Biological high-affinity H2 uptake in soil is the largest global sink for atmospheric H2. Soil pH often influences soil biological activity but the impact of pH on high-affinity H2 oxidizing bacteria (HOB) was not confirmed. We compared the activity and diversity of group 5/1h HOB in agricultural and forest soils across a gradient from pH 4 to pH 8. The potential H2 uptake activity was approximately 2 times higher in agricultural soil than in forest soil across the pH gradient. Both H2 oxidizing activity and HOB community structure were non-responsive to pH adjustment in these soils, and no pH optima was observed. Greater H2 oxidizing activity was associated with higher iron content and lower carbon and nitrogen concentrations in soil. Catabolic repression of HOB was likely triggered when more organic carbon was present, due to the mixotrophic metabolism in the HOB community. A few hhyL genotypes (5%) responded to pH manipulation, but preference for acidic or alkaline pH was not consistent at the HOB taxonomic level. We conclude that pH preference is not an ecological trait that predicts group 5/1h HOB distribution in soil.

Sinks contaminated with opportunistic pathogens are a source of hospital-acquired infections, responsible for morbidity and mortality in neonatal intensive care units (NICUs). Understanding pathogen behavior in sinks is essential for preventing their spread. Only a few studies have examined how sink environments affect pathogen distribution through changes in drain microbiota. This research uses an integrative approach to study three major bacterial pathogens: Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Serratia marcescens. Sink drains in two NICUs were sampled during 2-month and 5-month periods. The diversity and abundance of opportunistic pathogens were determined at the genotypic level. Their occurrence was analyzed considering microbial communities, water parameters, faucet design, and sink usage. P. aeruginosa, S. marcescens, and S. maltophilia were found in 47%, 39%, and 67% of drain samples, respectively. Low genotype diversity was observed within sinks, with 1-3 genotypes per species/sample. Dominant genotypes persisted throughout the sampling periods, showing the persistence of opportunistic pathogen strains in drains. Quantification of the studied bacterial sequence types ranged from 103 to 107 DNA copies/mL. The heterogeneous spatial distribution of the three species between individual sink drains was primarily attributed to changes in community composition, chlorine concentrations, and faucet design. We isolated a strain of Delftia tsuruhatensis (Dt1S33), whose presence in the sink environment was negatively correlated with the three opportunistic pathogens. Dt1S33 reduced the capacity of the pathogens to form biofilms in laboratory co-cultures. These findings underscore the key roles of biotic and abiotic factors in the colonization of sink drains by pathogens.IMPORTANCEHospital sinks are critical reservoirs for opportunistic pathogens (OPs), increasing the risk of healthcare-associated infections, especially in vulnerable populations such as neonatal intensive care unit (NICU) patients. Our study found that 39%-67% of sink drains were persistently colonized by Pseudomonas aeruginosa, Serratia marcescens, and Stenotrophomonas maltophilia, with a limited number of genotypes dominating for months. Colonization patterns in drains varied between NICUs, mainly influenced by microbial community composition and sink design. Notably, Delftia tsuruhatensis presence was negatively correlated with OP colonization and inhibited OP biofilm formation in vitro. These results highlight the interplay of abiotic and biotic factors in sink colonization and suggest that antagonistic bacteria could help reduce pathogen persistence. Understanding these dynamics is crucial for developing targeted interventions to mitigate infection risks in high-risk hospital settings.

Abstract Conophthorus coniperda (Coleoptera: Curculionidae; Schwarz), known as the white pine cone beetle, is a pest in white pine seed orchards. The insect was primarily studied in the United States of America during the late 1960’s to 1992. No contemporary studies have been performed since, despite the devastating damage the beetle causes to white pine seed orchards, and the seeds they produce for reforestation purposes. To help future research on potential biological control, this work revisits the ontogeny of the white pine cone beetle. The biology of the insect was studied over two years in 2022 and 2023 in a seed orchard (Québec, Canada). Observations were complemented with data collected from the same orchard and other sites in 2009 and in 2012. Except in 2022, the emergence of the insect occurred around 53.6 ± 1.98 °C.d above a threshold of 6.5 °C. A shorter developmental cycle was observed compared with the ones described in 1965 and 1976. The relationship between cone size and the number of insects per cone was statistically significant but explained only a small proportion of the variance and showed high variability. These results will help improve survey timing and sampling strategies for this species.

