Publications

Dissolved organic nitrogen (DON) is increasingly being recognized as a major component of the terrestrial nitrogen cycle, however, the factors that regulate its behaviour in soil remain poorly understood. The aim of this study was to investigate the impact of agricultural land use on the amount of DON in soil. At 94 sites, representing seven contrasting agricultural land use types, we extracted soil solution during the growing season. DON was high in all land use types constituting 57±8% of the total dissolved N (TDN) pool and generally followed the series citrus > vegetable > forest = arable > grassland = wetland > heathland . The TDN pool was dominated by DON in less intensive agricultural systems. In relative contrast to DON, the amount of dissolved inorganic N (DIN) varied widely upon land use with intensive agricultural systems being dominated by NO3 − and low input systems dominated by NH4 +. We conclude that DON represents a significant N pool in all agroecosystems but its concentration is less sensitive to land use system than DIN.

Soil microbial communities are drivers of carbon (C) and nitrogen (N) cycling in terrestrial ecosystems and provide early indicators of how management affects soil quality. Microbial community structure and function are affected by soil pH and N fertilization and may be affected by lime and gypsum, but there is a gap in the knowledge on the interaction with N, particularly in integrated systems. We evaluated the short-term effects of superficial lime and gypsum application along with N-fertilizer on soil properties and microbial communities, via phospholipid fatty acid profiling and Illumina 16S ribosomal RNA amplicon sequencing. Soil pH proved to be the most important characteristic regulating soil microbial structure in this tropical oxisol. In the absence of N fertilization, lime and gypsum alleviated acidity stress, decreased the Gram-positive to Gram-negative bacterial ratio (−8 %), and increased the fungal-to-bacterial ratio (+38 %). In addition, arbuscular mycorrhizal fungi (AMF) were enhanced (+36 %). Lime and lime+gypsum favored the relative abundance of important taxonomic groups involved in the N cycle. N-fertilizer application also increased the relative abundance of groups involved in N cycling, except for bacterial genera involved in N2 fixation. We conclude that alleviation of acid stress by the application of lime ± gypsum increased the relative abundance of beneficial microbial groups (i.e. AMF, Gram- and N cycling bacteria) resulting in shifts in microbial community composition, potentially promoting both C and N cycling.

Background: Microbial spatial distribution has been widely investigated in sediment. However, there is poorly available information on microbial distribution patterns in sediment of Bohai Sea coastal zone. Results: Here, we investigated the bacterial community composition and diversity in riverine and marine surface sediment around and in the Bohai Sea using high-throughput sequencing. Bacterial communities mainly comprised Proteobacteria, Bacteroidetes, and Firmicutes. Salinity, dissolved oxygen, pH, and magnetic susceptibility played the main role in determining bacterial α-diversity and community composition in this region. Of the total bacterial community composition variation, environmental factors (explained 29.41% of the total microbial community composition variation) played a more important role than spatial variables (explained 3.03%) in conditioning the bacterial community composition. Meanwhile, the significantly pure spatial effect and distance-decay tendency suggested that dispersal limitation was also an influential factor in shaping the bacterial biogeographical pattern. The presence of magnetite center might shape the geographical distribution of five genera Lactococcus , Clostridium , Caulobacter , Gillisia and Sphingomonas probably by affecting their iron-related geochemical cycle. Conclusion: Our results may provide a better understanding of present-day bacterial biogeography and the correlation between microbial communities and key environmental variables in a typical coastal area. Depending on these information, coastal resources could be efficiently predicted, assessed and used.

Antimicrobial resistance (AMR) is a global health challenge, with hospitals and wastewater treatment plants (WWTPs) serving as significant pathways for the dissemination of antibiotic resistance genes (ARGs). This study investigates the potential of wastewater-based epidemiology (WBE) as an early warning system for assessing the burden of AMR at the population level. In this comprehensive year-long study, effluent was collected weekly from three large hospitals, and treated and untreated wastewater were collected monthly from three associated community WWTPs. Metagenomic analysis revealed a significantly higher relative abundance and diversity of ARGs in hospital wastewater than in WWTPs. Notably, ARGs conferring resistance to clinically significant antibiotics such as β-lactams, aminoglycosides, sulfonamides, and tetracyclines were more prevalent in hospital effluents. Conversely, resistance genes associated with rifampicin and MLS (macrolides-lincosamide-streptogramin) were more commonly detected in the WWTPs, particularly in the treated effluent. Network analysis identified the potential bacterial hosts, which are the key carriers of these ARGs. The study further highlighted the variability in ARG removal efficiencies across the WWTPs, with none achieving complete elimination of ARGs or a significant reduction in bacterial diversity. Additionally, ARG profiles remained relatively consistent in hospital and community wastewater throughout the study, indicating a persistent release of a baseload of ARGs and pathogenic bacteria into surface waters, potentially polluting aquatic environments and entering the food chain. The study underscores the need for routine WBE surveillance, enhanced wastewater treatment strategies, and hospital-level source control measures to mitigate AMR dissemination into the environment.

