Bacterial Indicators Research Articles

Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant.

The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.

Freshwater monitoring by nanopore sequencing.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

Variable fecal source prioritization in recreational waters routinely monitored with viral and bacterial general indicators

Somatic and F+ coliphage methods are under consideration as potential routine surface water quality monitoring tools to identify unsafe levels of fecal pollution in recreational waters. However, little is known about the cooccurrence of these virus-based fecal indicators and host-associated genetic markers used to prioritize key pollution sources for remediation. In this study, paired measurements of cultivated coliphage (somatic and F+) and bacterial (E. coli and enterococci) general fecal indicators and genetic markers indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal pollution sources were assessed in 365 water samples collected from six Great Lakes Basin beach and river sites over a 15-week recreational season. Water samples were organized into groups based on defined viral and bacterial fecal indicator water quality thresholds and average log10 host-associated genetic marker fecal score ratios were estimated to compare pollutant source inferences based on variable routine water quality monitoring practices. Eligible log10 fecal score ratios ranged from -0.051 (F+ coliphage, GFD) to 2.08 (enterococci, Rum2Bac). Using a fecal score ratio approach, findings suggest that general fecal indicator selection for routine water quality monitoring can influence the interpretation of host-associated genetic marker measurements, in some cases, prioritizing different pollutant sources for remediation. Variable trends were also observed between Great Lake beach and river sites suggesting disparate management practices may be useful for each water type.

Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.

The Clinical Characteristics and Risk Factors of Severe COVID-19

Objective: We aim to investigate the clinical characteristics and risk factors for the severe cases of coronavirus disease 2019 (COVID-19) in comparison with the non-severe patients. Methods: We searched PubMed, EMBASE, Web of Science, and CNKI to collect all relevant studies published before July 26, 2020, and a total of 30 papers were included in this meta-analysis. Results: In the severe COVID-19 patients, 60% (95% CI = 56–64%) were male, 25% (95% CI = 21–29%) were over 65 years old, 34% (95% CI = 24–44%) were obese, and 55% (95% CI = 41–70%) had comorbidities. The most prevalent comorbidities were hypertension (34%, 95% CI = 25–44%), diabetes (20%, 95% CI = 15–25%), and cardiovascular disease (CVD; 12%, 95% CI = 9–16%). The most common blood test abnormalities were elevated C-reactive protein (CRP; 87%, 82–92%), decreased lymphocyte count (68%, 58–77%), and increased lactate dehydrogenase (69%, 95% CI = 57–81%). In addition, abnormal laboratory findings revealing organ dysfunctions were frequently observed in the severe cases, including decrease in albumin (43%, 95% CI = 24–63%) and increase in aspartate aminotransferase (47%, 95% CI = 38–56%), alanine aminotransferase (28%, 95% CI = 16–39%), troponin I/troponin T (TnI/TnT; 29%, 95% CI = 13–45%), and serum Cr (SCr; 10%, 95% CI = 5–15%). Conclusion: The male, elderly and obese patients and those with any comorbidities, especially with hypertension, diabetes, and CVD, were more likely to develop into severe cases. But the association between hypertension, diabetes, CVD, and severity of COVID-19 was declined by the increase of age. A significant elevation in cardiac TnI/TnT, the hepatic enzymes, and SCr and the reduction in lymphocytes with elevated CRPs are important markers for the severity. Specific attention should be given to the elderly male and obese patients and those with indications of severe immune injury in combination with bacterial infection and indication of multi-organ dysfunction or damages.

