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This study describes microbial and chemical source tracking approaches for water pollution in rural and urban catchments. Culturable faecal indicator bacteria, represented by Escherichia coli, were quantified. Microbial source tracking (MST) using host-specific DNA markers was applied to identify the origins of faecal contamination. Chemical source tracking (CST) was conducted to determine contaminants of emerging concern (CEC) of human/anthropogenic origin, including pharmaceuticals and personal care products (PPCPs) and endocrine-disrupting chemicals (EDCs). In addition, the eutrophication-causing macronutrients nitrogen and phosphorus were studied. MST tests revealed both anthropogenic and zoogenic faecal origins, with a dominance of human sources in the urban stream; non-human/environmental sources were prevalent in the rural creek. CST analyses revealed a higher number of CECs in the urban stream than in the rural watercourse. Positive correlations between PPCPs and both E. coli and the human DNA marker were uncovered in the urban stream, while in the rural creek, PPCPs were only highly correlated with the anthropogenic marker. Interestingly, macronutrients were strongly associated with primary faecal pollution origins in both watercourses. This correlation pattern determines the main pollutant contributors (anthropogenic or zoogenic) to eutrophication.

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Summary Faecal contamination is one of the major factors affecting biological water quality. In this study, we investigated microbial taxonomic diversity of faecally polluted lotic ecosystems in Norway. These ecosystems comprise tributaries of drinking water reservoirs with moderate and high faecal contamination levels, an urban creek exposed to extremely high faecal pollution and a rural creek that was the least faecally polluted. The faecal water contamination had both anthropogenic and zoogenic origins identified through quantitative microbial source tracking applying host‐specific Bacteroidales 16S rRNA genetic markers. The microbial community composition revealed that Proteobacteria and Bacteroidetes (70–90% relative abundance) were the most dominant bacterial phyla, followed by Firmicutes, especially in waters exposed to anthropogenic faecal contamination. The core archaeal community consisted of Parvarchaeota (mainly in the tributaries of drinking water reservoirs) and Crenarchaeota (in the rural creek). The aquatic microbial diversity was substantially reduced in water with severe faecal contamination. In addition, the community compositions diverge between waters with dominant anthropogenic or zoogenic pollution origins. These findings present novel interpretations of the effect of anthropo‐zoogenic faecal water contamination on microbial diversity in lotic ecosystems. The aquatic microbial diversity was substantially reduced in water with severe faecal contamination. In addition, the community compositions diverge between waters with dominant anthropogenic or zoogenic pollution origins. These findings present novel interpretations of the effect of anthropo‐zoogenic faecal water contamination on microbial diversity in lotic ecosystems.

Purpose: Rice production in paddy soil is important for food security, and nitrogen fertilisation is important to achieve high yields. Digestate, the organic rest from biogas production can be a good fertilizer, but relatively little is known about its use in paddy soil, which is investigated here.Method: Nitrogen transformations and rice growth in soil waterlogged and at field capacity after application of digestate and digestate products were assessed in a pot experiment. Nitrogen transformations and nitrous oxide (N2O) emissions with the same digestates were also assessed in an incubation.Results: One of the tested digestates had as good fertilizer effect as urea. Nitrogen transformations went mostly as expected under given water status, but digestates were more affected by waterlogging than urea. Some instability appeared about 10 days after fertilizer application. Then nitrite levels were high, responsive microbial populations peaked and N2O emissions started. Whilst emissions after mineral fertilizer application (urea) were not affected by waterlogging, emission after application of one of the examined digestate was high at field capacity but almost zero under waterlogging. N2O emissions from all other digestate and water treatments were also low.Conclusion: Digestates have great potential as organic fertilizers in rice production, but N2O emissions under aerobic soil conditions are of concern and warrants further investigation and mitigation strategy.

