Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system

Viruses are thought to control bacterial abundance, affect community composition and influence ecosystem function in natural environments. Yet their dynamics have seldom been studied in engineered systems, or indeed in any system, for long periods of time. We measured virus abundance in a full-scale activated sludge plant every week for two years. Total bacteria and ammonia oxidising bacteria (AOB) abundances, bacterial community profiles, and a suite of environmental and operational parameters were also monitored. Mixed liquor virus abundance fluctuated over an order of magnitude (3.18 × 10⁸-3.41 × 10⁹ virus's mL^-1) and that variation was statistically significantly associated with total bacterial and AOB abundance, community composition, and effluent concentrations of COD and NH₄⁺- N and thus system function. This suggests viruses play a far more important role in the dynamics of activated sludge systems than previously realised and could be one of the key factors controlling bacterial abundance, community structure and functional stability and may cause reactors to fail. These findings are based on statistical associations, not mechanistic models. Nevertheless, viral associations with abiotic factors, such as pH, make physical sense, giving credence to these findings and highlighting the role that physical factors play in virus ecology. Further work is needed to identify and quantify specific bacteriophage and their hosts to enable us to develop mechanistic models of the ecology of viruses in wastewater treatment systems. However, since we have shown that viruses can be related to effluent quality and virus quantification is simple and cheap, practitioners would probably benefit from quantifying viruses now.

Turbulence accelerates the growth of drinking water biofilms

Biofilms are found at the inner surfaces of drinking water pipes and, therefore, it is essential to understand biofilm processes to control their formation. Hydrodynamics play a crucial role in shaping biofilms. Thus, knowing how biofilms form, develop and disperse under different flow conditions is critical in the successful management of these systems. Here, the development of biofilms after 4 weeks, the initial formation of biofilms within 10 h and finally, the response of already established biofilms within 24-h intervals in which the flow regime was changed, were studied using a rotating annular reactor under three different flow regimes: turbulent, transition and laminar. Using fluorescence microscopy, information about the number of microcolonies on the reactor slides, the surface area of biofilms and of extracellular polymeric substances and the biofilm structures was acquired. Gravimetric measurements were conducted to characterise the thickness and density of biofilms, and spatial statistics were used to characterise the heterogeneity and spatial correlation of biofilm structures. Contrary to the prevailing view, it was shown that turbulent flow did not correlate with a reduction in biofilms; turbulence was found to enhance both the initial formation and the development of biofilms on the accessible surfaces. Additionally, after 24-h changes of the flow regime it was indicated that biofilms responded to the quick changes of the flow regime. Overall, this work suggests that different flow conditions can cause substantial changes in biofilm morphology and growth and specifically that turbulent flow can accelerate biofilm growth in drinking water.

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells

The factors that affect microbial community assembly and its effects on the performance of bioelectrochemical systems are poorly understood. Sixteen microbial fuel cell (MFC) reactors were set up to test the importance of inoculum, temperature and substrate: Arctic soil versus wastewater as inoculum; warm (26.5°C) versus cold (7.5°C) temperature; and acetate versus wastewater as substrate. Substrate was the dominant factor in determining performance and diversity: unexpectedly the simple electrogenic substrate delivered a higher diversity than a complex wastewater. Furthermore, in acetate fed reactors, diversity did not correlate with performance, yet in wastewater fed ones it did, with greater diversity sustaining higher power densities and coulombic efficiencies. Temperature had only a minor effect on power density, (Q₁₀: 2 and 1.2 for acetate and wastewater respectively): this is surprising given the well-known temperature sensitivity of anaerobic bioreactors. Reactors were able to operate at low temperature with real wastewater without the need for specialised inocula; it is speculated that MFC biofilms may have a self-heating effect. Importantly, the warm acetate fed reactors in this study did not act as direct model for cold wastewater fed systems. Application of this technology will encompass use of real wastewater at ambient temperatures.

