Biology subjects

Schubert, H.

Publications and source records attributed to Schubert, H..

14 recordsLinked to original sources

bioRxiv2026

Local Temperature and Humidity are Associated with Proportion of Antimicrobial-Resistant Escherichia coli isolates in Farm Environments: Considerations for On-Farm Surveillance

Evidence suggests that increased local temperatures are associated with higher prevalence of antimicrobial resistance (AMR) in environmental bacteria. This study investigates the association between local climate and the proportion of antimicrobial-resistant Escherichia coli isolated from 2,766 farm environment samples from 53 English dairy farms. To do this, a non-linear Bayesian model that specifically accounts for decreased test sensitivity at low E. coli abundance was developed and used to estimate the proportion of isolates resistant to four antimicrobials (amoxicillin, cephalexin, streptomycin and tetracycline) from colony count data. Mean 7-day temperature and relative humidity at the farm location was modelled using a generalised additive model formulation. A higher proportion of E. coli isolates were resistant to cephalexin and streptomycin in samples collected from adult cow collecting yards, than heifer housing sheds. In contrast, a greater proportion of E. coli isolates from heifer housing sheds were resistant to amoxicillin and tetracycline. Evidence that local temperature is associated with an increase in the proportion of E. coli isolates resistant to streptomycin (20{degrees}C increase associated with a 5.0-fold increase; 95% CI: 1.03-33.0) and tetracycline (2.6-fold increase; 90% CI: 1.1-5.2) was observed. Additionally, relative humidity was associated with an increase in the proportion of isolates resistant to amoxicillin streptomycin and tetracycline. The influence of weather on the proportion of antimicrobial-resistant E. coli varied between samples collected from adult animals in collecting yards and heifers in housing sheds. These findings highlight the importance of considering weather conditions, sample characterises and seasonality when designing on-farm AMR surveillance systems. ImportanceUnderstanding how environmental conditions are associated with variability in AMR prevalence is critical for developing robust livestock AMR surveillance and anticipating the potential effects of climate change. The non-linear Bayesian modelling approach developed here adjusts for E. coli abundance associated variability in test sensitivity, enabling the influence of risk factors associated with the proportion of antimicrobial-resistant E. coli within samples to be more accurately estimated. Applying this approach to 2,766 faecal samples from 53 dairy farms in Southwest England indicated that the proportion of antimicrobial-resistant E. coli generally increased under warmer and wetter conditions. These findings suggest that environmental conditions can influence the prevalence of AMR E. coli in dairy farm environments and demonstrate the importance of accounting for weather related variability in livestock AMR surveillance. Adjusting for these associations in livestock AMR surveillance could improve the accuracy of modelling AMR trends and strengthen the assessment of climate-associated AMR risks.

microbiology↗

bioRxiv2024

The structure of full-length AFPK supports the ACP linker in a role that regulates iterative polyketide and fatty acid assembly

We present the full structures of two animal fatty acid synthase (FAS)-like polyketide synthases (AFPKs), PKS1 and PKS2 from Elysia chlorotica. Unlike the related FAS enzymes that use malonate to produce reduced lipids, EcPKS1 and EcPKS2 accept methylmalonyl-CoA to produce oxidized polypropionate products. When incubated with inhibitory malonyl-CoA (MC), the resulting EcPKS2(MC) structure revealed MC bound to the acyltransferase active site and the phosphopantetheinylated acyl carrier protein (ACP-pPant) bound to the ketosynthase (KS) active site. Remarkably, the entire linker from one modifying region to the ACP was visible in full-length EcPKS2(MC), revealing an asymmetric mega-enzyme structure. Mutations disrupting the affinity between the ACP linker and modifying domains altered substrate selectivity and active site selection, despite an expectation that the interactions are transient and that the wild-type linker alternates between the observed ordered and disordered conformations during the competing catalytic cycles of the homodimeric protein. A second structure, EcPKS2(AC), was acylated both on the KS catalytic cysteine and on the ACP-pPant. The ACP was docked at the dehydratase site, revealing further interactions between ACP and these FAS-like enzymes. The results suggest an unexpected role for the ACP linker in the control of substrate and product selectivity across the AFPK/FAS clade in animals and highlight ACP interfaces and mega-enzyme dynamics over the course of the catalytic cycle.

biochemistry↗

bioRxiv2024

Chara canescens part I: Oospore differentiation of parthenogenic and dioecious strains and salt-dependent oospore sizes