Fate and persistence of antibiotic-resistant bacteria and genes through a multi-barrier treatment facility for direct potable reuse

Abstract Given the availability of technological solutions and guidelines for safe drinking water, direct potable reuse of reclaimed water has become a promising option to overcome severe lack of potable water in arid regions. However, the growing awareness of the presence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) in corresponding raw wastes has led to new safety concerns. This study investigated the fate of ARB and intracellular and extracellular ARG after each treatment step of an advanced water treatment facility in Windhoek, Namibia. The New Goreangab Water Reclamation Plant (NGWRP) produces drinking water from domestic secondary wastewater treatment plant effluent and directly provides for roughly a quarter of Windhoek's potable water demand. Procedures to study resistance determinants were based on both molecular biology and culture-based microbiological methods. TaqMan real-time PCR was employed to detect and quantify intracellular resistance genes sul1, ermB, vanA, nptII and nptIII as well as extracellular resistance gene sul1. The NGWRP reduced the amount of both culturable bacterial indicators as well as the resistance genes to levels below the limit of detection in the final product. The main ozonation and the ultrafiltration had the highest removal efficiencies on both resistance determinants.

Rumen bacterial community, indicators of reproduction and milk productivity at different levels of protein concentrate in the diets of dairy cows

The use of new sources of by-pass protein in the cow diets to optimize milk production and herd reproduction performance indicators in modern economic conditions is relevant. The article presents data on the use of a protein concentrate containing plant and animal components and its effect on the quality of the milk obtained, the state of the rumen bacterial community and reproduction indicators. The use of protein concentrate of both 1.0 kg and 1.5 kg/head/day contributed to improving the quality and increasing the yield of dry matter of cow's milk by 0.17-0.43 %. During the days in milk, with the use of protein concentrate it was observed that increase the content of Selenomonas by 1.7 % and 4.1%, which cleave the urea, indicates a more efficient use of nitrogen in the diet. The inclusion of protein concentrate in the composition of daily diets helps to improve reproduction indicators, reduce the duration of the service period and the number of semen doses spent.

Increased sanitization potency of hydrogen peroxide with synergistic O3 and intense pulsed light for non-woven polypropylene.

Supplies of respiratory masks have recently become a concern due to the onset of the SARS-CoV-2 pandemic. Sanitization and reuse of masks can alleviate high mask consumption and production stresses. In the present work, improved sanitization potency of vaporous hydrogen peroxide (VHP) treatment of resilient bacterial spores while retaining polymeric filter performance was explored. A batch fumigation chamber with hydrogen peroxide (H2O2) vapor and ozone (O3) is featured, followed by intense pulsed light (IPL) flash treatments. A resilient bacterial indicator, Geobacillus stearothermophilus (G. stearothermophilus), was utilized to compare the efficacy of various H2O2 concentrations in combination with O3 and IPL. It was found that exposure to 30 minutes of 4.01 L min−1 0.03% H2O2 aqueous vapor and 3 g h−1 O3 followed by 10 IPL flashes per side completely inactivated G. stearothermophilus. The xenon sourced IPL irradiation was found to synergistically enhance radical production and strengthen the complementary biocidal interaction of H2O2 with O3. Due to the synergistic effects, H2O2 was able to sanitize at a diluted concentration of 0.03% H2O2. The physical properties, such as surface potential, tensile strength, hydrophobicity, and filtration efficiency of >300 nm saline water aerosol of fibrous polypropylene (PP) sheets, were maintained. In addition, no residue of sanitizers was detected, thus confirming the biosafety and applicability of this method to disposable masks. Performance was benchmarked and compared with commercially available processes. The synergistic regime was found to achieve sterilization of G. stearothermophilus at drastically reduced H2O2 concentrations and in ambient conditions relative to commercial methods.

Bacterioplankton composition as an indicator of environmental status: proof of principle using indicator value analysis of estuarine communities