The stability of conventional single-stage anaerobic digestion has limitations and requires strategies to enhance biogas production, including two-stage anaerobic digestion (TSAD) and trace metals addition (Ni2+). This research was focused on determining the effect of the supplementation of different concentrations of Ni2+ on a TSAD compared with a conventional process. In the first stage (hydrogen-producing reactor), the Ni2+ concentrations evaluated were 0, 0.1, and 0.5 mg Ni2+/gVSinoculum. The acidogenic effluents were fed in the second stage to produce CH4-rich biogas. The results showed that it was possible to increase the CH4-productivity and the specific methane production by 72% and 105%, respectively, by operating in TSAD compared with the conventional anaerobic digester. The Ni2+ addition improved the stability of the first and second stages, allowing higher biogas production. The microbial communities' composition at the phylum level changed in each stage.

Every year, soil microbial-mediated hydrogen (H2) oxidation removes about 80 % of the global atmospheric H2, an indirect greenhouse gas. Soil-dwelling high-affinity H2 oxidizing bacteria use this trace gas as an energy source to persist when other substrates are limited or to meet their maintenance energy requirements during dormancy. However, there is limited knowledge of the distribution, composition, diversity, and functions of this group of bacteria, particularly their ecological traits (i.e., characteristics that influence their interactions with the environment and other organisms). This is because the high-affinity H2-oxidizing bacteria are not phylogenetically conserved, potentially due to the horizontal transfer of their functional gene, which still needs to be demonstrated. This makes it difficult to answer ecological questions related to the distribution, functional role, and ecological contribution of H2-oxidizing bacteria in the soil H2 cycle, as well as their responses to environmental factors. Such information is needed to estimate the contribution of the H2-oxidizing bacteria to the global H2 cycle. Although many H2-oxidizing bacteria are not culturable, they may share similar ecological traits when responding to environmental changes, such as pH, moisture content, and H2 concentrations. Therefore, a community or guild-level trait-based approach (defined as the analysis of functional traits shared by groups of bacteria (guilds) that perform similar ecological roles) could be useful to synthesize complex genomic and phylogenetic information. This review discusses the impact of soil environmental factors on soil H2 uptake (by oxidation), and identifies ecological response traits under controlled conditions. Our approach connects the biological activity of the H2-oxidizing bacteria to their resident environment, for scaling up and estimating the capacity of soil microbial communities to mitigate global warming linked to increased atmospheric H2.

Soil high‐affinity H 2 uptake activity can be affected by many factors, including the soil pH. However, the method to determine how pH affects high‐affinity H 2 uptake activity should be updated. The effect of pH on the biological high‐affinity H 2 uptake in agricultural soils was compared using three pH buffer systems in the pH 4–8 range. Soil pH was adjusted to the target pH using a buffer system (1 g soil/5 mL pH buffer). Soil slurries were treated with heat (autoclaving) or a chemical (25% v/w of toluene addition, microbial inhibitor) to inhibit biological activity. Sterile pH buffer was used as a negative control. The sterile soil slurry (heat sterilization) was the optimal reference control for measuring biological high‐affinity H 2 uptake activity. Biological H 2 uptake activity was resistant to toluene, particularly at extreme pH levels. Overall, soil pH ( p = 0.95) and pH buffer systems ( p = 0.46) did not affect the high‐affinity H 2 uptake activity in the tested agricultural soils. We provide an updated method to accurately measure the potential high‐affinity H 2 uptake activity in soil, with an emphasis on the importance of controlling the soil pH.

Trace gas degradation is a widespread metabolic adaptation in microbial communities, driving chemosynthesis and providing auxiliary energy that enhances persistence during nutrient starvation. In particular, carbon monoxide and hydrogen degradation can be of crucial importance for pioneering microbial communities colonising new, oligotrophic environmental niches, such as fresh volcanic deposits or the aerial interface of the phyllosphere. After volcanic eruptions, trace gas metabolism helps pioneer colonisers to initiate soil formation in ash deposits and on recently solidified lava, a vital ecosystem service. Similarly, in the phyllosphere, bacteria colonising newly emerging leaves and shoots, and/or persisting on the oligotrophic surface of plants, also benefit from trace gas oxidation and, given the global size of this habitat, likely constitute a significant sink for these trace gases affecting atmospheric chemistry. Herein, we review the current state of knowledge surrounding microbial oxidation of carbon monoxide and hydrogen and discuss how this may contribute to niche colonisation in oligotrophic ecosystems.