Chara canescens Loisel. is one of two European species of the section Desvauxia R.D. Wood of the genus Chara L. Whereas most populations of C. canescens reproduce parthenogenetically, a few sites with sexual reproducing populations are known. Studies of European C. canescens oospore morphology led to open questions about the taxonomic status. Here we investigated nearly 1000 oospores from 16 European populations originated from plant release, sediments, germination experiments and herbaria and two Asian populations resulting in a regional determination key for studied populations as well as important database implications regarding origin, oospore plant position and equipment used. The impact of salinisation on oospore morphology were tested by artificial salt levels. The longest but smallest oospores were formed at 3 PSU, whereas the widest at 0.1 PSU and the shortest at 5 PSU. Basal width and shape, on the other hand, seem to be only affected by higher salt contents. This study contributes the lacking oospore-information for both reproduction modes of European of C. canescens - populations.

plant biology↗

bioRxiv2023

The cell walls of different Chara species (Charophyceae) are characterized by branched galactans rich in 3-O-methylgalactose and absence of arabinogalactan-proteins

Streptophyte algae are the closest relatives of land plants and their latest common ancestor performed the most drastic adaptation that happened in plant evolution around 500 million years ago: the conquest of land. Beside other adaptations, this step required changes in cell wall composition. Today knowledge on cell walls of streptophyte algae and especially presence of arabinogalactan-proteins (AGPs), which are important signaling molecules of all land plants, is limited. To get deeper insights in cell walls of streptophyte algae, especially of the Charophyceae, we performed sequential cell wall extractions of four Chara species. The three species Chara globularis, Chara subspinosa and Chara tomentosa revealed comparable cell wall compositions with pectins, xylans and xyloglucans, whereas Chara aspera was outstanding with higher amounts of uronic acids in the pectic fractions and lack of reactivity with antibodies binding to xylan- and xyloglucan epitopes. Search for AGPs in the four Chara species and also Nitellopsis obtusa revealed presence of galactans with pyranosidic galactose in 1,3-, 1,6- and 1,3,6-linkage, which are typical galactan motifs of land plant AGPs. A unique feature of these branched galactans were high portions of 3-O-methylgalactose. Only Nitellopsis contained substantial amounts of Ara. Bioinformatic search for prolyl-4-hydroxylase necessary for biosynthesis of AGPs revealed one possible functional sequence in the genome of Chara braunii, but no hydroxyproline could be detected in the four Chara species and Nitellopsis obtusa. We conclude that AGPs typical for land plants are absent at least in these members of the Charophyceae.

plant biology↗

bioRxiv2023

Photosynthetic response of Chara braunii towards different bicarbonate concentrations

A variety of inorganic carbon acquisition modes have been proposed in Characean algae, however, the specific inorganic carbon uptake mechanism is unknown for the genus Chara. In the present study, we analyzed if C. braunii can efficiently use HCO3- as a carbon source for photosynthesis. For this purpose, C. braunii was exposed to different concentrations of NaHCO3- for different time scales. The photosynthetic electron transport through photosystem I (PSI) and II (PSII), the maximal electron transport rate (ETRmax), the efficiency of the electron transport rate (, the initial slope of the ETR), and the light saturation point of photosynthesis (Ek) were evaluated. Additionally, pigment contents (chlorophyll a, chlorophyll b, and carotenoids) were determined. Bicarbonate addition positively affected ETRmax after direct HCO3- application of both PSII and PSI, but this effect decreased after 1 h and 24 h. Similar trends were seen for Ek, but no significant effect was observed for . Pigment contents showed no significant changes in relation to different HCO3- concentrations. To evaluate if cyclic electron flow around PSI was involved in active HCO3- uptake, the ratio of PSI ETRmax/PSII ETRmax was calculated but did not show a distinctive trend. These results suggest that C. braunii can utilize NaHCO3- in short time periods as a carbon source but relies on other carbon acquisition mechanisms over prolonged time periods. These observations differentiate C. braunii from other examined Chara spp. and suggest a minor direct role of HCO3- as a carbon source for photosynthesis in this alga.

plant biology↗

bioRxiv2022

Plastid DNA sequences and oospore characters of some European species of Tolypella section Tolypella (Obtusifolia, Characeae) indicate a new cryptic Tolypella species from the Mediterranean island Sardinia

