Publications

This work investigated the microbial content of nodules from alders to determine how many ribotypes of Frankia were present and which, if any, other bacteria existed within nodes from the nodules. The bacterial content of alder nodules was investigated by 454 sequencing of 16S rDNA genes. Over half of the sequences were from a single ribotype of Frankia, with nearly all other sequences coming from the chloroplast of the host plant, and other sequences (including other ribotypes of Frankia) being at < 1%. It is concluded that a single ribotype of Frankia is the major, although not unique, bacterium present in an individual lobe from an alder nodule.

Wastewater-based epidemiology (WBE) is a powerful approach to study antimicrobial resistance (AMR) dynamics at the population level. Using genome-resolved metagenomics, we recovered 3978 metagenome-assembled genomes (MAGs) from archived metagenome sequences generated under the national wastewater surveillance programme across Wales, UK. Taxonomic profiling of MAGs revealed a diverse bacterial community, with significant compositional shifts observed across seasons and sample sources. Approximately 13.6 % of the MAGs carried one or more antimicrobial resistance genes (ARGs), with genes conferring resistance to tetracycline and oxacillin being the most prevalent within the wastewater microbiomes. We also recovered yet-uncultivated microbial genomes- often referred to as "microbial dark matter" harbouring clinically relevant ARGs, offering insights into previously uncharacterised resistance reservoirs in wastewater. ARG-host associations shifted between untreated influent and treated effluent, with effluent profiles also varying significantly between secondary and tertiary treatments, revealing the impact of treatment type on ARG host composition. This study represents the first comprehensive genome-resolved metagenomic characterisation of ARG carriers across both hospital and municipal wastewater in Wales, effectively bridging clinical and environmental compartments. Our findings highlight the need to integrate high-resolution genome-resolved metagenomic surveillance into national AMR monitoring frameworks to track emerging threats, characterise ARG reservoirs and inform targeted public health interventions.

No abstract is provided for this article.

Many studies have shown that the microbial biomass content in paddy soils is much higher than that in upland soils, but a comprehensive review of the underlying mechanisms and processes is lacking. We conducted a meta-analysis of published literature on the microbial biomass content in continuous paddy soils (>1700 data pairs) and paddy-upland rotation soils (>1100 data pairs) as compared to that in adjacent upland soils (>360 data pairs), measured by the fumigation extraction or fumigation incubation method. The microbial biomass carbon (MBC) content in paddy soils was double that in upland soils. This MBC surplus in paddy soils compared to upland soils was explained by (1) higher input of root C and rhizodeposits by rice plants compared with upland crops; (2) lower oxygen availability and consequently slower microbial turnover; (3) higher microbial C assimilation efficiency in paddy soils; and (4) additional C stabilization on iron (oxyhydr)oxides in paddy soils. The proportion of MBC in total soil organic C in paddy-upland rotation, paddy, and upland soils was 3.5%, 2.5%, and 2.1%, respectively. The higher microbial biomass C/N ratio in paddy soils (12.4 ± 0.11) compared to upland soils (9.9 ± 0.21) reflects greater N losses (through nitrate leaching and denitrification) in relation to slower C losses under anoxic conditions. Despite higher temperature and better water availability, microbial biomass turnover was 1.1–1.6 times slower in paddy soils than in upland soils because of oxygen limitation. Multiple stepwise regression and redundancy analyses showed that microbial biomass in continuous paddy and paddy-upland rotation soils was affected by similar soil factors (such as total N and organic C), whereas microbial biomass in upland soils was mainly affected by pH and the organic C content. Paddy-upland rotation soils undergo oxic–anoxic cycles and consequently can absorb and coprecipitate organic compounds with iron (oxyhydr)oxides as an additional advantage for C stabilization. We conclude that the reduced microbial activity and slower microbial turnover under oxygen-limited conditions lead to nearly two times higher microbial biomass content in paddy than in upland soils.