Purpose: Soils are the largest store of carbon in the biosphere, but soils can also act as the key sources of greenhouse gases. Rice cultivation in paddy soil is anoxic, thus creating an optimal condition for methane production. Digestate, a potential biofertilizer, contains a microbial consortium adapted for methane production because it comes from biogas production where methane production is optimised. In this study, we explored digestate as fertiliser in paddy soil, focussing on the effects of carbon sequestration and methane emission.Method: A number of digestates and digestate products were incubated in the soils, both waterlogged and at field capacity. The effects of thermal treatment of the digestates were assessed to understand if the microbial community applied with the digestate played a role.Results: Carbon dioxide emission was 53% higher in the soil with a history of mineral fertiliser application, than in the soil with digestate application history under waterlogging, at field capacity it was 13% smaller. Methane emissions came later when the digestate was heat-treated, indicating that the microbial community in the digestate could change the timing of emissions, but not the amount. Otherwise, some digestates increased methane emissions, whilst others had little effect. The supply of available carbon appeared to be an important factor to explain differences.Conclusion: Digestate can increase carbon sequestration in paddy soil, although the interaction between waterlogging and soil history is not fully understood. The microbial community applied with the digestate can make methane emission start earlier, but it does not increase total emission.

To meet increasing demand for animal protein, swine have been raised in large Chinese farms widely, using antibiotics as growth promoter. However, improper use of antibiotics has caused serious environmental and health risks, in particular Antimicrobial resistance (AMR). This paper reviews the consumption of antibiotics in swine production as well as AMR and the development of novel antibiotics or alternatives in China. The estimated application of antibiotics in animal production in China accounted for about 84240 tons in 2013. Overuse and abuse of antibiotics pose a great health risk to people through food-borne antibiotic residues and selection for antibiotic resistance. China unveiled a national plan to tackle antibiotic resistance in August 2016, but more support is needed for the development of new antibiotics or alternatives like plant extracts. Antibiotic resistance has been a major global challenge, so international collaboration between China and Europe is needed.

Giant panda could have bamboo as their exclusive diet for about 2 million years because of the contribution of numerous enzymes produced by their gut bacteria, for instance laccases. Laccases are blue multi-copper oxidases that catalyze the oxidation of a broad spectrum of phenolic and aromatic compounds with water as the only byproduct. As a “green enzyme,” laccases have potential in industrial applications, for example, when dealing with degradation of recalcitrant biopolymers, such as lignin. In the current study, a bacterial laccase, Lac51, originating from Pseudomonas putida and identified in the gut microbiome of the giant panda’s gut was transiently expressed in the non-food plant Nicotiana benthamiana and characterized. Our results show that recombinant Lac51 exhibits bacterial laccase properties, with optimal pH and temperature at 7–8 and 40°C, respectively, when using syringaldazine as substrate. Moreover, we demonstrate the functional capability of the plant expressed Lac51 to oxidize lignin using selected lignin monomers that serve as substrates of Lac51. In summary, our study demonstrates the potential of green and non-food plants as a viable enzyme production platform for bacterial laccases. This result enriches our understanding of plant-made enzymes, as, to our knowledge, Lac51 is the first functional recombinant laccase produced in plants.

The aquatic microbiota is known to be an important factor in the sustainability of the natural water ecosystems. However, the microbial community also might include pathogens, which result in very serious waterborne diseases in humans and animals. Faecal pollution is the major cause of these diseases. Therefore, it is of immense importance to assess the potential impact of faecal pollution, originating from both anthropogenic and zoogenic sources, on the profile of microbial communities in natural water environments. To this end, the microbial taxonomic diversity of lotic ecosystems in different regions of Norway, representing urban and rural areas, exposed to various levels of faecal pollution, was investigated over the course of a 1-year period. The highest microbial diversity was found in rural water that was the least faecally polluted, while the lowest was found in urban water with the highest faecal contamination. The overall diversity of the aquatic microbial community was significantly reduced in severely polluted water. In addition, the community compositions diverged between waters where the dominant pollution sources were of anthropogenic or zoogenic origin. The results provide new insight into the understanding of how faecal water contamination, specifically that of different origins, influences the microbial diversity of natural waters.

Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.

Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.