The recent discovery of atmospheric chemosynthesis has caused a paradigm shift in the way H2-oxidizing bacteria (HOB) are examined. The field has transitioned from the consideration of HOB as a specialized functional group benefiting from the energy potential of H2 for mixotrophic growth or persistence to a versatile group of bacteria using multiple trace gases. We discuss four life history strategies supported by H2, namely chemolithoautotrophic growth, mixotrophic growth, persistence, and atmospheric chemosynthesis. There is experimental evidence supporting the role of HOB in various ecosystem services beyond the uptake of H2 including, for instance, carbon cycling, plant growth promotion, and primary production. Decoupling between the intensity of HOB activation in soil and compositional change of microbial communities remains puzzling, highlighting our poor understanding of the ecological role of HOB. We call for new experimental approaches to delineate the interactions between HOB and the other members of the community. We propose a dedicated framework integrating life history strategies of HOB for mechanistic assessment of microbial interactions and processes supported by H2 in soil.

The tomato brown rugose fruit virus (ToBRFV) poses a considerable threat to tomato production worldwide. Substantial experimental evidence supports the role of infected seeds as a contamination route, but the epidemiologic portrait of the virus has received less attention. This study reports the first survey of ToBRFV prevalence in commercial greenhouses. The aim was to examine the distribution of the virus in relation to greenhouse size and management practices in Québec (Canada). Plant samples collected at three production stages in 31 commercial greenhouses were subjected to ToBRFV detection and genome sequencing. The virus was detected in seven commercial greenhouses (11 positive samples out of 311 analyzed). Retrieved partial genome sequences formed a cluster with ToBRFV variants from Canada and Mexico, suggesting cross-border propagation through commercial trades. There was no link between greenhouse features and ToBRFV diagnosis, indicating that no specific profile is more susceptible to infection than others.

Background N2-fixing nodules release molecular hydrogen (H2) in the rhizosphere of legumes. The process activates H2-oxidizing bacteria (HOB) in soil, leading to multiple effects on biogeochemical processes and a potential biofertilization effect. The legacy effect of the energy potential of H2 on the soil microbial community structure and the population density of HOB has received little attention. The aim of the current study is to evaluate how the legacy effect of HOB, previously activated in soil microcosms exposed to elevated H2 concentrations (eH2), affects biomass production yield of common vetch (Vicia sativa), the abundance of HOB, and the composition of the rhizosphere microbiome. Methods Contrasting soil samples displaying more than 60% difference in H2 oxidation activity were used as growth substrate for vetch. Soil microbial community composition and diversity were examined by bacterial 16S rRNA polymerase chain reaction (PCR) amplicon sequencing, and dry weight (DW) of the above- and below-ground biomass of vetch was analyzed to assess the impact of HOB enrichment on plant growth. The population density of high-affinity HOB was estimated by using the droplet digital polymerase chain reaction (ddPCR) technique to target the hhyL gene, encoding for the large subunit of group 1H/5 [NiFe]-hydrogenase. Results The abundance of HOB possessing group 1H/5 [NiFe]-hydrogenase was indistinguishable between the treatments, indicating that soil nutrient content (inorganic and organic carbon) and the energy potential of H2 were insufficient to support their growth. Aeromicrobium spp. and Ramlibacter spp. were favored by eH2 exposure at the activation stage, but their response was lost after vetch growth. The root biomass and the root/shoot ratio were reduced in soil conditioned with eH2 compared to control soil exposed to ambient H2, suggesting that the plant growth-promotion activity of HOB reduces root proliferation for nutrient prospection. These results provide new experimental evidence suggesting the biofertilization effect of H2 is not universal and requires specific conditions that are yet to be identified.

The minimal sampling effort required to report the microbiome composition of insect surveyed in natural environment is often based on empirical or logistical constraints. This question was addressed with the white pine cone beetle, Conophthorus coniperda (Schwarz), a devastating insect pest of seed orchards. It attacks and stop the growth of the cones within which it will spend its life, on the ground. To survive, the bark beetle probably interacts with microorganisms involved in alimentation, cold adaptation, and dormancy stage. Deciphering the drivers and benefits of these microorganisms in an orchard first requires methodological development addressing variability of the white pine cone beetle microbiome. The number of insect guts integrated in composite samples prior to DNA extraction and the number of surveyed trees are two features expected to induce variability in recovered microbiome profiles. These two levels of heterogeneity were examined in an orchard experimental area where 12 white pine trees were sampled and 15 cones from each tree were grouped together. For each tree, 2, 3 and 4 insects were selected, their intestinal tract dissected, and the microbiome sequenced. The number of insects caused no significant incidence on the coverage of bacterial and fungal communities’ composition and diversity (p > 0.8). There was more variability among the different trees. A sampling effort including up to 33 trees in an area of 1.1 ha is expected to capture 98% of the microbial diversity in the experimental area. Spatial variability has important implications for future investigations of cryptic insect microbiome.

