestedness) and underlying drivers remain poorly understood. Based on two alternative approaches (that is, the beta diversity partitioning proposed by Baselga and the Local Contributions to Beta Diversity (LCBD) partitioning proposed by Legendre), we examined the patterns of beta diversity components of lacustrine benthos, from bacteria to diatoms and chironomids, in the surface sediments along a 100-m water-depth gradient in Lugu Lake. We further quantified the relative importance of spatial, environmental and biotic variables in explaining water-depth patterns in beta diversity. Based on the Baselga's framework, there was a taxonomic dependency for the patterns of beta diversity components with water-depth, showing a significant species turnover pattern for bacteria, while diatoms and chironomids showed significant nestedness. This dependency was also evident in the patterns of community uniqueness with water-depth because based on Legendre's framework, the LCBD decreased with water depth for bacteria whereas increased with depth for diatoms. The total beta diversity and species turnover of bacteria could be explained by the pure effects of spatial, environmental and biotic variables. A total of 26.8% and 23.6% of the nestedness component of diatoms and chironomids was explained by environmental variables, respectively, while species turnover was mostly related to spatial variables. Bacteria total LCBD and species replacement were driven only by environmental variables. For diatoms and chironomids, however, most of the total LCBD and its two components were explained by spatial variables, and biotic variables were most important for the diatom replacement component. Our findings provide insights into the mechanisms responsible for community organizations along water-depth gradients from the perspective of beta diversity components.

The Role of Retardation, Attachment and Detachment Processes during Microbial Coal-Bed Methane Production after Organic Amendment

Microbially enhanced coal-bed methane could allow for a more sustainable method of harvesting methane from un-mineable coaldbeds. The model presented here is based on a previously validated batch model; however, this model system is based on upflow reactor columns compared to previous experiments and now includes flow, transport and reactions of amendment as well as intermediate products. The model implements filtration and retardation effects, biofilm decay, and attachment and detachment processes of microbial cells due to shear stress. The model provides additional insights into processes that cannot be easily observed in experiments. This study improves the understanding of complex and strongly interacting processes involved in microbially enhanced coal-bed methane production and provides a powerful tool able to model the entire process of enhancing methane production and transport during microbial stimulation.

Exploring flow-biofilm-sediment interactions: Assessment of current status and future challenges

Biofilm activities and their interactions with physical, chemical and biological processes are of great importance for a variety of ecosystem functions, impacting hydrogeomorphology, water quality and aquatic ecosystem health. Effective management of water bodies requires advancing our understanding of how flow influences biofilm-bound sediment and ecosystem processes and vice-versa. However, research on this triangle of flow-biofilm-sediment is still at its infancy. In this Review, we summarize the current state of the art and methodological approaches in the flow-biofilm-sediment research with an emphasis on biostabilization and fine sediment dynamics mainly in the benthic zone of lotic and lentic environments. Example studies of this three-way interaction across a range of spatial scales from cell (nm - µm) to patch scale (mm - dm) are highlighted in view of the urgent need for interdisciplinary approaches. As a contribution to the review, we combine a literature survey with results of a pilot experiment that was conducted in the framework of a joint workshop to explore the feasibility of asking interdisciplinary questions. Further, within this workshop various observation and measuring approaches were tested and the quality of the achieved results was evaluated individually and in combination. Accordingly, the paper concludes by highlighting the following research challenges to be considered within the forthcoming years in the triangle of flow-biofilm-sediment: i) Establish a collaborative work among hydraulic and sedimentation engineers as well as ecologists to study mutual goals with appropriate methods. Perform realistic experimental studies to test hypotheses on flow-biofilm-sediment interactions as well as structural and mechanical characteristics of the bed. ii) Consider spatially varying characteristics of flow at the sediment-water interface. Utilize combinations of microsensors and non-intrusive optical methods, such as particle image velocimetry and laser scanner to elucidate the mechanism behind biofilm growth as well as mass and momentum flux exchanges between biofilm and water. Use molecular approaches (DNA, pigments, staining, microscopy) for sophisticated community analyses. Link varying flow regimes to microbial communities (and processes) and fine sediment properties to explore the role of key microbial players and functions in enhancing sediment stability (biostabilization). iii) Link laboratory-scale observations to larger scales relevant for management of water bodies. Conduct field experiments to better understand the complex effects of variable flow and sediment regimes on biostabilization. Employ scalable and informative observation techniques (e.g., hyperspectral imaging, particle tracking) that can support predictions on the functional aspects, such as metabolic activity, bed stability, nutrient fluxes under variable regimes of flow-biofilm-sediment.