In Europe, the genus Tolypella (Characeae) comprises four to eight Tolypella species in sections Rothia and Tolypella that have been distinguished by vegetative morphology and gametangial characters such as antheridial size and oospore cell wall ornamentation. However, morphological species differentiation is difficult in some cases due to overlapping and variable vegetative features, which in many cases are difficult to observe clearly. To clarify the taxonomic status of the five European species of Tolypella in section Tolypella, sequence data of the plastid genes atpB, rbcL and psbC for Tolypella glomerata (Desv.) Leonh., Tolypella hispanica Allen, Tolypella nidifica (O.F. Mull.) A. Braun, Tolypella normaniana (Nordst.) Nordst. and Tolypella salina Cor. were combined with data on oospore morphology, including oospore wall ornamentation. Gene sequence data identified five distinct clusters, but they differed from the morphologically identified five species. T. glomerata consisted of some of the samples morphologically identified as T. glomerata and seven samples of T. normaniana, while the remaining T. glomerata samples clustered with specimens of unclear affiliation ("Tolypella. sp."). T. hispanica I consisted of samples from various locations, whereas "T. hispanica II" consisted of samples of T. hispanica from the Mediterranean island, Sardinia. The remaining cluster consisted of all the specimens that had been determined as T. salina or T. nidifica in addition to two specimens of T. normaniana. Oospore morphology was most clearly distinguishable for T. glomerata. Oospore characteristics for all other taxa were not as informative but showed some geographical and/or environmentally influenced differences, especially for T. nidifica and T. salina. Our results suggest a significantly different taxonomy of Tolypella sect. Tolypella in which specimens normally identified as T. glomerata might be two different species, T. glomerata and an unidentified species; T. nidifica and T. salina are not separate species; T. normaniana is a diminutive variant of T. nidifica or T. salina; and T. hispanica comprises two different species, one from the Mediterranean island Sardnia.

plant biology↗

bioRxiv2022

Mesopredator-mediated trophic cascade can break persistent phytoplankton blooms in coastal waters

Managing eutrophied systems only bottom-up (nutrient decreases) can be economically and ecologically challenging. Top-down controls (consumption) were sometimes found to effectively control phytoplankton blooms. However, mechanistic insights, especially on possible trophic cascades, are less understood in brackish, species-poor coastal waters, where large cladocera are absent. In this study, we set-up large mesocosms for three consecutive years during growth season. One set of mesocosms was controlled by mesopredator (gobies and shrimp), whereas the other mesocosms had no such mesopredator present. The results were standardized to monitoring data of the ecosystem to denote possible differences between treatments and the system. We found that mesopredator mesocosms showed lower turbidity, phytoplankton biomass, and nutrients compared to no-mesopredator mesocosms and the ecosystem. This decrease allowed macrophytes to colonize water depths only sparsely colonized in the ecosystem. Rotifer biomass increased in mesopredator mesocosms compared to the ecosystem and no-mesopredator mesocosms. Likewise, copepod biomass that potentially grazes upon rotifers and other microzooplankton decreased in mesopredator mesocosms. No-mesopredator mesocosms were colonized by an omnivorous mesograzer (Gammarus tigrinus), potentially creating additional pressure on macrophytes and increasing grazing-mediated nutrient release. Zooplankton was not able to control the non-nutrient limited phytoplankton. We propose a new mechanism, where a higher mesopredator density will increase grazing on phytoplankton by promoting microzooplankton capable of grazing on picophytoplankton. This proposed mechanism would contrast with freshwater systems, where a decrease of zooplanktivorous fish would promote larger phytoplankton grazer like cladocera. Biomanipulation in such species-poor eutrophic coastal waters may be more successful, due to less trophic pathways that can cause complex top-down controls. Stocking eutrophic coastal waters with gobies and shrimps may be an alternative biomanipulative approach rather than selectively remove large piscivorous or omnivorous fish from eutrophic coastal waters.

ecology↗

bioRxiv2021

Factors Influencing the Detection of Antibacterial Resistant Escherichia coli in Faecal Samples from Individual Cattle

