Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling

The responses of microbial metabolic activity, bacterial community and resistance genes under the coexistence of nanoplastics and quaternary ammonium compounds in the sewage environment

Nanoplastics (NPs) and quaternary ammonium compounds (QACs) are frequently detected in sewage. However, little is known about the risks of coexistence of NPs and QACs. In this study, the responses of microbial metabolic activity, bacterial community and resistance genes (RGs) to the exposure of polyethylene (PE), polylactic acid (PLA), silicon dioxide (SiO₂) and dodecyl dimethyl benzyl ammonium chloride (DDBAC) were focused on 2nd and 30th day of incubation in sewer environment. Bacterial community contributed 25.01 % to shape RGs and mobile genetic elements (MGEs) after two days of incubation in sewage and plastisphere. After 30 days of incubation, the most important individual factor (35.82 %) was turned to microbial metabolic activity. The metabolic capacity of the microbial communities in plastisphere was stronger than that from SiO₂ samples. Moreover, DDBAC inhibited the metabolic capacity of microorganisms in sewage samples, and increased the absolute abundances of 16S rRNA in plastisphere and sewage samples which might be similar to the hormesis effect. After 30 days of incubation, Aquabacterium was the predominant genus in plastisphere. As for SiO₂ samples, Brevundimonas was the predominant genus. QACs RGs (qacEdelta1-01, qacEdelta1-02) and antibiotic RGs (ARGs) (aac(6')-Ib, tetG-1) significantly enriched in plastisphere. There was also co-selection among qacEdelta1-01, qacEdelta1-02 and ARGs. In addition, VadinBC27 which enriched in plastisphere of PLA NPs was positively correlated with the potentially disease-causing genus Pseudomonas. It showed that after 30 days of incubation, plastisphere had an important effect on distribution and transfer of pathogenic bacteria and RGs. Plastisphere of PLA NPs also carried the risk of spreading disease.

Dynamic responses of carbon metabolism of sediment microbial communities to Ag nanoparticles: Effects of the single and repeated exposure scenarios

The widespread use of nanosilver will inevitably lead to their release into aquatic environment, threating the health of freshwater ecosystem. The toxic effects of silver nanoparticles (AgNPs) on sediment microbial diversity, community composition, and functional enzyme activity are well established, while little is known about how sediment microbes dynamically respond to the stress of different AgNPs exposure scenarios. Herein, microcosm experiments were performed to investigate the impacts of repeated (1 mg/L, applied every 6 days for 10 times) and single (10 mg/L) exposure scenarios of AgNPs on the specific functions of sediment microbes (5-60 days). The carbon metabolism of sediment microbial communities was measured using BIOLOG ECO microplates, and carbon metabolic rate and functional diversity indices were calculated. Compared to control group, the maximum carbon source utilization capacity of the microbial community increased by 6.6 and 15.4 % in the single and repeated exposure group, respectively. And the metabolic rates of sediment microorganisms were significant increased by 6.1 % in the repeated exposure group, which suggested that repetitive low-dosing of AgNPs induce a larger alteration of both capacity and rate of microbial carbon metabolism. Notably, different AgNPs exposure scenarios resulted in a shift in the carbon source preference of the microorganisms. After exposure for 60 days, compared with the controls, the ability to utilize polymers was significantly increased by 51.5 and 21.7 % in the single and repeated exposure groups, respectively, and decreased by 33.7 and 10.5 % in the utilization of miscellaneous, both exhibiting significant differences (P < 0.05), implying that AgNPs exposure scenarios affected the microbial-mediated carbon cycling processes in sediment. These results highlight that different exposure scenarios of AgNPs have different effects on the carbon metabolism capacity of microbial communities, thus affecting the carbon cycling processes in which microorganisms are involved.

Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe

When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes-especially tet(M)-were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas.