Investigation of nanoparticle transport inside coarse-grained geological media using magnetic resonance imaging

Quantifying nanoparticle (NP) transport inside saturated porous geological media is imperative for understanding their fate in a range of natural and engineered water systems. While most studies focus upon finer grained systems representative of soils and aquifers, very few examine coarse-grained systems representative of riverbeds and gravel based sustainable urban drainage systems. In this study, we investigated the potential of magnetic resonance imaging (MRI) to image transport behaviors of nanoparticles (NPs) through a saturated coarse-grained system. MRI successfully imaged the transport of superparamagnetic NPs, inside a porous column composed of quartz gravel using T(2)-weighted images. A calibration protocol was then used to convert T(2)-weighted images into spatially resolved quantitative concentration maps of NPs at different time intervals. Averaged concentration profiles of NPs clearly illustrates that transport of a positively charged amine-functionalized NP within the column was slower compared to that of a negatively charged carboxyl-functionalized NP, due to electrostatic attraction between positively charged NP and negatively charged quartz grains. Concentration profiles of NPs were then compared with those of a convection-dispersion model to estimate coefficients of dispersivity and retardation. For the amine functionalized NPs (which exhibited inhibited transport), a better model fit was obtained when permanent attachment (deposition) was incorporated into the model as opposed to nonpermanent attachment (retardation). This technology can be used to further explore transport processes of NPs inside coarse-grained porous media, either by using the wide range of commercially available (super)paramagnetically tagged NPs or by using custom-made tagged NPs.

Quantifying the tensile strength of microbial mats grown over noncohesive sediments

Biofilms in marine and fluvial environments can comprise strong bacterial and diatom mats covering large areas of the bed and act to bind sediments. In this case the bed material becomes highly resistant to shear stresses applied by the overlying fluid motion and detachment, when it does occur, is manifest in patches of biofilm of the order cm(2) being entrained into the flow. This article is the first to report tensile test data specific to the centimeter scale using moist biofilm/sediment composite materials; the strain (ε)-stress (σ) relationships permit quantification of the elasticity (Young's modulus, E) and cohesive strength of each specimen. Specifically, we compare the mechanical strength of cyanobacterial biofilm-only samples to that of biofilm cultured over sediment samples (glass beads or natural sands of d ~ 1 mm) for up to 8 weeks. The range of tensile strength (1,288-3,283 Pa) for composite materials was up to three times higher than previous tensile tests conducted at smaller scale on mixed culture biofilm [Ohashi et al. (1999) Water Sci Technol 39:261-268], yet of similar range to cohesive strength values recorded on return activated sludge flocs [RAS; Poppele and Hozalski (2003) J Microbiol Methods 55:607-615]. Composite materials were 3-6 times weaker than biofilm-only samples, indicating that adhesion to sediment grains is weaker than cohesion within the biofilm. Furthermore, in order to relate the tensile test results to the more common in-situ failure of bio-mats due to shear flow, controlled erosion experiments were conducted in a hydraulic flume with live fluid flow. Here, the fluid shear stress causing erosion was 3 orders of magnitude lower than tensile stress; this highlights both the problem of interpreting material properties measured ex-situ and the need for a better mechanistic model of bio-mat detachment.

Towards the design of diversity: stochastic models for community assembly in wastewater treatment plants

We believe that the engineering of wastewater treatment systems would be improved if we could predict and manipulate the composition, that is, the diversity of such systems. This ability would complement our established ability to predict the size of treatment communities. The theoretically based design of diversity in wastewater treatment systems is held by some to be unnecessary and by others to be impossible. In this paper we point to important phenomena in wastewater treatment, such as acclimation, adaptation and functional redundancy that would benefit from the ability to confidently design diversity. We set out a rationale and a mathematical framework for a stochastic approach to the design of diversity and show that, in principle, this approach works with two important functional groups in wastewater treatment. The implications for design and theory are briefly discussed.