Long-term changes in soil microbial communities during primary succession

Soil microbial communities (SMCs) play a critical role in the cycling of carbon and nutrients in terrestrial ecosystems, as well as regulating plant productivity and diversity. However, very little is known about long-term (decades-centuries) structural changes in these communities. The development of aboveground-belowground linkages during century-scale succession is also poorly understood. Our study addressed this knowledge gap by investigating SMC and plant communities undergoing primary succession on an 850-year chronosequence of lava flows in Iceland. We hypothesised that communities of microfungi and bacteria would respond to progressive changes in vegetation and that SMC diversity would increase with terrain age. Soil samples were collected from three lava flows at different stages of primary succession (165, 621 and 852 years after lava flow emplacement). Plant community composition was surveyed as the samples were collected. The composition of the SMCs present in the soil was determined using amplicon pyrosequencing. The physical and chemical properties of the soil were also analysed. The results of the study indicated changes in plant and fungal communities with increasing terrain age. Distinct plant and fungal assemblages were identified on the three sites and both communities became richer and more diverse with increasing terrain age. There was also evidence to suggest the development of mycorrhizal associations on older sites. In contrast, the composition and structure of the bacterial communities did not change systematically with terrain age. Similarly, there were few changes in soil properties: SOM concentrations and pH, both of which have been demonstrated to be important to SMCs, were constant across the chronosequence. These results suggest that plant community composition is significant for fungal communities, but less relevant for bacterial communities. This finding has implications for studies of primary succession and the biogeochemical impact of vegetation change in high-latitude ecosystems.This work was funded by a Small Ecological Project Grant from the British Ecological Society (grant number 2812/3507) and grants from the John Fell Fund, University of Oxford (grant number 091/148) and Trinity College, University of Cambridge.This is the accepted manuscript. The final version is available at http://www.sciencedirect.com/science/article/pii/S003807171300429X

Using molecular and crowd‐sourcing methods to assess breeding ground diet of a migratory brood parasite of conservation concern

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordThe research data supporting this publication are openly available from Dryad at https://doi.org/10.5061/dryad.v6wwpzgsp and from NCBI Sequence Read Archive under BioProject number PRJNA606798Breeding ground food availability is critical to the survival and productivity of adult birds. The common cuckoo Cuculus canorus is a brood‐parasitic Afro‐Palearctic migrant bird exhibiting long‐term (breeding) population declines in many European countries. Variation in population trend between regions and habitats suggests breeding ground drivers such as adult food supply. However, cuckoo diet has not been studied in detail since before the most significant population declines in Europe began in the mid‐1980s. 20th century studies of cuckoo diet largely comprised field observations likely to carry bias towards larger prey taxa. Here we demonstrate the potential value of 1) using high‐throughput DNA sequencing of invertebrate prey in faeces to determine cuckoo diet with minimal bias towards large prey taxa, and 2) using crowd‐sourced digital photographs from across Britain to identify lepidopteran cuckoo prey taxa during recent years post‐decline (2005‐2016). DNA analysis found a high frequency of Lepidoptera, including moths of family Lasiocampidae, prominent within the past literature, but also grasshoppers (Orthoptera) and flies (Diptera) that may be overlooked by field observation methodologies. The range of larval lepidopteran prey identified from photographs largely agreed with those previously documented, with potential signs of reduced diversity, and identities of key adult prey taxa were supported by molecular results. Notably, many identified cuckoo prey taxa have shown severe declines due to agricultural intensification, suggesting this has driven spatial patterns of cuckoo loss. Landscape‐scale, lowland rewilding interventions provide opportunities to understand the scale of reversal of previous agricultural intensification that may be necessary to restore prey populations sufficiently to permit recolonization by cuckoos.Dartmoor National Park AuthorityNatural Environment Research Council (NERC)University of ExeterRoyal Society for the Protection of Birds (RSPB

The elderly in the psychiatric emergency service (PES); a descriptive study

<p>Abstract</p> <p>Background</p> <p>The impact of an aging population on the psychiatric emergency service (PES) has not been fully ascertained. Cognitive dysfunctions aside, many DSM-IV disorders may have a lower prevalence in the elderly, who appear to be underrepresented in the PES. We therefore attempted to more precisely assess their patterns of PES use and their clinical and demographic characteristics.</p> <p>Methods</p> <p>Close to 30,000 visits to a general hospital PES (Montreal, Quebec, Canada) were acquired between 1990 and 2004 and pooled with over 17,000 visits acquired using the same methodology at three other services in Quebec between 2002 and 2004.</p> <p>Results</p> <p>The median age of PES patients increased over time. However, the proportion of yearly visits attributable to the elderly (compared to those under 65) showed no consistent increase during the observation period. The pattern of return visits (two to three, four to ten, eleven or more) did not differ from that of patients under 65, although the latter made a greater number of total return visits per patient. The elderly were more often women (62%), widowed (28%), came to the PES accompanied (42%) and reported « illness » as an important stressor (29%). About 39% were referred for depression or anxiety. They were less violent (10%) upon their arrival. Affective disorders predominated in the diagnostic profile, they were less co-morbid and more likely admitted than patients under 65.</p> <p>Conclusion</p> <p>Although no proportional increase in PES use over time was found the elderly do possess distinct characteristics potentially useful in PES resource planning so as to better serve this increasingly important segment of the general population.</p