Increasing awareness of environmental impacts caused by anthropogenic activities highlights the need to determine indicators of environmental status that can be routinely assessed at large spatial and temporal scales. Microbial communities comprise the greatest share of biological diversity on Earth and can rapidly reflect recent environmental changes while providing a record of past events. However, they have rarely been targeted in the search for ecological indicators of habitat types, environmental conditions, or environmental changes. Here, as a proof of principle, we analysed the bacterioplankton community composition of 4 estuaries in North and South America, Europe, and Asia, and looked for indicators of groups of samples defined using partition techniques, according to primary physicochemical variables typically monitored to infer water quality. Indicator value analysis (IndVal) was conducted to identify indicator operational taxonomic units (OTUs; analogous to species in other fields of ecology) in each group. These bacterioplankton-based indicators exhibited a high capacity to predict the group membership of the samples within each estuary and to correctly assign the samples to the appropriate estuary in a combined data set, employing different machine learning techniques. The indicators were composed of OTUs belonging to several bacterial phyla, which responded significantly and differentially to the environmental variables used to define the groups of samples. Moreover, the predictive values of these bacterial indicators were generally higher than those of other biological assemblages commonly used for environmental monitoring. Therefore, this approach appears to be a promising tool to complement existing strategies for monitoring and conservation of aquatic systems worldwide.

The microbiome of the seagrass Halophila ovalis: community structuring from plant parts to regional scales

Seagrass meadows are critical marine ecosystems. They are significant carbon sinks and play numerous important roles in coastal areas. They help to prevent shoreline erosion and serve as nursery grounds for many marine species. Like their terrestrial counterparts, seagrasses form symbiotic relationships with diverse communities of bacteria that help to promote and maintain host fitness. In this study, we sampled the seagrass Halophila ovalis throughout Singapore and Peninsular Malaysia to characterise the associated bacterial communities and distributions in this acknowledged seagrass biodiversity hotspot. Three different parts of the seagrass (leaves, roots and rhizomes) were collected, and a sediment sample was collected in close proximity to each host. We used high-throughput 16S rRNA amplicon sequencing to examine the bacterial communities associated with each plant part and location. Our analyses indicated that bacterial assemblages associated with H. ovalis were distinct among locations, and different plant parts harboured divergent bacterial communities. We uncovered a significant distance-decay relationship, suggesting that dispersal limitations could explain the observed bacterial community structuring. We further identified bacterial indicator amplicon sequence variants (ASVs) that were associated with degraded or healthy seagrass meadows. The identification of indicator ASVs that are indicative of anthropogenically stressed seagrass, or a declining environment, could be used to implement proactive seagrass conservation and management schemes. This study addresses a current scientific gap within the characterisation of seagrass microbiomes, specifically of those from Southeast Asia, a region of acute seagrass losses, and provides a solid foundation for future seagrass research in the region.

Kondisi Pencemaran Lingkungan Berdasarkan Parameter Mikrobiologis di Sekitar Muara Sungai Cimandiri, Teluk Pelabuhan Ratu, Jawa Barat

The Gulf waters of Pelabuhan Ratu are important waters for fisheries and tourism. However, currently anthropogenic pollution carried by river flows threatens water quality, especially around the Cimandiri estuary. This study aims to analyze a water quality around Cimandiri estuary based on the abundance of fecal pollution indicator bacteria and patogenic bacteria on water samples taken from 15 stations. Fecal pollution indicator bacteria were enumerated using filtration method and plate count agar, while patogenic bacteria was detected using selective media and biochemical tests. The results of the study in March 2017 showed that domestic waste pollution occurred in Cimandiri estuary. The presence of pollution indicator bacteria colliform, E. coli and patogenic bacteria were found in the water column with varying density levels. The highest density of coliform bacteria was found in the mouth of Cimandiri estuary as much as 4.56x10 5 CFU / 100 ml and E. coli as much as 2.59x10 4 CFU/100 ml. Geomean of the total coliform bacteria and E. coli respectively 4.61x10 3 CFU/100 ml and 7.61x10 2 CFU/100 ml. The abundance of bacterial pollution indicators in Cimandiri Estuary has been already exceeded Indonesian water quality standard determined by the Ministry of Environment Decree. Patogenic bacteria i.e Vibrio sp. and Aeromonas sp. most found at Cimandiri Estuary.