Organic inputs to soils can accelerate soil organic matter (SOM) decomposition via so-called priming effects, but at the same time microbial biomass turnover can be accelerated – that will be termed as apparent priming effect. However, only a few studies have been set up to quantify the contribution of extra CO2 production from apparent priming. Here, we labeled the microbial biomass by 14C-glucose in pre-incubation and then added labile carbon (C; 12C or 14C glucose) and nitrogen (N; NH4 +) in soil and incubated over 120 days to investigate the contribution of apparent priming to total SOM priming. After 120 days of pre-incubation, 48 % of added glucose was released as CO2, and 34 % of added glucose was recovered in microbial biomass. After glucose addition, microbial biomass and salt extractable organic C were similar between glucose and water addition. However, glucose addition increased the contribution of 14C-glucose to microbial biomass by 2.5-folds and to CO2 by 10-folds. This increased contribution of 14C-glucose indicated accelerated microbial biomass turnover by labile C. Furthermore, 10 and 47 μg C g−1 of previously added and incorporated into microbial biomass 14C and 12C were replaced by new 14C, which contributed to 10 % and 33 % of primed CO2 emissions, respectively. On the contrary, N addition reduced previously added 14C in both microbial biomass pool and released CO2. This may reflect that the faster microbial turnover contributes to microbial necromass and further to stable SOM formation. Similar total apparent priming (∼1.5 μg C g−1 in 120 days, mainly in the first 20 days) was observed after glucose and N addition, which contributed around 1–4 % of total priming. Unlike after glucose and N additions, the 14C released as CO2 (8 % of the remaining previously added 14C-glucose) after water addition was mainly derived from reutilization of microbial necromass. This was supported by the absence of changes in either the 14C or total C in microbial biomass. Overall, the turnover of the microbial biomass pool – the apparent priming – should not be ignored, since microbial biomass acts not only as a major determinant of SOM turnover but also as a C pool.

Whilst the scale of food poisoning in the home is not fully understood, the increase in sporadic cases of Campylobacter continues to place focus on home hygiene and domestic food safety practices. Domestic hygiene has rarely been identified as a risk factor for the incidence of campylobacteriosis but due to the high levels of sporadic cases of Campylobacter, cross contamination from kitchen practices remains of significant interest. Due to the complexities of human nature, finding the true risk perceptions and practices that take place in the kitchen is challenging, with social desirability bias affecting the results of surveys and optimistic bias influencing risk perceptions. This study looks at self-reported kitchen behaviours and perceptions of people who have had campylobacteriosis in comparison to people who have not had food poisoning. It also investigates microbiological kitchen hygiene within a smaller sample. The survey crucially includes a longitudinal element to investigate any change that may take place after a period of six months has elapsed. Optimistic bias was evident in both groups and no significant difference in perception was noted in the baseline study. However, the longitudinal study showed that individuals who had not had food poisoning increased their optimism, introducing a significant difference in optimistic bias between the two groups after six months had elapsed. Self-reported kitchen behaviours also exhibited a difference between the two groups, with the individuals who had campylobacteriosis responding more favourably with the exception of washing chicken and washing salad leaves sold in a bag. No evidence of kitchen hygiene differences could be found between the people who had suffered campylobacteriosis in comparison to people who had not had food poisoning. The results of the survey demonstrate that more effective food safety communication is required. Important messages such as ‘not washing chicken’ seem not to have been absorbed and the good practices become routine. These messages need particularly to be aimed towards people who may not perceive themselves as being at risk of getting food poisoning, such as the young, although the challenge of changing the practice of those who perceive themselves to be at low risk remains.

Micro and macroplastics are emerging contaminants in agricultural settings, yet their impact on nitrogen (N) cycling and partitioning in plant-soil-microbial systems is poorly understood. In this mesocosm-scale study, spring barley (Hordeum vulgare L.) was exposed to macro or microplastic produced from low density polyethylene (LDPE) or biodegradable plastic at concentrations equivalent to 1, 10 and 20 years of plastic mulch film use. Partitioning of 15N-labelled fertiliser into plant biomass, soil and leachate yielded a partial mass balance. Soil N partitioning was probed via compound-specific 15N-stable isotope analyses of soil microbial protein. Concentration-dependent decreases in plant 15N uptake occurred with increased leached nitrogen for LDPE microplastic. Assimilation into soil microbial protein was higher for biodegradable plastics, which we associate with early-stage biodegradable plastic degradation. Partitioning of 15N into inorganic soil N pools was affected by LDPE size, with lower assimilation into the microbial protein pool. While microplastics and macroplastics altered soil N cycling, the limited impacts on plant health indicated the threshold for negative effects was not reached at agriculturally relevant concentrations. This study highlights the difference between conventional and biodegradable plastics, and emphasises that the interplay of micro and macroplastics on soil N cycling must be considered in future studies.

Contamination of water with the zoonotic pathogen Escherichia coli O157 can have severe public health implications and has led to many large disease outbreaks. Although the gastrointestinal tract of ruminants is the recognised reservoir of this organism, E. coli O157 can persist for significant periods of time in animal manure and contaminated soil, from where it can be transferred to watercourses during periods of heavy rainfall. Freshwater ecosystems are often at the interface between agriculture and the wider environment and can play an important role in human exposure to E. coli O157, e.g. though contaminating drinking water, recreational surface waters and shellfish harvesting areas. To mitigate the risk of disease outbreaks, it is essential to have a rapid, robust and reproducible method for the detection of waterborne E. coli O157. Because of the very low infective dose and the high background levels of non-target microbes, detection methods need to be extremely sensitive, and display a high level of specificity. In this review, we briefly outline the environmental pathways for the movement of E. coli O157 into watercourses, and critically assess the methods that are currently used to detect E. coli O157 in freshwater systems. Finally, we determine the suitability of each method for the rapid, accurate and affordable detection of waterborne E. coli O157 and consider some future directions for detecting human pathogens in the environment.

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