New index of functional specificity to predict the redundancy of ecosystem functions in microbial communities

An ecosystem function is suggested to be more sensitive to biodiversity loss (i.e. low functional redundancy) when focusing on specific-type functions than broad-type functions. Thus far, specific-type functions have been loosely defined as functions performed by a small number of species (facilitative species) or functions involved in utilizing complex substrates. However, quantitative examination of functional specificity remains underexplored. We quantified the functional redundancy of 33 ecosystem functions in a freshwater system from 76 prokaryotic community samples over three years. For each function, we used a sparse regression model to estimate the number of facilitative Amplicon Sequence Variants (ASVs) and to define taxon-based functional specificity. We also used Bertz structural complexity to determine substrate-based functional specificity. We found that functional redundancy increased with the taxon-based functional specificity defined as the proportion of facilitative ASVs ( = facilitative ASV richness/ facilitative ASV richness + repressive ASV (ASVs reducing functioning) richness). When using substrate-based functional specificity, functional redundancy was influenced by Bertz complexity per se and by substrate acquisition mechanisms. Therefore, taxon-based functional specificity is a better predictive index for evaluating functional redundancy than substrate-based functional specificity. These findings provide a framework to quantitatively predict the consequences of diversity losses on ecosystem functioning.

The microbial metabolic activity on carbohydrates and polymers impact the biodegradability of landfilled solid waste

Biological waste degradation is the main driving factor for landfill emissions. In a 2-year laboratory experiment simulating different landfill in-situ aeration scenarios, the microbial degradation of solid waste under different oxygen conditions (treatments) was investigated. Nine landfill simulation reactors were operated in triplicates under three distinct treatments. Three were kept anaerobic, three were aerated for 706 days after an initial anaerobic phase and three were aerated for 244 days in between two anaerobic phases. In total, 36 solid and 36 leachate samples were taken. Biolog® EcoPlates™ were used to assess the functional diversity of the microbial community. It was possible to directly relate the functional diversity to the biodegradability of MSW (municipal solid waste), measured as RI₄ (respiration index after 4 days). The differences between the treatments in RI₄ as well as in carbon and polymer degradation potential were small. Initially, a RI₄ of about 6.5 to 8 mg O₂ kg^-1 DW was reduced to less than 1 mg O₂ kg^-1 DW within 114 days of treatment. After the termination of aeration, an increase 3 mg O₂ kg^-1 DW was observed. By calculating the integral of the Gompertz equation based on spline interpolation of the Biolog® EcoPlates™ results after 96 h two substrate groups mainly contributing to the biodegradability were identified: carbohydrates and polymers. The microbial activity of the respective microbial consortium could thus be related to the biodegradability with a multilinear regression model.

Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany

The contribution of fungi to the degradation of plant litter and transformation of dissolved organic matter (humic substances, in particular) in freshwater ecosystems has received increasing attention recently. However, the role of Saprolegniales as one of the most common eukaryotic organisms is rarely studied. In this study, we isolated and phylogenetically placed 51 fungal and 62 Saprolegniales strains from 12 German lakes. We studied the cellulo-, lignino-, and chitinolytic activity of the strains using plate assays. Furthermore, we determined the capacity of 10 selected strains to utilize 95 different labile compounds, using Biolog FF MicroPlates™. Finally, the ability of three selected strains to utilize maltose and degrade/produce humic substances was measured. Cladosporium and Penicillium were amongst the most prevalent fungal strains, while Saprolegnia, Achlya, and Leptolegnia were the most frequent Saprolegniales strains. Although the isolated strains assigned to genera were phylogenetically similar, their enzymatic activity and physiological profiling were quite diverse. Our results indicate that Saprolegniales, in contrast to fungi, lack ligninolytic activity and are not involved in the production/transformation of humic substances. We hypothesize that Saprolegniales and fungi might have complementary roles in interacting with dissolved organic matter, which has ecological implications for carbon cycling in freshwater ecosystems.

