Christina Hazard

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.

Nitrososphaeria, an archaeal class containing all ammonium-oxidizing archaea (AOA) and their closely related clades (e.g. Ca. Caldarchaeales), is a widely distributed archaeal lineage across diverse ecosystems. Due to the difficulty of isolation and cultivation, the viral diversity and evolution associated with non-marine AOA lineages and Ca. Caldarchaeales remain largely uncharacterized. Here, based on globally sampled genomes and metagenomes, we assembled a genomic catalogue associated with AOA, including 283 species-level viruses and 415 species-level mobile genetic elements (MGEs). Notably, 259 previously unrecognized species-level viruses or MGEs associated with Ca. Caldarchaeales were identified. Across the two major Nitrososphaeria lineages, we uncovered an expansion of archaeal viral families: 11 families associated with AOA, including seven new head-tailed lineages, one of which comprises a mega archaeal virus with a genome size exceeding 220 kb; ten families associated with Ca. Caldarchaeales, including four novel head-tailed groups and two previously unknown rod-shaped family (Demeterviridae and Gaiaviridae).Phylogenetic inference showed that rod-shaped viruses associated with Ca. Caldarchaeales and methanogens are phylogenetically intertwined and likely share a common ancestor with Hoswirudivirus, a Sulfolobales-associated rod-shaped virus characterized by two copies of the coat gene. Through structural modelling, a rare fusion of the coat protein in Demeterviridae was observed, in which a single open reading frame within a gene island adjacent to a glycosyl transferase appears capable of forming a complete capsomer. This provides new insights into the origin and evolution of Adnaviria viral realm. Functional genomics analyses further revealed that these novel rod-shaped viruses encode virus-specific rare quinone biosynthesis genes and arsenic response transcriptional regulator genes, providing potential clues to their mechanisms of adaptation to hyperthermal environments. Collectively, our work uncovers the hidden genomic, evolution and functional diversity of Nitrososphaeria viromes for the first time and closes a long-standing gap in archaeal virome research.

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.

Soil rewetting after a long dry season results in a burst of microbial activity accompanied by succession of both microbial and DNA viral communities. We hypothesized that RNA viruses, like DNA viruses, would exhibit temporal succession following rewetting. Moreover, we expected their response would change with the addition of phosphate, since viral proliferation may lead to phosphorus (P) limitation due to their low C:N:P ratio. We used a replicated time-series of soil metatranscriptomes collected after rewetting to identify parameters affecting RNA viral community composition over three weeks. P amendment led to a decrease in RNA viral community diversity and evenness, significantly impacting beta diversity over time. As has been observed for DNA viruses, the spatial distribution of RNA viruses in dry soil was highly heterogeneous. Most viruses were predicted to infect bacteria or fungi, and a small fraction was predicted to infect protists, plants, and animals. The amount of RNA extracted from phages of the class Leviviricetes increased significantly after one week in P-amended soil, contrasting with unamended soil. This suggests that P availability plays an important role in RNA phage proliferation. We estimate that the number of bacteria infected by RNA phages is on the order of 107–109 per gram soil, comparable to the range of total cells in soil. This implies that RNA phages likely have a profound effect on the bacterial community following soil wet-up when P is not a limiting factor.

Wetlands can be a significant source of N2O under current global climate change regime with the soil-water interface representing a biogeochemical hotspot for microbial activity. However, the role of soil-water interface in controlling N2O emissions remains poorly understood. We hypothesized that the millimeter-scale redox gradient across the soil-water interface generates corresponding distinct niche for N-cycling microorganisms that collectively regulate the production and consumption of N2O over the same spatial scale. The abundance, transcriptional activity and spatial organization of different N-cycling guilds across the soil-water interface were characterized in mesocosms from three different paddy soils with different N2O emissions. Results demonstrated millimeter-scale stratification of N-cycling microbial activity across the soil-water interface, and in particular within the first 10 mm of flooded soils. Ammonia-oxidizing microorganisms were only transcriptionally active in the top 4 mm, suggesting a previously underestimated contribution to N2O emissions from wetlands. Variation in N2O accumulation was observed across the soil-water interface, with the highest concentrations measured at either the soil-water interface or in the deeper anoxic layer of paddy soils. Despite this difference, N2O-reducing microorganisms exhibited high transcriptional activity at the soil-water interface in all soils, suggesting that there is a microbial-mediated sink for N2O across the soil-water interface that can reduce N2O produced from both oxic and anoxic layers. This work demonstrate an underappreciated and essential role of the microbial hot zones at soil-water interface in regulating N2O emissions from wetlands.