Metagenomic assessment of the diversity and ubiquity of antimicrobial resistance genes in Bangladeshi aquaculture ponds

This is the final version. Available on open access from Elsevier via the DOI in this recordData Availability: Raw sequencing reads were deposited in the ENA under BioProject PRJEB53918. Scripts for all bioinformatic processes are available on GitHub (https://github.com/ash-bell/Bangladesh_ARG_analysis/).In Bangladesh, fish provide over 60% of animal-source food with 56.2% of this coming from aquaculture produced predominantly in rural freshwater ponds. Increasing demand for fish products is driving intensification and resulting in higher disease prevalence, posing a risk to food security. Biosecurity is often absent in rural aquaculture practices in Bangladesh and antibiotics are commonly used to treat and prevent disease outbreaks. Antibiotics are often administered incorrectly - a key factor associated with the development of antimicrobial resistance (AMR). AMR can be disseminated rapidly within microbial ecosystems via mobile genetic elements, posing a risk for humans and animals infected with AMR pathogens as treatments with antibiotics become ineffective. Early AMR detection and understanding of the spread of antimicrobial resistance genes (ARGs) in rural aquaculture practices is critical for both food security, human health protection and food safety. Here, we apply a metagenomic approach to assess the ARG composition in pond water from six finfish (tilapia and pangasius) farms in the Mymensingh division of North-central Bangladesh. We found microbial communities within the ponds had similar alpha and beta diversities, with multiple ARGs predicted to confer resistance to eighteen different classes of antimicrobials. The most common ARGs conferred resistance to aminoglycosides and sulphonamides and were present in taxa associated with both fish and human pathogens. This ARG diversity potentially confers resistance to a wide variety of antibiotic classes and questions the effectiveness of current and future treatment of diseases with antibiotics in earthen aquaculture ponds. The microbial and ARG compositions between fish ponds within each farm were similar, which may relate to parallels in farming practices creating similar microbial selection pressures and thus comparable microbial populations. Without a more controlled approach towards antibiotic usage, we will inevitably further exacerbate the challenges in treating and preventing disease outbreaks as aquaculture production intensifies in Bangladesh.Biotechnology & Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC

The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

This is the final version. Available on open access from MDPI via the DOI in this recordData Availability: The raw RNA-seq data are available in the NCBI Sequence Read Archive under BioProject number PRJNA604966. The assembled genome sequence of Bangladesh TiLV isolate BD-2017 is available in NCBI GenBank, accession numbers MN939372-MN939381 (segments 1–10). QualiMap output from genome assembly is Supplementary data 1 and on Figshare, Viruses 2020, 12, 258 5 of 17 10.6084/m9.figshare.11812143. Multiple sequence alignments of partial segments 1, 2, 3, 4 and 9 are available as Supplementary data 2 and on Figshare, doi:10.6084/m9.figshare.11617563. Multiple sequence alignments of full coding regions of all ten segments are available as Supplementary data 3 and on Figshare, doi:10.6084/m9.figshare.11617545. Results from each quartet analysis are available as Supplementary data 4 and on Figshare, doi:10.6084/m9.figshare.11625774.Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.Newton FundDepartment for International DevelopmentIndian Department of BiotechnologyBiotechnology and Biological Sciences Research Council (BBSRC)Economic and Social Research Council (ESRC

Antimicrobial Resistance in Aquaculture Environments: Unravelling the Complexity and Connectivity of the Underlying Societal Drivers

This is the final version. Available on open access from the American Chemical Society via the DOI in this recordFood production environments in low- and middle-income countries (LMICs) are recognized as posing significant and increasing risks to antimicrobial resistance (AMR), one of the greatest threats to global public health and food security systems. In order to maximize and expedite action in mitigating AMR, the World Bank and AMR Global Leaders Group have recommended that AMR is integrated into wider sustainable development strategies. Thus, there is an urgent need for tools to support decision makers in unravelling the complex social and environmental factors driving AMR in LMIC food-producing environments and in demonstrating meaningful connectivity with other sustainable development issues. Here, we applied the Driver-Pressure-State-Impact-Response (DPSIR) conceptual framework to an aquaculture case study site in rural Bangladesh, through the analysis of distinct social, microbiological, and metagenomic data sets. We show how the DPSIR framework supports the integration of these diverse data sets, first to systematically characterize the complex network of societal drivers of AMR in these environments and second to delineate the connectivity between AMR and wider sustainable development issues. Our study illustrates the complexity and challenges of addressing AMR in rural aquaculture environments and supports efforts to implement global policy aimed at mitigating AMR in aquaculture and other rural LMIC food-producing environments.UK Government ODA-funded projectEngineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC)Global Challenges Research Fund (GCRF

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: Raw sequencing reads were deposited in the European Nucleotide Archive under the accession PRJEB46984. Data processing, analysis scripts and final ASV tables are accessible at https://github.com/jamiemcm/Malawi_Tilapia_MicrobiomesIntensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus the likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin — the most widely farmed finfish globally — and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provide the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset.Biotechnology & Biological Sciences Research Council (BBSRC)Newton FundWorldFis

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

Peer reviewedPublisher PD