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.

Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment

Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System

Dissolved organic nitrogen (DON) represents a unique challenge in prechlorinated raw water distribution systems (PRWDSs) because of its contribution to the formation of harmful nitrogen-disinfection byproducts, influence upon biogeochemical processes, and unclear molecular characteristics. Here, Fourier transform ion cyclotron resonance mass spectrometry in combination with high-throughput sequencing was applied to elucidate the molecular changes of DON and biofilm microbial communities in a PRWDS in Yixing, China. Our study revealed that dynamic characteristics of DON are significantly correlated with the biofilm. The accumulation of refractory lignin-like compounds and C_nH_mO_pN₁ contributes to the higher recalcitrance molecular characteristics of DON in the effluent associated with Alphaproteobacteria, Planctomycetes, and Bacteroidetes. Additionally, with the help of prechlorination, the biofilm may change the DON characteristics and lead to higher oxygenation, higher m/z, and lower saturation during transportation. Despite the promotion of C_nH_mO_pN₁ and C_nH_mO_pN₃ at the early stage, we suggest that appropriate concentration of chlorine can add to the front end of raw water distribution pipes. Prechlorination may control the nitrification process and stabilize the rapid growth of diversity and concentration of low molecular weight DON, especially the refractory C_nH_mO_pN₁ in the effluent, which may help to improve treatment efficiency of drinking water treatment plants.

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

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

Niche partitioning of microbial communities in riverine floodplains

Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor β (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.

Microbial biofilm formation and community structure on low-density polyethylene microparticles in lake water microcosms

The occurrence of microplastics (MPs) in the environment has been gaining widespread attention globally. MP-colonizing microorganisms are important links for MPs contamination in various ecosystems, but have not been well understood. To partially address this issue, the present study investigated biofilm formation by microorganisms originating from lake water on low-density polyethylene (LDPE) MPs using a cultivation approach and the surface-related effects on the MP-associated microbial communities using 16S rRNA high-throughput sequencing. With the addition of nonionic surfactants and UV-irradiation pretreatment that changed the surface properties of LDPE MPs, more microorganisms were colonized on LDPE surface. Microbial community analysis indicated that LDPE MPs were primarily colonized by the phyla Proteobacteria, Bacteroidetes and Firmicutes, and the surface roughness and hydrophobicity of MP were important factors shaping the LDPE MP-associated microbial community structure. Half of the top 20 most abundant genera colonizing on LDPE were found to be potential pathogens, e.g., plant pathogens Agrobacterium, nosocomial pathogens Chryseobacterium and fish pathogens Flavobacterium. This study demonstrated rapid bacterial colonization of LDPE MPs in lake water microcosms, the role of MPs as transfer vectors for harmful microorganisms in lake water, and provided a first glimpse into the effect of surface properties on LDPE MP-associated biofilm communities.

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

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

Transport and instream removal of the Cry1Ab protein from genetically engineered maize is mediated by biofilms in experimental streams

The majority of maize planted in the US is genetically-engineered to express insecticidal properties, including Cry1Ab protein, which is designed to resist the European maize borer (Ostrinia nubilalis). After crop harvest, these proteins can be leached into adjacent streams from crop detritus left on fields. The environmental fate of Cry1Ab proteins in aquatic habitats is not well known. From June-November, we performed monthly short-term additions of leached Cry1Ab into four experimental streams with varying benthic substrate to estimate Cry1Ab transport and removal. At the start of the experiments, when rocks were bare, we found no evidence of Cry1Ab removal from the water column, but uptake steadily increased as biofilm colonized the stream substrate. Overall, Cry1Ab uptake was strongly predicted by measures of biofilm accumulation, including algal chlorophyll a and percent cover of filamentous algae. Average Cry1Ab uptake velocity (vf = 0.059 ± 0.009 mm s-1) was comparable to previously reported uptake of labile dissolved organic carbon (DOC; mean vf = 0.04 ± 0.008 mm s-1). Although Cry1Ab has been shown to rapidly degrade in stream water, benthic biofilms may decrease the distance proteins are transported in lotic systems. These results emphasize that once the Cry1Ab protein is leached, subsequent detection and transport through agricultural waterways is dependent on the structure and biology of receiving stream ecosystems.