Few attempts have been made to examine the diversity and functions that characterize microbial communities compatible with and beneficial to the biotechnologically relevant mushroom Pleurotus ostreatus. The quest for complementarity is complicated by the variable nature of beneficial traits, impairing the rational assembly of synthetic communities to improve bioprocesses. This study investigated whether the compatibility between P. ostreatus and microbial enrichments is lessened in conditions favoring saprophyte metabolism and is enhanced when a combination of recalcitrant and labile carbon is integrated in the enrichment. The microbial diversity of enrichment cultures and substrates colonized by P. ostreatus was analyzed through PCR amplicon sequencing, and the proliferation of P. ostreatus was assessed by quantitative image analysis. In general, co-inoculation of lignocellulosic substrate with microbial enrichment reduced the growth of P. ostreatus. The saprophytic enrichment conditions were more conducive to the development of antagonistic communities inhibiting P. ostreatus growth than enrichment cultures integrating labile carbon substrates. Both microbial community analyses and in vitro assays led to the identification of a single phylotype affiliated with Brevundimonas spp., which displayed neutral interaction with P. ostreatus. Recalcitrant and labile carbon degradation functions were not primary factors driving beneficial microbial communities for P. ostreatus. Additional functions beyond carbon metabolism are likely to promote beneficial interactions. Directed enrichment cultures, integrating the mushroom in the earliest stage of the procedure, are expected to promote more beneficial interactions than top-down approaches.IMPORTANCELignocellulosic biomass upcycling biotechnologies integrating solid-state fermentation by fungi are aligned with sustainable development perspectives. While the recalcitrance of this biomass imposes a challenge for the implementation of these bioprocesses converting the lignocellulosic feedstock into bioenergy and bioproducts, pretreatment of lignocellulose biomass with fungi is efficient and generates fewer by-products than chemical approaches. Optimization and stabilization of this bioprocess by integrating microbial consortia has received little attention. The significance of our research is to bridge that knowledge gap by examining how interactions between the biotechnologically relevant basidiomycete Pleurotus ostreatus and microbial communities influence fungal growth in lignocellulosic substrate. Directed enrichment cultures integrating Pleurotus ostreatus as a selective agent are expected to trigger more beneficial interactions promoting mushroom growth than our top-down approaches, due to a dominance of antagonistic mushroom-bacteria interactions.

Soil H2 oxidizing bacteria metabolize H2 from the atmosphere, but soil carbon substrates and environmental factors influence their distribution in the soil profile. We conducted a field survey of the spatial distribution of H2 content and high-affinity H2 oxidation activity in the soil profile (5 cm, 15 cm, and 35 cm) and between the soybean rhizosphere and bulk soil. We found the H2 content declined exponentially with soil depth, but potential H2 oxidation activity was consistent at all soil depths. The rhizosphere soil had 66% more high-affinity H2 oxidation activity than bulk soil. Simultaneous presence of H2 and carbon likely facilitates mixotrophic growth of H2 oxidizing bacteria in the rhizosphere.

Objective Evaluate the effects of five disinfection methods on bacterial concentrations in hospital sink drains, focusing on three opportunistic pathogens (OPs): Serratia marcescens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. Design Over two years, three sampling campaigns were conducted in a neonatal intensive care unit (NICU). Samples from 19 sink drains were taken at three time points: before, during, and after disinfection. Bacterial concentration was measured using culture-based and flow cytometry methods. High-throughput short sequence typing was performed to identify the three OPs and assess S. marcescens persistence after disinfection at the genotypic level. Setting This study was conducted in a pediatric hospitals NICU in Montr & eacute;al, Canada, which is divided in an intensive and intermediate care side, with individual rooms equipped with a sink. Interventions Five treatments were compared: self-disinfecting drains, chlorine disinfection, boiling water disinfection, hot tap water flushing, and steam disinfection. Results This study highlights significant differences in the effectiveness of disinfection methods. Chlorine treatment proved ineffective in reducing bacterial concentration, including the three OPs. In contrast, all other drain interventions resulted in an immediate reduction in culturable bacteria (4-8 log) and intact cells (2-3 log). Thermal methods, particularly boiling water and steam treatments, exhibited superior effectiveness in reducing bacterial loads, including OPs. However, in drains with well-established bacterial biofilms, clonal strains of S. marcescens recolonized the drains after heat treatments. Conclusions Our study supports thermal disinfection (>80 degrees C) for pathogen reduction in drains but highlights the need for additional trials and the implementation of specific measures to limit biofilm formation.