Reduction and partitioning of viral and bacterial indicators in a UASB reactor followed by high rate algal ponds treating domestic sewage

Human enteric pathogens are a major global concern, as they are responsible for thousands of preventable deaths every year. New pathogens in wastewater are constantly emerging. For example, SARS-CoV-2 has been recently detected in domestic sewage and primary sludge. Knowledge about the reduction of viruses in wastewater treatment and their partitioning between the treated liquid effluent versus the sludge or biosolids is still very scarce, especially in countries with emerging economies and tropical climates. Upflow anaerobic sludge blanket (UASB) reactors are among the top three most commonly used technologies for the treatment of sewage in Latin America and the Caribbean, and their use has become increasingly common in many other low- and middle-income countries. High-rate algal ponds (HRAP) are regarded as a sustainable technology for the post-treatment of UASB effluent. This study evaluated the overall reduction and the liquid-solid partitioning of somatic coliphages, F-specific coliphages, and E. coli in a pilot-scale system comprised of a UASB reactor followed by HRAPs treating real wastewater. Average log removal for somatic and F-specific coliphages were 0.40 and 0.56 for the UASB reactor, and 1.15 and 1.70 for HRAPs, respectively. The overall removal of both phages in the system was 2.06-log. Removal of E. coli was consistently higher. The number of viruses leaving the system in the UASB solids and algal biomass was less than 10% of the number leaving in the clarified liquid effluent. The number of E. coli leaving the system in solids residuals was estimated to be approximately one order of magnitude higher than the number of E. coli leaving in the liquid effluent. Results from this study demonstrate the suitability of UASB-HRAP systems to reduce viral and bacterial indicators from domestic sewage and the importance of adequately treating sludge for pathogen reduction before they are used as biosolids.

A Review of Current and Emerging Approaches for Water Pollution Monitoring

The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.

Fate and removal of bacteria and antibiotic resistance genes in horizontal subsurface constructed wetlands: Effect of mixed vegetation and substrate type

This study aimed to investigate the influence of cropping method and substrate type on the fate and the removal of bacterial and antibiotic resistance genes (ARGs) indicators from primary wastewater by constructed wetlands (CWs) during startup and maturation stages. Four small-scale CWs differing in their plantation pattern (monoculture vs. polyculture) and substrate type were constructed and operated under field conditions. While for bacteria, the greatest impact of the cropping method and substrate type on removal was during the startup stage rather than the maturation stage, for ARGs, such impact was significant at both stages. During startup, the removal efficiencies of heterotrophic bacteria, fecal coliforms, E. coli, 16S rRNA genes and lacZ increased with the operation time. At maturation, the removal efficiencies were constant and were within the range of 89.2–99.4%, 93.7–98.9%, 89–98.8%, 94.1–99.6% and 92.9–98.7%, respectively. The removal efficiencies of intl1, tetM, intl1, sul1, ermB and total ARGs were also increased with the operation time. However, they were ARG type and configuration-dependent; at maturation they ranged between 50.7%–89.4%, 85.9%–97%, 49.6%–92.9%, 58.2%–96.7% and 79.9–94.3%, respectively. The tuff-filled serially planted CW was also the only one capable of removing these genes at similar high efficiency. Metagenomic analysis showed that none of the ARGs was among the most common ARGs in water and biofilm samples; rather most ARGs belonged to bacterial efflux transporter superfamilies. Although ARGs were removed, they were still detected in substrate biofilm and their relative concentrations were increased in the effluents. While the removal of both bacteria and ARGs was higher during summer compared to winter, the season had no effect on the removal pattern of ARGs. Hence, combination of the serial plantation with substrate having high surface area is a potential strategy that can be used to improve the performance of CWs.