AimsTo investigate whether on-farm antibacterial usage (ABU), environmental antibacterial resistant (ABR) Escherichia coli prevalence, and sampling and sample handling methodologies are associated with ABR E. coli positivity in individual faecal samples from dairy heifers. Methods and ResultsThree hundred and sixty-four heifers from 37 farms were sampled via rectal or faecal pat sampling. Samples were stored at -80{degrees}C for variable periods before microbiological analysis. Data analysis was through a multilevel, multivariable logistic regression approach. Individual rectal samples had increased odds of positivity for amoxicillin, cefalexin and tetracycline-resistant E. coli. Sample storage for 6-12 month was associated with decreased odds of finding amoxicillin and tetracycline-resistant E. coli. On-farm ABU had little influence, and environmental ABR E. coli prevalence had no significant influence on on the odds of sample-level positivity for ABR E. coli. ConclusionsSampling methodology and sample handling have a greater association than on-farm factors with the detection of ABR E. coli in individual faecal samples from dairy heifers. Significance and Impact of the StudySampling and storage methodologies should be considered carefully at the point of designing ABR surveillance studies in livestock and their environments and, where possible, standardised between and within future studies.

microbiology↗

bioRxiv2021

Fluoroquinolone-Resistant Escherichia coli Originating on Dairy Farms are an Infrequent Cause of Bacteriuria in Humans Living in the Same Geographical Region

SynopsisO_ST_ABSBackgroundC_ST_ABSOur primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms were a significant cause of bacteriuria in humans living in the same 50 x 50 km geographical region located in South West England. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms. MethodsFQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularisation approach. ResultsOf 489 FQ-R human isolates, 255 were also 3rd generation cephalosporin-resistant (3GC-R), with strong genetic linkage between aac(6)Ib-cr and blaCTX-M-15. We identified possible farm-to-human sharing for pairs of ST744 and ST162 isolates, but core genome SNP distances (71 and 63, respectively) were smaller in pairs of ST744 and ST162 isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli while total dry cow therapy use showed a negative association. ConclusionsThis work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population, however, this appears greater than observed for 3GC-R E. coli when studied in parallel. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli, and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.

microbiology↗

bioRxiv2019

Molecular epidemiology of cefotaxime-resistant Escherichia coli from dairy farms in South West England identifies a dominant plasmid encoding CTX-M-32

Third-generation cephalosporin resistance (3GC-R) in Escherichia coli is a rising problem in human and farmed animal populations. We conducted whole genome sequencing analysis of 138 representative 3GC-R isolates previously collected from dairy farms in South West England and confirmed by PCR to carry acquired 3GC-R genes. This analysis identified blaCTX-M (131 isolates: encoding CTX-M-1, -14, -15, -32 and the novel variant, CTX-M-214), blaCMY-2 (6 isolates) and blaDHA-1 (one isolate). A highly conserved plasmid was identified in 73 isolates, representing 27 E. coli sequence types. This novel ~220 kb IncHI2 plasmid carrying blaCTX-M-32 was sequenced to closure and designated pMOO-32. It was found experimentally to be stable in cattle and human transconjugant E. coli even in the absence of selective pressure and was found by multiplex PCR to be present on 26 study farms representing a remarkable range of transmission over 1500 square kilometres. However, the plasmid was not found amongst human urinary E. coli we have recently characterised from people living in the same geographical location, collected in parallel with farm sampling. There were close relatives of two blaCTX-M plasmids circulating amongst eight human and two cattle isolates, and a closely related blaCMY-2 plasmid found in one cattle and one human isolate. However, phylogenetic evidence of recent sharing of 3GC-R strains between farms and humans in the same region was not found. ImportanceThird-generation cephalosporins (3GCs) are critically important antibacterials and 3GC-resistance (3GC-R) threatens human health, particularly in the context of opportunistic pathogens such as Escherichia coli. There is some evidence for zoonotic transmission of 3GC-R E. coli through food, but little work has been done examining possible transmission (e.g. via interaction of people with the local near-farm environment). We characterised acquired 3GC-R E. coli found on dairy farms in a geographically restricted region of the United Kingdom and compared these with E. coli from people living in the same region, collected in parallel. Whilst there is strong evidence for recent farm-to-farm transmission of 3GC-R strains and plasmids - including one epidemic plasmid that has a remarkable capacity to transmit - there was no evidence that 3GC-R found on study farms had a significant impact on circulating 3GC-R E. coli strains or plasmids in the local human population.

microbiology↗

bioRxiv2019

Characterisation of AmpC Hyper-Producing Escherichia coli from Humans and Dairy Farms Collected in Parallel in the Same Geographical Region