Two-stage anaerobic digestion and trace metals (TM) supplementation are promising techniques to improve biogas production. Fe 2+ and Ni 2+ can improve process stability since they are part of the cofactors of enzymes and microorganisms’ growth. This work attempted to evaluate the effect of Fe 2+ and Ni 2+ addition on H 2 -rich biogas production from organic solid waste and the CH 4 -rich biogas production from the acidogenic effluents (AEs) enriched with TM. The TM concentrations that enhanced the hydrogen yield in the batch were 0.25 mg/L of Ni 2+ and 334 mg/L of Fe 2+ . These concentrations were evaluated in a two-stage system. The substrate for the batch tests and fermentative reactor (first stage) was OSW. The AE generated in the first stage was the substrate to produce CH 4 -rich biogas in the second stage. In the first stage, the productivity achieved was 1823 ± 160 mL H 2 /L/day. However, TM supplementation decreased productivity by 65% since the VS removal increased. Megasphaera genus predominated in the first stage. Regarding the methanogenic reactor, the undiluted AE without TM caused the fast decay of the process. Nevertheless, the reactor operated stably after using AE enriched with TM as a substrate, and CH 4 yields increased by 42%. The highest productivity achieved in the second stage was 1278 ± 42 mL CH 4 /L/day, operating with an organic loading rate of 2.8 gVS/L/day. The genera Proteiniphilum , Thermovirga , DMER64 , Anaerovorax , and Syntrophomonas predominated in the second stage. In conclusion, AE enriched with TM can be used to recover the stability of anaerobic digesters, increasing methane production.

Labile carbon and nutrients of the rhizosphere promote the activity of trace gas oxidizing bacteria (TGOB), but the capacity of the rhizosphere effect to support their persistence upon activation has received less attention. Here, we hypothesized that the activation response of TGOB in soil before planting is proportional to the persistence of their activity after wheat growth. The TGOB were activated in sandy-loam and peat soils under a static atmosphere containing elevated concentration of hydrogen (H2), carbon monoxide (CO) or methane (CH4). Our hypothesis was proven to hold true in sandy-loam soil, whereas higher organic matter in peat soil was less favourable for the persistence of TGOB activity. We conclude that the energy potential of the trace gas oxidation reaction and soil nutrients both intervein in the persistence of TGOB activity.

Trees can play different roles in the regulation of fluxes of methane (CH4), a greenhouse gas with a warming potential 83 times greater than that of carbon dioxide. Forest soils have the greatest potential for methane uptake compared to other land uses. In addition to their influence on soil CH4 fluxes, trees can act directly as a source or sink of CH4, by transporting CH4 produced in the soil and harbouring the key microorganisms involved in CH4 production and consumption (methanogens and methanotrophs). Tree CH4 fluxes can vary between species characterized by different traits that influence transport and modify the availability of CH4 reaction substrates as well as the habitat for methanogens and methanotrophs. Despite their important role in modulating CH4 fluxes from forest ecosystems, the identity and role of tree traits influencing these fluxes are poorly consolidated in the literature. The objectives of this paper are to 1) Review the functional traits of trees associated with their role in the regulation of CH4 emissions; 2) Assess the importance of inter-specific variability in CH4 fluxes via a global analysis of tree methane fluxes in the literature. Our review highlights that differences in CH4 fluxes between tree species and individuals can be explained by a diversity of traits influencing CH4 transport and microbial production of CH4 such as wood density and secondary metabolites. We propose a functional classification for trees based on the key traits associated with a function in CH4 emissions. We identified the fast-growing species with low wood density, species adapted to flood and species vulnerable to rot as functional groups which can be net sources of CH4 in conditions favorable to CH4 production. The global analysis further demonstrated the importance of taxonomy, with other factors such as land type and season in explaining variability in tree CH4 fluxes.

Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.