Forfeiting the priority effect: turnover defines biofilm community succession

Microbial community succession is a fundamental process that affects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are often poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the ecological contribution of colonizers? We performed a succession experiment within a hypersaline ecosystem to investigate how different processes contributed to the turnover of founder species. Bacterial and eukaryotic colonizers were identified during primary succession and tracked through a defined, 79-day biofilm maturation period using 16S and 18S rRNA gene sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate successional patterns of primary producers and nitrogen fixers. The majority of the founder species did not maintain high abundance throughout succession. Species replacement (versus loss) was the dominant process shaping community succession. We also asked if different ecological processes acted on bacteria versus Eukaryotes during succession and found deterministic and stochastic forces corresponded more with microeukaryote and bacterial colonization, respectively. Our results show that taxa and functions belonging to different kingdoms, which share habitat in the tight spatial confines of a biofilm, were influenced by different ecological processes and time scales of succession.

Taxonomic relatedness and environmental pressure synergistically drive the primary succession of biofilm microbial communities in reclaimed wastewater distribution systems

Compared to drinking water, the higher bacterial abundance, diversity, and organic matter concentration in reclaimed wastewater suggest that it is more likely to form biofilms. Nevertheless, little is known regarding many important aspects of the biofilm ecology in reclaimed wastewater distribution systems (RWDS), such as the long-term microbial community succession and the underlying driving factors. In the present study, by sampling and analysing microbial compositions of pipe wall biofilms from six frequently used pipe materials under NaClO_disinfection (sodium hypochlorite-treated), NON_disinfection (without disinfection), and UV_disinfection (UV-treated) treatments over one year, it was found that the succession of microbial community structure followed a primary succession pattern. This primary succession pattern was reflected as increases in live cell number and α-diversity, along with metagenic succession in taxonomic composition. Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Verrucomicrobia comprised the dominant phyla in biofilm samples. Compared to biofilms in the NaClO_disinfection reactor, the bacterial communities of biofilms in NON_disinfection and UV_disinfection reactors were distributed more evenly among different bacterial phyla. Principal component analysis revealed a clear temporal pattern of microbial community structures in six kinds of pipe wall biofilms albeit a difference in microbial community structures among the three reactors. Adonis testing indicated that the microbial community composition variation caused by disinfection methods (R² = 0.283, P < 0.01) was more pronounced than that from the time variable (R² = 0.070, P < 0.01) and pipe material (R² = 0.057, P < 0.01). Significantly positive correlation between average local abundance and occupancy was observed in biofilm communities of the three reactors, suggesting that the 'core-satellite' model could be applied to identify biofilm-preferential species under specific disinfection conditions in RWDS. The prevalence of family Sphingomonadaceae, known to show chlorine tolerance and powerful biofilm-forming ability in NaClO_disinfection reactors, evidenced the habitat filtering consequent to environment pressure. Correlation-based network analysis revealed that taxonomic relatedness such as similar niches, cooperation, taxa overdispersion, and competition all functioned toward driving the bacterial assembly succession in RWDS.

Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing

Clogging of drippers due to the development of biofilms weakens the advantages and impedes the implementation of drip irrigation technology. The objective of this study was to characterise the bacterial community of biofilms that develop in a drip irrigation system supplied with treated wastewater. High-throughput sequencing of 16S rRNA gene amplicons indicated that the bacterial community composition differed between drippers and pipes, mainly due to changes in the abundance of the genus Aquabacterium. Cyanobacteria were found to be involved in the biological fouling of drippers. Moreover, bacterial genera including opportunistic pathogenic bacteria such as Legionella and Pseudomonas were more abundant in dripper and pipe biofilms than in the incoming water. Some genera such as Pseudomonas were mostly recovered from drippers, while others (ie Bacillus, Brevundimonas) mainly occurred in pipes. Variations in the hydraulic conditions and properties of the materials likely explain the shift in bacterial communities observed between pipes and drippers.