ObjectivesTo characterise putative AmpC hyper-producing 3rd generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships as well as to identify risk factors for their presence; to assess evidence for their zoonotic transmission into the local human population\n\nMethodsProteomics was used to explain differences in antimicrobial susceptibility. Whole genome sequencing allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors.\n\nResultsIncreased use of amoxicillin-clavulanate was associated with an increased risk of finding AmpC hyper-producers on farms. Expansion of cephalosporin resistance in AmpC hyper-producers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring 4th generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyper-producers but there was no evidence for acquisition of farm isolates by members of the local human population.\n\nConclusionsIn this two-year surveillance study of 53 dairy farms, AmpC hyper-production was the cause of cefotaxime resistance in 46.2% of E. coli. There was evidence of recent farm-to-farm transmission and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce 3rd generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyper-producers. The finding that amoxicillin-clavulanate use was associated with increased risk of finding AmpC hyper-producers is important because this is not currently categorised as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.

microbiology↗

bioRxiv2019

Evidence for reduced CTX-M carriage in cattle-associated Escherichia coli at low temperatures and on publicly accessible farmland: implications for surveillance and potential for farm-to-human transmission

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g. CTX-M {square}-lactamase-positive Escherichia coli). Here, we collected samples, monthly over a two-year period, on 53 dairy farms in the South West of England, and data for 610 variables concerning antimicrobial usage, management practices and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin streptomycin and tetracycline, respectively, in 2754/4145 (66%), 263/4145 (6%), 1475/4145 (36%) and 2874/4145 (69%) of all samples from faecally contaminated sites. E. coli positive for blaCTX-M were detected in 224/4145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibiotic dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with increased odds of blaCTX-M positivity. Low temperature was associated with reduced odds of blaCTX-M E. coli positivity in samples and to reduced odds of finding E. coli resistant to each of the four test antibacterials. This was additional to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had increased odds of having E. coli resistance to each antibacterial or positive for blaCTX-M. Samples collected on pastureland had reduced odds of having E. coli resistant to amoxicillin or tetracycline, and being positive for blaCTX-M. ImportanceAntibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including to track the impacts of interventions aimed at reducing the prevalence of resistance. In this epidemiological survey of dairy farm antibacterial resistance, we show that local temperature, as it changes over the course of a year, is associated with the prevalence of antibacterial resistant E. coli. Also, that prevalence of resistant E. coli is higher in indoor environments and in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time-point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm with regard to the presence or number of resistant E. coli.

microbiology↗

bioRxiv2017

Evaluation of Metrics for Benchmarking Antimicrobial Use in the United Kingdom Dairy Industry

The issue of antimicrobial resistance is of global concern across human and animal health. In 2016 the UK government committed to new targets for reducing antimicrobial use (AMU) in livestock. However, though a number of metrics for quantifying AMU are defined in the literature, all give slightly different interpretations.\n\nThis paper reviews a selection of metrics for AMU in the dairy industry: total mg, total mg/kg, daily dose and daily course metrics. Although the focus is on their application to the dairy industry, the metrics and issues discussed are relevant across livestock sectors.\n\nIn order to be used widely, a metric should be understandable and relevant to the veterinarians and farmers who are prescribing and using antimicrobials. This means that clear methods, assumptions (and possible biases), standardised values and exceptions should be published for all metrics. Particularly relevant are assumptions around the number and weight of cattle at risk of treatment and definitions of dose rates and course lengths; incorrect assumptions can mean metrics over- or under-represent AMU.\n\nThe authors recommend that the UK dairy industry work towards UK-specific metrics using UK-specific medicine dose and course regimens as well as cattle weights in order to monitor trends nationally.

epidemiology↗

bioRxiv2017

Eelgrass leaf surface microbiomes are locally variable and highlycorrelated with epibiotic eukaryotes

Eelgrass (Zostera marina) is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes) as well as eukaryotic epibionts in-and outside lagoons on the German Baltic Sea coast. Bacterial microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both bacterial and eukaryotic community composition. Communities of bacterial and eukaryotic epibionts were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surface biofilms are a mosaic of the microbiomes of several eukaryotes, in addition to that of the eelgrass itself, and underlines that eukaryotic microbial diversity should be taken into account in order to explain microbiome assembly and dynamics in aquatic environments.

microbiology↗