Carbon labels inform consumers about the amount of greenhouse gases (GHGs) released during the production and consumption of goods, including food. In the future consumer and legislative responses to carbon labels may favour goods with lower emissions, and thereby change established supply chains. This may have unintended consequences. We present the carbon footprint of three horticultural goods of different origins supplied to the United Kingdom market: lettuce, broccoli and green beans. Analysis of these footprints enables the characterisation of three different classes of vulnerability which are related to: transport, national economy and supply chain specifics. There is no simple relationship between the characteristics of an exporting country and its vulnerability to the introduction of a carbon label. Geographically distant developing countries with a high level of substitutable exports to the UK are most vulnerable. However, many developing countries have low vulnerability as their main exports are tropical crops which would be hard to substitute with local produce. In the short term it is unlikely that consumers will respond to carbon labels in such a way that will have major impacts in the horticultural sector. Labels which require contractual reductions in GHG emissions may have greater impacts in the short term.

The accurate detection of pathogens in environmental matrices, such as sediment, is critical in understanding pathogen fate and behavior in the environment. In this study, we assessed the usefulness of methods for the detection and quantification of

In the Amazonian region of Brazil, the combination of different inoculation forms of Azospirillum brasilense and N rates has not been studied for its effect on photosynthetic N use efficiency and yield in maize plants. The effects of inoculation forms of A. brasilense and N rates on photosynthetic N use efficiency and maize yield were evaluated. Two field trials were conducted, combining four N rates (0 to 180 kg ha−1) with different inoculation forms of A. brasilense (seed, leaf, or control). Photosynthetic N use efficiency (photosynthesis per unit leaf N) was taken at the beginning of tasseling stage, while yield and N use efficiency components were evaluated at physiological maturity. Photosynthesis and specific leaf N increased with increasing N rates, regardless of inoculation forms. Azospirillum-inoculated seeds, along with 114 kg ha−1 of N provided the maximum yield (6.0 Mg ha−1). Without N, seed inoculation increased yield by 33% and photosynthesis by 31% compared to the control. Averaged across N rates, seed inoculation increased photosynthetic N use efficiency by 17%–24% compared to the control. Azospirillum-inoculated seeds improved N use efficiency compared to the control under low N available. The results show that the Azospirillum-inoculated seeds could potentially decrease N rates from 180 to 114 kg ha−1 of N, while increasing yield by 9%. Besides, Azospirillum-inoculated seeds could enhance photosynthetic N use efficiency in a sustainable manner on low-fertility soils. Therefore, the benefits of the A. Brasiliense drive a sustainable agriculture by improving yield and reducing the need for N inputs.

&amp;lt;p&amp;gt;Afforestation with pure and mixed-species is an important strategy to improve soil organic carbon (SOC) stocks and restore degraded lands. However, what remains unclear is the stability of SOC to microbial degradation after afforestation and the effect of tree species composition. Moreover, it is important to reveal how sensitive the SOC in afforestation lands is to environmental changes, such as warming. To study the combined effects of warming and the tree species composition on decomposition of SOC by microorganisms and enzyme activities, soils were collected from the monocultural and mixtures of Silver birch (Betula Pendula) and European beech (Fagus Silvatica) (BangorDiversity, UK, 12 years since afforestation) and were incubated for 169 days at 0, 10, 20, 30 &amp;amp;#176;C at 60 % of WHC. The field experiment is arranged into a completely randomized design with n=4. The CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; efflux was measured constantly, whereas activities of &amp;amp;#946;-glucosidase, chitinase and acid phosphatase, and content of microbial biomass C (MBC) were obtained at the end of the incubation.&amp;amp;#160;Results showed that soil cumulative CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; efflux increased by 34.7&amp;amp;#8211;107% with the temperature. Potential enzyme activities were dependent on tree species composition. Warming, but not tree species exhibited a significant impact on the temperature sensitivity (Q10) of soil cumulative CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; efflux and enzyme activities. The greatest temperature sensitivity (Q&amp;lt;sub&amp;gt;10&amp;lt;/sub&amp;gt;) of total CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; efflux was found at 10&amp;amp;#8211;20 &amp;amp;#176;C and was 2.0&amp;amp;#8211;2.1, but that of enzyme activities were found as 0.9&amp;amp;#8211;1.1 at 0&amp;amp;#8211;10 &amp;amp;#176;C. These results suggest that warming has an asynchronous effect on the SOC decomposition and enzyme activity, and enzymes cannot account for the temperature sensitivity of soil respiration. Thus, thermal adaptations of SOC mineralization is independent of the adaptation of the enzyme pool.&amp;lt;/p&amp;gt;