FACTORS AFFECTING THE PERFORMANCE OF HORIZONTAL FLOW CONSTRUCTED WETLAND VEGETATED WITH CYPRUS PAPYRUS FOR MUNICIPAL WASTEWATER TREATMENT

The impact of hydraulic loading rate (HLR) and hydraulic retention time (HRT) on the bioremediation of municipal wastewater using a horizontal flow constructed wetland (HFCW) vegetated with Cyprus papyrus was investigated. Three different HLRs were applied with values of 0.18, 0.10 and 0.07 m3/m2.d with corresponding HRT of 1.8, 3.2 and 4.7 days. The flow rate was 8.3 m3/d and the average organic loading rate was 0.037kg BOD/m3/d. Results showed that the performance of HFCW is linearly affected by decreasing HLR and increasing the HRT. The remediation for the heights HRT (4.7) days and lowest HLR (0.07 m3/m2.d) produced high quality effluent in terms of reduction of chemical oxygen demand (COD; 86%), biochemical oxygen demand (BOD; 87%) and total suspended solids (TSS; 80%) as well satisfactory nutrient removal. Also, removal of 2-3 logs of bacterial indicators was achieved. The dry biomass of Cyprus papyrus was 7.7 kg/m2. Moreover, Cyprus papyrus plant proved to be very efficient in nitrification processes due to high diversity of the roots that increase the treatment surface area.

Chemically enhanced primary treatment of municipal wastewater with ferrate(VI).

Chemically enhanced primary treatment (CEPT) with ferrate(VI), a multifunctional treatment agent, was investigated for the treatment of municipal wastewater in a laboratory-scale study. The treatment performance was evaluated at different ferrate(VI) doses (0.0-9.0mg/L as Fe) and pH (6.0 and 7.5). The optimal removals of total suspended solids (TSS) (52%), total chemical oxygen demand (COD) (34%), and total phosphorus (47%) were achieved at the highest ferrate(VI) dose (9.0mg/L as Fe) and the weakly alkaline condition (pH 7.5). The pollutant abatements principally ascribed to the formation of large-sized aggregate and ensuing sedimentation fell within the reported ranges of CEPT with traditional coagulants. However, different from conventional CEPT, ferrate(VI) appreciably removed recalcitrant dissolved organic phosphorus (49%) and simultaneously inactivated total coliform (3.30 log removal) and Escherichia coli (3.67 log removal) at 9.0mg/L Fe(VI) and pH 7.5. The CEPT with ferrate(VI) offers an innovative alternative for improving municipal wastewater treatment. PRACTITIONER POINTS: Ferrate(VI) represents a promising agent for chemically enhanced primary treatment (CEPT) of municipal wastewater. CEPT with ferrate(VI) can effectively alleviate TSS, total COD, and total P via the formation of large-sized aggregates and ensuing sedimentation. Ferrate(VI) can substantially remove recalcitrant dissolved organic phosphorus in municipal wastewater. Different from other CEPT coagulants, ferrate(VI) can appreciably inactivate bacterial indicators during CEPT. Higher ferrate(VI) dose and weakly alkaline pH favor the performance of ferrate(VI) CEPT.

Comprehensive water testing analyses for improved water management: coliforms, coliphage and cholesterol

Abstract The use of faecal coliforms as indicators is the traditional approach of testing water quality. Unfortunately, for a comprehensive water quality analysis, there is an increasing body of evidence that demonstrates coliforms as insufficient indicators for water quality assessment. Therefore, during the last two decades, alternative water testing approaches such as the use of coliphage as well as cholesterol detection have gained popularity. In the present study, we evaluated and compared the reliability of data from three different indicators that included coliforms (Streptococcus), coliphage and cholesterol. Four sites were chosen for sample collection and these included one site from Haart river (HR1) and three sites from Barberspan (BP1, 2 and 3) in the North West Province of South Africa. Samples were collected during winter and summer seasons. Collected samples were subjected to different analyses for detection of coliphage, coliforms and cholesterol. Faecal indicator bacteria were detected at all sites and in some cases were relatively high (HR1: 287 cfu/100 mL faecal coliform and 228.6 cfu/100 mL faecal streptococci; BP1: 1,730 cfu/100 mL Escherichia coli). The HR1 site consistently had the highest levels of bacterial faecal indicators of the four sampling sites. Most notably, faecal streptococci were detected in higher numbers than any other bacterial indicator. A significant finding was the general higher levels of faecal indicator markers at the BP3. Based on the outcome of this study, a combination of these indicators offers a comprehensive and promising approach for monitoring water quality.

