Graeme W. Nicol

Mineral fertilizers have sustained food security for decades, yet the long-term impacts on soil microbial communities underpinning soil health remain virtually unknown. We combine standardized field surveys with a meta-analysis to assemble a global dataset of 501 long-term agricultural experiments (≥5 years, median duration 25 years) to evaluate the impacts of sustained mineral fertilization on soil properties and microbial communities. Long-term mineral fertilization increases soil organic carbon by 14% and decreases soil pH by 0.31 units on average relative to unfertilized controls. Soil organic carbon accumulation largely explains increased microbial biomass carbon and living bacterial biomass. Mineral fertilizer-induced acidification primarily reshapes dominant bacterial taxa, with the relative abundance of Proteobacteria increasing and Firmicutes declining, whereas fungal community composition remains stable. Virulent bacteriophages increase in association with shifts in bacterial hosts. Microbial activities reveal a decoupling of more nitrogen- and phosphorus-acquisition enzymes from the unchanged production of carbon-mineralization enzymes. Microbial communities are taxonomically reorganized without reducing richness or promoting fungal pathogens. These responses are evaluated in the context of agroecosystem type, fertilization regime, and cropping regime. Our findings provide global-scale evidence for the consequences of long-term mineral fertilization on soil health, which is integral to guiding fertilizer management for sustainable agriculture.

A critical step in developing new biosensing devices is to ensure biofilm adaptability to electrochemical conditions and responsiveness to varying environmental factors. In this study, we investigated the biofilm enrichment from French vertical flow treatment wetland (VFTW) sludge in air-cathode MFCs with varying external resistances (100 and 1000 Ω). Electrochemical Impedance Spectroscopy, Environmental Scanning Electron Microscope, and metagenomic analysis showed that the 100 Ω condition promoted higher current output, lower anode resistance, thicker biofilm formation, and stronger enrichment of the Geobacteraceae. In contrast, 1000 Ω condition resulted lower current output and a reduced abundance of electroactive bacteria. This was aligned with the limited biofilm coverage and pseudocapacitive behavior, which could offer advantages for long-term biosensor operation by controlling electrode fouling and enabling continuous electron transfer. Interestingly, spatial biofilm heterogeneity along the anode depth promoted distinct microbial community compositions. The internal biofilm layers presented an increase in the relative expressions of c-type cytochrome omcB, omcE, omcM, which could potentially regulate its extracellular electron transfer (EET). These findings demonstrate the high adaptability of VFTWs-enriched electroactive biofilms and provide valuable insight for designing strategies to influence biofilm dynamics and stable signal output, fostering the application of MFCs for clogging indication in French VFTWs.

Nitrobacter strain NHB1 is a nitrite-oxidizing bacterium previously demonstrated to form a consortium capable of nitrification under acidic conditions when cocultivated with a neutrophilic ammonia-oxidizing bacterium. Here, we characterize the growth of isolated NHB1 under different pH and nitrite (NO2−) concentrations, as well as its influence on the activity of obligately acidophilic soil ammonia-oxidizing archaea (AOA) isolated from acidic soils when grown in coculture. NHB1 is acidotolerant with optimal growth at pH 6.0 (range: 5.0–7.5) at an initial NO2− concentration of 500 μM. However, at lower NO2− concentrations, closer to those found in soil, its pH optimum decreases to 5.0 and with detectable growth extended to pH 3.5. In coculture, NHB1 enhances the growth of the acidophilic AOA Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2, which are highly sensitive to NO2-derived compounds and typically oxidize only ~200 to 300 μM ammonia (NH3) when grown in batch cultures as isolates. However, in coculture with NHB1, both strains oxidized up to ~3 mM NH3, limited only by the buffering capacity of the medium, and their pH range was also extended downward by ~0.5 units. NHB1 also possesses a cyanase, enabling reciprocal cross-feeding through cyanate-derived NH3 production while utilizing AOA-derived NO2−. These findings suggest that NO2− removal is essential for ammonia oxidizer growth in acidic soils and emphasize the importance of considering substrate and metabolic product concentrations when characterizing ecophysiology. Genome analysis reveals that NHB1 is distinct from validated species, and we propose the name “Nitrobacter laanbroekii.”

Single species tests on surrogate organisms from different trophic levels constitute a cornerstone in aquatic and terrestrial ecotoxicology, representing a major tool for assessing pesticide ecotoxicity. However, there are no assays approved under the EU regulatory framework that specifically target soil microorganisms, despite their pivotal role in ecosystems. This study evaluated the toxicity of pesticides on ammonia-oxidizing microorganisms (AOM), recognized as potential indicators of pesticide toxicity in soil, using a single species in vitro testing system. We assessed the toxicity of ten pesticides of major categories (insecticides, fungicides, herbicides) on a range of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and functionally associated nitrite-oxidizing bacteria (NOB) in liquid cultures, representing all major soil lineages of both groups. Toxicity end points (EC₅₀) were calculated for each strain-pesticide combination. Nitrosotalea sinensis ND2, Nitrosospira briensis and Candidatus Nitrobacter laanbroekii NHB1 were the most sensitive AOA, AOB and NOB, respectively. Fungicides and insecticides were more toxic to AOM than NOB, whereas herbicides had a wide range of toxicity across all groups of nitrifiers. Our study introduces a novel testing approach that includes a range of phylogenetically and ecophysiologically distinct nitrifier strains for assessing pesticides toxicity on soil microorganisms that could potentially, upon standardization, serve as a tier I assay in environmental risk analysis.

The climate crisis presents an urgent challenge for Earth’s living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth’s ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173 kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.

Bacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection of host communities across ecological gradients and co-evolutionary processes may influence both the distribution of phages and the susceptibility of individual hosts through virus interactions and local adaptation within distinct ecological niches. Metagenomic-based analyses have revealed that soil pH selects for distinct populations and community structures for both phage and hosts at local and global scales. However, whether contrasting soil pH represents a selective barrier for phages capable of infecting an individual host is unknown. To examine the influence of pH on individual host-virus interactions, two closely related Bacillus strains were isolated and characterized from pH 7.5 soil associated with a long-term contiguous pH gradient (pH 4.5 to 7.5). Phages infecting each strain were subsequently enriched from soils across the pH gradient (pH 4.5, 5.5, 6.5 and 7.5), enumerated using a plaque assay, and characterized via metagenomic analysis. Phages infecting each strain were cultivated from all soils but their community composition and abundance varied with pH. Phage populations infecting each of the two strains were distinct despite the close relatedness of the two hosts, indicating relatively narrow host ranges for each virus. These results suggest that while phage community structures vary substantially across an ecological gradient, soil pH alone does not represent a barrier for the distribution of phages capable of infecting an individual host.

Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1^T and Nd2^T, respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1^T does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1^T were small angular rods 0.5–1 µm in length and grew at pH 4.2–5.6 and at 20–30 °C. Cells of Nd1^T were small angular rods 0.5–1 µm in length and grew at pH 4.0–6.1 and at 20–42 °C. Nd1^T and Nd2^T are distinct with respect to genomic and physiological features and are assigned as the type strains for the species Nitrosotalea devaniterrae sp. nov. (type strain, Nd1^T=NCIMB 15248^T=DSM 110862^T) and Nitrosotalea sinensis sp. nov. (type strain, Nd2^T=NCIMB 15249^T=DSM 110863^T), respectively, within the genus Nitrosotalea gen. nov. The family Nitrosotaleaceae fam. nov. and order Nitrosotaleales ord. nov. are also proposed officially.