Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.     

Towards a unified data infrastructure to support European and global microbiome research: a call to action

High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.     

Residual nitrogen contribution from grain legumes to succeeding wheat and rape and related microbial process

The residual N contribution from faba bean (Vicia faba L.), pea (Pisum sativum L.) and white lupin (Lupinus albus L.) to microbial biomass and subsequent wheat (Triticum aestivum L.) and oilseed rape (Brassica napus L.) was studied in a greenhouse experiment. The grain legumes were ¹⁵N labelled in situ with a stem feeding method before incorporated into the soil, which enables the determination of N rhizodeposition. Wheat and rape were subsequently grown on the soil containing the grain legume residues (incl. ¹⁵N-labelled rhizodeposits) and were harvested either twice at flowering and at maturity or once at maturity, respectively. The average total N uptake of the subsequent crops was influenced by the legume used as precrop and was determined by the residue N input and the N₂-fixation capacity of the legume species. The succeeding crops recovered 8.6–12.1% of the residue N at maturity. Similar patterns were found for the microbial biomass, which recovered 8.2–10.6% of the residue N. Wheat and rape recovered about the same amount of residue N. The absolute contribution of soil derived N to the subsequent crops was similar in all treatments and averaged 149 mg N pot^–1 at maturity. At flowering 17–23% of the residue derived N was recovered in the subsequent wheat and in the microbial biomass; 70% of the residue N was recovered in the microbial biomass in the flowering stage and decreased to about 50% at maturity. In contrast, the recovery in wheat and rape constituted only 30% at flowering and increased to 50% at maturity in all treatments, indicating that the residual N uptake by the subsequent wheat was apparently supplied by mobilisation of residue N temporarily immobilised in the microbial biomass.     

Recurrent soil freeze-thaw cycles enhance grassland productivity.

Ongoing global warming will increase the frequency of soil freeze-thaw cycles (FTCs) in cool-temperate and other high-latitude regions. The spatial relevance of seasonally frozen ground amounts to c. 55% of the total land area of the northern hemisphere. Evidence suggests that FTCs contribute to nutrient dynamics. Knowledge of their effects on plant communities is scarce, although plants may be the decisive factor in controlling ecosystem functions such as nutrient retention. Here, the effects are analysed of five additional FTCs in winter for the above- and below-ground productivity of experimental grassland communities and soil enzymatic activity over the following growing season. Freeze-thaw cycles increased the above-ground productivity but reduced root length over the whole subsequent growing season. In summer, no changes in soil enzymatic activities representing the carbon, nitrogen and phosphorus cycles were observed in the FTC-manipulated plots, except for an increased cellobiohydrolase activity. Changes in productivity resulting in an increased shoot-to-root ratio and shifts in timing are capable of altering ecosystem stability and ecosystem services, such as productivity and nutrient retention.     

A TaqMan-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies

Real-time TaqMan-PCR assays were developed for detection, differentiation and absolute quantification of the pathogenic subspecies of Clavibacter michiganensis (Cm) in one single PCR run. The designed primer pair, targeting intergenic sequences of the rRNA operon (ITS) common in all subspecies, was suitable for the amplification of the expected 223-nt DNA fragments of all subspecies. Closely related bacteria were completely discriminated, except of Rathayibacter iranicus, from which weak PCR product bands appeared on agarose gel after 35 PCR cycles. Sufficient specificity of PCR detection was reached by introduction of the additional subspecies specific probes used in TaqMan-PCR. Only Cm species were detected and there was clear differentiation among the subspecies C. michiganensis sepedonicus (Cms), C. michiganensis michiganensis (Cmm), C. michiganensis nebraskensis (Cmn), C. michiganensis insidiosus (Cmi) and C. michiganensis tessellarius (Cmt). The TaqMan assays were optimized to enable a simultaneous quantification of each subspecies. Validity is shown by comparison with cell counts.     

Free Radicals in Mercury-Resistant Bacteria Indicate a Novel Metabolic Pathway

A mercury resistant-soil bacterium P.10.15, identified as a close relative of Pseudomonas veronii, was shown to accumulate a specific compound in the stationary phase of growth. This compound is converted to a long-lived free radical under oxidizing conditions, as registered by its EPR signal at room temperature. The compound was purified by ion-exchange and gel-filtration chromatography and identified by mass spectroscopy, 2D NMR, and EPR as a trisaccharide -D-GlcpNOH,CH₃-(16)--D-Glcp-(11)--D-Glcp, or, in other words, as 6-O-(2-deoxy-2-{N-methyl}hydroxylamino--D-glucopyranosyl)---trehalose, previously discovered in Micrococcus luteus (lysodeikticus) and named lysodektose. It is suggested that the compound is a novel intermediate of a previously unknown basic metabolic pathway of trehalose transformation in bacteria, a potential target for antibacterial drug development.     

Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition

Global change, especially land‐use intensification, affects human well‐being by impacting the delivery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is a major component of global change effects on multifunctionality in real‐world ecosystems, as in experimental ones, remains unclear. Therefore, we assessed biodiversity, functional composition and 14 ecosystem services on 150 agricultural grasslands differing in land‐use intensity. We also introduce five multifunctionality measures in which ecosystem services were weighted according to realistic land‐use objectives. We found that indirect land‐use effects, i.e. those mediated by biodiversity loss and by changes to functional composition, were as strong as direct effects on average. Their strength varied with land‐use objectives and regional context. Biodiversity loss explained indirect effects in a region of intermediate productivity and was most damaging when land‐use objectives favoured supporting and cultural services. In contrast, functional composition shifts, towards fast‐growing plant species, strongly increased provisioning services in more inherently unproductive grasslands.     

A new cultivation independent approach to detect and monitor common Trichoderma species in soils

A set of primers was developed for the detection, identification and quantification of common Trichoderma species in soil samples. Based on a broad range master alignment primers were derived to amplify an approximate 540 bp fragment comprising the internal transcribed spacer region 1 (ITS 1), 5.8S rDNA and internal transcribed spacer region 2 (ITS 2) from all taxonomic Clades of the genus Trichoderma. The primer set was applied to test strains as well as community DNA isolated from arable and forest soil. For all tested isolates the corresponding internal transcribed spacer regions of Trichoderma spp. strains were amplified, but none of non-Trichoderma origin. PCR with community DNA from soil yielded products of the expected size. Analysis of a clone library established for an arable site showed that all amplified sequences originated exclusively from Trichoderma species mainly being representatives of the Clades Hamatum, Harzianum and Pachybasioides and comprising most of the species known for biocontrol ability. In a realtime PCR approach the primer set uTf/uTr also proved to be a suitable system to quantify DNA of Trichoderma spp. in soils.     

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.