Microbiological Quality of Cooked Chicken: Results of Monitoring in England (2013 to 2017)

Results from monitoring of the microbiological quality of 2,721 samples of ready-to-eat cooked chicken collected between 2013 to 2017 in England were reviewed: 70% of samples were from retail, catering or manufacture and 30% were imported and collected at English ports. Samples were tested for a range of bacterial pathogens and indicator organisms. Six samples (<1%) had unsatisfactory levels of pathogens which were potentially injurious to health. Neither Salmonella nor Campylobacter were recovered from any sample. Two samples from catering settings contained either an unsatisfactory level of Bacillus cereus (5 x 10 6 CFU/g) or an unsatisfactory level of coagulase positive staphylococci (1.6 x 10 4 CFU/g). Listeria monocytogenes was recovered from 36 samples (one at manufacture, 26 at catering and nine at retail) and in four instances, unsatisfactory levels (≥10 2 CFU/g) were detected (three samples collected at catering and one at retail). For L. monocytogenes there were no significant differences between the rates of contamination with between the samples collected from ports, manufacture, retail supermarkets and other retailers (p = 0.288). There were no differences between the rates of contamination for other potential pathogens detected between samples from different settings. The prevalence of hygiene indicators ( Escherichia coli , Enterobacteriaceae and Aerobic Colony Counts) at import was significantly lower than in samples collected from manufacturers, retail or catering (p < 0.01). Samples collected from catering gave poorer results than all other settings. Regardless of the stage in the food chain, samples from Thailand and from other non-EU countries were of significantly better microbiological quality with respect to indicator organisms than those from the UK or from other EU countries (p = <0.001).

Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study

Environmental DNA metabarcoding of benthic bacterial communities emerged as a very powerful technology to assess environmental disturbance effects of coastal salmon aquaculture. A prerequisite for the implementation of this approach into compliance monitoring regulations is its robustness and reproducibility of obtained results. In the framework of regular compliance monitoring of a Scottish salmon farm, we therefore collected sediment samples along a transect from the salmon cages to reference sites in duplicates (biological replicates). Aliquots of both biological replicate samples were then processed by two different laboratories using independently the same eDNA metabarcoding protocol (technical replicates). Measures of alpha diversity and beta diversity, as well as taxonomic profiles of benthic bacterial communities were highly congruent among technical replicates, which even showed less variations then the biological replicates that were processed within each laboratory. Both technical replicate datasets identified the same bacterial indicator taxon groups and ASVs that are characteristic for the environmental quality (EQ) categories to which each of the samples was assigned based on traditional macroinvertebrate biomonitoring of the same samples. In a supervised machine learning (SML) approach, we could classify all individual samples from one technical replicate dataset into the correct EQ category using all samples of the other technical replicate dataset as a training dataset for the SML algorithm. We conclude that eDNA metabarcoding is sufficiently robust that different laboratories come to the same conclusions regarding officially regulated action criteria for environmental impact assessments in salmon aquaculture.

Environmental and microbial controls on microbial necromass recycling, an important precursor for soil carbon stabilization

There is an emerging consensus that microbial necromass carbon is the primary constituent of stable soil carbon, yet the controls on the stabilization process are unknown. Prior to stabilization, microbial necromass may be recycled by the microbial community. We propose that the efficiency of this recycling is a critical determinant of soil carbon stabilization rates. Here we explore the controls on necromass recycling efficiency in 27 UK grassland soils using stable isotope tracing and indicator species analysis. We found that recycling efficiency was unaffected by land management. Instead, recycling efficiency increased with microbial growth rate on necromass, and was highest in soils with low historical precipitation. We identified bacterial and fungal indicators of necromass recycling efficiency, which could be used to clarify soil carbon stabilization mechanisms. We conclude that environmental and microbial controls have a strong influence on necromass recycling, and suggest that this, in turn, influences soil carbon stabilization.