Microbiomes and chemical components of feed water and membrane-attached biofilm in reverse osmosis system to treat membrane bioreactor effluents

Reverse osmosis (RO) system at a stage after membrane bioreactor (MBR) is used for the wastewater treatment and reclamation. One of the most serious problems in this system is membrane fouling caused by biofilm formation. Here, microbiomes and chemical components of the feed water and membrane-attached biofilm of RO system to treat MBR effluents were investigated by non-destructive confocal reflection microscopy, excitation-emission fluorescence spectroscopy and high-throughput sequencing of 16S rRNA genes. The microscopic visualization indicated that the biofilm contained large amounts of microbial cells (0.5 ± 0.3~3.9 ± 2.3 µm³/µm²) and the extracellular polysaccharides (3.3 ± 1.7~9.4 ± 5.1 µm³/µm²) and proteins (1.0 ± 0.2~1.3 ± 0.1 µm³/µm²). The spectroscopic analysis identified the humic and/or fulvic acid-like substances and protein-like substances as the main membrane foulants. High-throughput sequencing showed that Pseudomonas spp. and other heterotrophic bacteria dominated the feed water microbiomes. Meanwhile, the biofilm microbiomes were composed of diverse bacteria, among which operational taxonomic units related to the autotrophic Hydrogenophaga pseudoflava and Blastochloris viridis were abundant, accounting for up to 22.9 ± 4.1% and 3.1 ± 0.4% of the total, respectively. These results demonstrated that the minor autotrophic bacteria in the feed water played pivotal roles in the formation of polysaccharide- and protein-rich biofilm on RO membrane, thereby causing membrane fouling of RO system.

Succession of bacterial and fungal communities within biofilms of a chlorinated drinking water distribution system

Understanding the temporal dynamics of multi-species biofilms in Drinking Water Distribution Systems (DWDS) is essential to ensure safe, high quality water reaches consumers after it passes through these high surface area reactors. This research studied the succession characteristics of fungal and bacterial communities under controlled environmental conditions fully representative of operational DWDS. Microbial communities were observed to increase in complexity after one month of biofilm development but they did not reach stability after three months. Changes in cell numbers were faster at the start of biofilm formation and tended to decrease over time, despite the continuing changes in bacterial community composition. Fungal diversity was markedly less than bacterial diversity and had a lag in responding to temporal dynamics. A core-mixed community of bacteria including Pseudomonas, Massillia and Sphingomonas and the fungi Acremonium and Neocosmopora were present constantly and consistently in the biofilms over time and conditions studied. Monitoring and managing biofilms and such ubiquitous core microbial communities are key control strategies to ensuring the delivery of safe drinking water via the current ageing DWDS infrastructure.

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study

Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances.

Going with the flow: Planktonic processing of dissolved organic carbon in streams

A large part of the organic carbon in streams is transported by pulses of terrestrial dissolved organic carbon (tDOC) during hydrological events, which is more pronounced in agricultural catchments due to their hydrological flashiness. The majority of the literature considers stationary benthic biofilms and hyporheic biofilms to dominate uptake and processing of tDOC. Here, we argue for expanding this viewpoint to planktonic bacteria, which are transported downstream together with tDOC pulses, and thus perceive them as a less variable resource relative to stationary benthic bacteria. We show that pulse DOC can contribute significantly to the annual DOC export of streams and that planktonic bacteria take up considerable labile tDOC from such pulses in a short time frame, with the DOC uptake being as high as that of benthic biofilm bacteria. Furthermore, we show that planktonic bacteria efficiently take up labile tDOC which strongly increases planktonic bacterial production and abundance. We found that the response of planktonic bacteria to tDOC pulses was stronger in smaller streams than in larger streams, which may be related to bacterial metacommunity dynamics. Furthermore, the response of planktonic bacterial abundance was influenced by soluble reactive phosphorus concentration, pointing to phosphorus limitation. Our data suggest that planktonic bacteria can efficiently utilize tDOC pulses and likely determine tDOC fate during downstream transport, influencing aquatic food webs and related biochemical cycles.

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands

The effects of water flow on the leaf-biofilm interface of Vallisneria natans and Hydrilla verticillata were investigated using artificial plants as the control. Water flow inhibited the growth of two species of submerged macrophytes, reduced oxygen concentrations in plant leaves and changed oxygen profiles at the leaf-biofilm interface. The results from confocal laser scanning microscopy and multifractal analysis showed that water flow reduced biofilm thickness, changed biofilm topographic characterization and increased the percentages of single colony-like biofilm patches. A cluster analysis revealed that the bacterial compositions in biofilms were determined mainly by substrate types and were different from those in sediments. However, water flow increased the bacterial diversity in biofilms in terms of operational taxonomic unit numbers and Shannon Indices. Our results indicated that water flow can be used to regulate the biomass, distribution and bacterial diversities of epiphytic biofilms in constructed wetlands dominated by submerged macrophytes.