Bacterial diversity, community composition and metabolic function in Lake Tianmuhu and its dammed river: Effects of domestic wastewater and damming

Anthropogenic disturbances, such as pollution discharge and damming, can lead to a global decline in biodiversity in aquatic ecosystems. However, how such disturbances affect microbial community composition and function remains poorly understood. In November 2019, we explored bacterial diversity, community composition and metabolic function in Lake Tianmuhu, China, and in its upstream dammed river, using Illumina MiSeq sequencing and Biolog EcoPlate method based on carbon source utilization. Our results revealed higher variations in bacterial α- and β-diversity in the dammed river ecosystem than in the lake ecosystem. In addition, the dammed river and lake ecosystems were significantly different in bacterial community compositions and metabolic structures. No significant relationship between species richness and functional (metabolic) diversity was observed in this study. The site that was most impacted by domestic wastewater had the lowest taxonomic diversity but highest metabolic capacity and activity, suggesting that community composition rather than species diversity is more important in determining ecosystem functioning. Overall, our findings indicate that anthropogenic disturbances can significantly alter bacterial community and function, and taxonomic diversity is a weak proxy for ecosystem functioning in a natural freshwater habitat.

Distinct microbial metabolic activities of biofilms colonizing microplastics in three freshwater ecosystems

Concerns are growing about the increasing amounts of microplastics (MPs) and their ecological impacts, especially the influences of "plastisphere" in the freshwater ecosystems. Although the microbial structure and composition of biofilms are investigated, knowledge of their microbial functions remains limited. Herein, we investigated the functional diversity of carbon metabolism in biofilms colonizing one inert (glass) and two MPs as polyvinyl chloride (PVC) and polyethylene terephthalate (PET) substrates incubated for 44 days in situ in the Niushoushan River, the Qinhuai River, and Donghu Lake. 2D confocal laser scanning microscopy images visualized distinct micro-structures and biofilm compositions on three substrates. BIOLOG ECO microplates indicated variation on carbon utilization capacities of biofilms of inert and MPs in three freshwater ecosystems. Biofilms on PET showed lower capacities and carbon metabolism rates than those on glass and PVC, indicating the presence of substrate-specific functional diversity. The Shannon-Wiener diversity, Simpson diversity and Shannon evenness indices for the Niushoushan River and Donghu Lake were ordered as glass > PVC > PET. Besides to MPs-specific factors, environmental factors including nutrient (i.e., TN and TP) and turbidity largely shaped biofilm carbon metabolism. Overall findings demonstrated that as specific niches, MPs influenced microbial-mediated carbon cycling in the freshwater ecosystems and MPs-promoted microbial communities posed ecological significance.

Soil Bacterial Community Responds to Land-Use Change in Riparian Ecosystems

Riparian forests were frequently cleared and converted to agricultural pastures, but in recent times these pastures are often revegetated in an effort to return riparian forest structure and function. We tested if there is a change in the soil bacterial taxonomy and function in areas of riparian forest cleared for agricultural pasture then revegetated, and if soil bacterial taxonomy and function is related to vegetation and soil physicochemical properties. The study was conducted in six riparian areas in south-eastern Australia, each comprising of three land-use types: remnant riparian forest, cleared forest converted to pasture, and revegetated pastures. We surveyed three strata of vegetation and sampled surface soil and subsoil to characterize physicochemical properties. Taxonomic and functional composition of soil bacterial communities were assessed using 16S rRNA gene sequences and community level physiological profiles, respectively. Few soil physiochemical properties differed with land use despite distinct vegetation in pasture relative to remnant and revegetated areas. Overall bacterial taxonomic and functional composition of remnant forest and revegetated soils were distinct from pasture soil. Land-use differences were not consistent for all bacterial phyla, as Acidobacteria were more abundant in remnant soils; conversely, Actinobacteria were more abundant in pasture soils. Overall, bacterial metabolic activity and soil carbon and nitrogen content decreased with soil depth, while bacterial metabolic diversity and evenness increased with soil depth. Soil bacterial taxonomic composition was related to soil texture and soil fertility, but functional composition was only related to soil texture. Our results suggest that the conversion of riparian forests to pasture is associated with significant changes in the soil bacterial community, and that revegetation contributes to reversing such changes. Nevertheless, the observed changes in bacterial community composition (taxonomic and functional) were not directly related to changes in vegetation but were more closely related to soil attributes.

