SupplementaryInfo_Fowleretal_MBBR.docx from Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors

Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems

Biodegradation Kinetics of Fragrances, Plasticizers, UV Filters, and PAHs in a MixtureChanging Test Concentrations over 5 Orders of Magnitude

Biodegradation of organic chemicals emitted to the environment is carried out by mixed microbial communities growing on multiple natural and xenobiotic substrates at low concentrations. This study aims to (1) perform simulation type biodegradation tests at a wide range of mixture concentrations, (2) determine the concentration effect on the biodegradation kinetics of individual chemicals, and (3) link the mixture concentration and degradation to microbial community dynamics. Two hundred ninety-four parallel test systems were prepared using wastewater treatment plant effluent as inoculum and passive dosing to add a mixture of 19 chemicals at 6 initial concentration levels (ng/L to mg/L). After 1–30 days of incubation at 12 °C, abiotic and biotic test systems were analyzed using arrow solid phase microextraction and GC–MS/MS. Biodegradation kinetics at the highest test concentrations were delayed for several test substances but enhanced for the reference chemical naphthalene. Test concentration thus shifted the order in which chemicals were degraded. 16S rRNA gene amplicon sequencing indicated that the highest test concentration (17 mg C/L added) supported the growth of the genera Acidovorax, Novosphingobium, and Hydrogenophaga, whereas no such effect was observed at lower concentrations. The chemical and microbial results confirm that too high mixture concentrations should be avoided when aiming at determining environmentally relevant biodegradation data

Biodegradation in a Partially Saturated Sand Matrix: Compounding Effects of Water Content, Bacterial Spatial Distribution, and Motility

Bacterial pesticide degraders are generally heterogeneously distributed in soils, leaving soil volumes devoid of degradation potential. This is expected to have an impact on degradation rates because the degradation of pollutant molecules in such zones will be contingent either on degraders colonizing these zones or on pollutant mass transfer to neighboring zones containing degraders. In a model system, we quantified the role exerted by water on mineralization rate in the context of a heterogeneously distributed degradation potential. Alginate beads colonized by Pseudomonas putida KT2440 were inserted at prescribed locations in sand microcosms so that the initial spatial distribution of the mineralization potential was controlled. The mineralization rate was strongly affected by the matric potential (decreasing rate with decreasing matric potential) and by the initial distribution of the degraders (more aggregated distributions being associated with lower rates). The mineralization was diffusion-limited, as confirmed with a mathematical model. In wet conditions, extensive cell dispersal was observed for the flagellated wild type and, albeit to a lesser extent, for a nonflagellated mutant, partially relieving the diffusion limitation. Dry conditions, however, sustained low mineralization rates through the combined effects of low pollutant diffusivity and limited degrader dispersal

Antecedent Growth Conditions Alter Retention of Environmental <i>Escherichia coli</i> Isolates in Transiently Wetted Porous Media

The physical transport of Escherichia coli in terrestrial environments may require control to prevent its dissemination from potential high-density sources, such as confined animal feedlot operations. Biobarriers, wherein convective flows carrying pathogens pass through a porous matrix with high retentive capacity, may present one such approach. Eight environmental E. coli isolates were selected to conduct operational retention tests (ORT) with potential biobarrier materials Pyrax or dolomite, or silica glass as control. The conditions in the ORT were chosen to simulate conditioning by manure solutes, a pulse application of a bacterial load followed by rainfall infiltration, and natural drainage.Removal was limited, and likely caused by the relatively high velocities during drainage, and the conditioning of otherwise favorable adhesion sites. Flagella-mediated motility showed the strongest correlation to biobarrier retention. Significant variability was observed across the E. coli isolates, but consistently higher retention was observed for cells with external versus intestinal pregrowth histories. E. coli O157:H7 was retained the least with all examined matrices, while E. coli K-12 displayed moderate retention and may not serve as representative model strain. Pyrax is a good candidate biobarrier material given its superior removal ability across the tested E. coli strains

Evaluation of Bioaugmentation with Entrapped Degrading Cells as a Soil Remediation Technology

Soil augmentation with microbial degraders immobilized on carriers is evaluated as a potential remediation technology using a mathematical model that includes degradation within spatially distributed carriers and diffusion or advection-dispersion as contaminant mass transfer mechanisms. The total volume of carriers is a critical parameter affecting biodegradation performance. In the absence of advection, 320 and 20 000 days are required to mineralize 90% of the herbicide linuron by Variovorax sp. SRS16 encapsulated in 2 mm beads with 5 and 20 mm spacings, respectively. Given that many pesticide degraders have low intrinsic degradation rates and that only limited carrier to soil volume ratios are practically feasible, bioaugmented soils are characterized by low effective degradation rates and can be considered fully mixed. A simple exponential model is then sufficient to predict biodegradation as verified by comparisons with published experimental data. By contrast, the full spatially distributed model is needed to adequately model the degradation of faster degrading contaminants such as naphthalene and benzene which can be mass-transfer limited. Dimensionless Damköhler numbers are proposed to determine whether the spatially distributed model is required. Results show that field scale applications of immobilized degraders will be limited by the amount of carriers required to reach acceptable degradation rates

Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community

Wastewater treatment plants (WWTPs) have been suggested as reservoirs and sources of antibiotic resistance genes (ARGs) in the environment. In a WWTP ecosystem, human enteric and environmental bacteria are mixed and exposed to pharmaceutical residues, potentially favoring genetic exchange and thus ARG transmission. However, the contribution of microbial communities in WWTPs to ARG dissemination remains poorly understood. Here, we examined for the first time plasmid permissiveness of an activated sludge microbial community by utilizing an established fluorescent bioreporter system. The activated sludge microbial community was challenged in standardized filter matings with one of three multidrug resistance plasmids (pKJK5, pB10, and RP4) harbored by <i>Escherichia coli</i> or <i>Pseudomonas putida</i>. Different donor–plasmid combinations had distinct transfer frequencies, ranging from 3 to 50 conjugation events per 100000 cells of the WWTP microbial community. In addition, transfer was observed to a broad phylogenetic range of 13 bacterial phyla with several taxa containing potentially pathogenic species. Preferential transfer to taxa belonging to the predicted evolutionary host range of the plasmids was not observed. Overall, the ARG dissemination potential uncovered in WWTP communities calls for a thorough risk assessment of ARG transmission across the wastewater system, before identification of possible mitigation strategies

Additional file 3 of Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle

Additional file 3: Table S2: Overview of the genetic content of the recovered metagenome-assembled genomes

Additional file 1 of Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle

Additional file 1: Supplemental Information, Supplementary Figures and Table S3

Additional file 2 of Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle

Additional file 2: Table S1:  Quality,  abundance and taxonomy of the recovered metagenome-assembled genomes