Microbial carbon metabolic functions of biofilms on plastic debris influenced by the substrate types and environmental factors

As an artificial type of microbial carrier, plastic debris has been widely detected in freshwater habitats, and the potential impacts of the plastisphere (biofilms colonized on plastics) in aquatic ecosystems have drawn increasing attention. Distinct community compositions and structures of biofilms in plastic and natural substrates have been recorded in freshwater environments. However, the microbial metabolic functioning of the plastisphere was underestimated, especially in freshwater environments. In this study, the effects of substrate types on the carbon metabolic functions of biofilms were studied by in situ cultivation of biofilms on plastics (polyvinyl chloride, PVC and polyethylene, PE) and natural substrate (cobblestone) for 44 days in two rivers (the Niushoushan River and the Qinhuai River) and two lakes (Donghu Lake and Xuanwu Lake). Biofilms on plastics showed higher biomasses than those on natural substrates in all ecosystems. Variations in the micro-structure and compactness of biofilms developed under different substrates were observed from scanning electron microscope and confocal laser scanning microscope image analyses. The carbon metabolic activities of the biofilms evaluated by BIOLOG EcoPlate were different between plastics (PVC and PE) and natural substrate (cobblestone) in the four freshwater ecosystems. In the Niushoushan River, PE-associated biofilms had different capacity in using carbon sources from cobblestone-associated biofilms as illustrated by the Shannon-Wiener diversity index and Shannon evenness index. Additionally, the metabolic functional diversity profiles of biofilms on PVC were significantly different from those on cobblestone in the other three aquatic ecosystems. Moreover, results from variation partitioning analysis suggested that the impact of environmental factors (contribution: 21%) on microbial carbon metabolic functions was much greater than that of substrate types (contribution: 6%). These findings illustrated distinct microbial functions of biofilms inhabited on plastics, and environmental factors play a decisive role in the differentiation and specificity of carbon metabolism of the plastisphere. This study offers new insights that plastics serving as artificial microbial niches have the ability to affect the microbial-mediated carbon cycling process in aquatic ecosystems.

Effects of wastewater disinfectants on the soil: Implications for soil microbial and chemical attributes

In most cases, chlorination is used for effluent disinfection. However, this process can lead to the formation of byproducts hazardous to the environment and public health. Therefore, new disinfectants, such as calcium hypochlorite (CH) and peracetic acid (PAA), were investigated as alternatives. This study aimed at determining doses of the disinfectants PAA and CH to be applied to the soil and analyzing the possible changes in the major chemical and microbiological attributes of the soil, thus encouraging the practice of reusing wastewater in agriculture. Initially, toxicity bioassays were conducted with lettuce (Lactuca sativa L.) seeds in order to determine which concentrations affected germination and also which would be analyzed. From these trials, three concentrations of each disinfectant were chosen to be subjected to basal respiration, microbial biomass carbon and metabolic quotient analyses. Doses of 3, 5 and 10 mg L^-1 were used for PAA, and concentrations of 25, 32 and 64 mg L^-1 for CH. Thus, it was observed that the greater concentration of each disinfectant provided a significant increase in the metabolic potential of microorganisms. However, it was observed that PAA increased ecotoxicity besides promoting changes in the chemical attributes of the soil, compared to CH. On the other hand, concentrations of 3 mg L^-1 and 25 mg L^-1 of PAA and CH, respectively, did not cause large impacts and could be an alternative in effluent disinfection with the aim of recycling it in agriculture.