H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

International audienceSoil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

International audienceThe atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes

Dose-response relationships between environmentally-relevant H 2 concentrations and the biological sinks of H 2 , CH 4 and CO in soil

International audienceLocal H2 accumulations can be found in soil, especially within legume crop agroecosystems, where H2 is an obligate by-product of nitrogen fixation. Recent investigations show that diffusive fluxes of H2 act as additional energy inputs shaping microbial community structure and function in soil. The goal of this study is thus to define dose-response relationships between H2 exposure and soil microbial community dynamics. Community structure and trace gases (i.e. H2, CH4 and CO) oxidation activities were investigated following soil incubation to environmentally-relevant H2 mixing ratios. Despite no evidence of an alteration of microbial diversity, coordinated dose-response relationships between trace gases oxidation rates and H2 exposure were recorded. Measured H2 oxidation rates were implemented into a theoretical framework modeling H2 decay as a function of distance from H2-emitting point sources. Theoretical H2 concentration profiles and dose-response relationships between H2 concentration and trace gases oxidation rates were integrated to predict the impact of H2 on microbial community functioning. While most H2 is oxidized within 1 cm of H2 point sources, trace gases oxidation is predicted to be altered within a 10 cm radius. High-affinity CH4 and CO oxidation capacities dropped by up to 78% and 84% along H2 concentration gradients, respectively. Theoretical distances from H2-emitting point sources required to reactivate 50% of maximal CH4 oxidation rate were 0.3 cm in farmland soil and 0.2 cm in poplar soil. A longer distance was required to reactivate 50% of CO oxidation rate, i.e. 1.5 and 2.7 cm in farmland and poplar soils, respectively. Loss of CH4 oxidation potential observed under elevated H2 exposure was correlated with a gain of low-affinity H2 oxidation activity, while a substrate inhibition of high affinity H2 oxidation rate was paralleled with a decreasing trend of CO oxidation activity. In addition to shedding light on potential interactions between H2, CH4 and CO biogeochemical processes in soil, these novel findings provide evidence that H2 supports metabolic and energetic flexibility in microorganisms supplying a variety of ecosystem services

Roles of bacterial and epistylis populations in aerobic granular SBRs treating domestic and synthetic wastewaters

International audienceAerobic granular sludge (AGS) has been recently studied and developed as a way to circumvent the poor settling and biomass retention capacity of conventional activated sludge. While it is known that AGS allows the simultaneous presence of oxic and anoxic zones on the surface or within granules, respectively, the actual composition dynamics of those granules in relation to their underlying wastewater influent have receive little attention. The main goal of this study is thus to assess the relationship between wastewater composition, microbial community structure and epistylis abundance. Two SBRs (sequencing batch reactors) comprising the same inoculum and fed with either domestic or synthetic wastewater were used in this regard. The more complex composition of domestic wastewater promoted a higher bacterial richness than their synthetic counterparts. Indeed, the vast majority of the bacterial community in the SBR fed with synthetic wastewater was dominated by the genus Thauera. The SBR fed with domestic wastewater also showed a more thorough granulation and greater treatment efficiency. Surprisingly, the abundance of epistylis was positively correlated with remaining suspended solids, hinting that ciliates might be responsible for SS (suspended solids) removal and would be a desirable trait to include in wastewater treatment plants. In sum, our study gives insight into the differing population dynamics shaped by domestic and synthetic wastewaters inoculated with the same initial consortium, along with their overall pollutant removal efficiency

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities

Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H2-oxidation activity measured in three soils exposed to H2

International audienceInferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H2 as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H2 oxidation rate measured in soil collected in poplar monoculture, larch plantation and farmland. Shotgun metagenomic and metatranscriptomic analyses of soil samples exposed to elevated or low H2 concentration led to the identification of 45 genes encoding the large subunit of [NiFe]-hydrogenases belonging to 8 distinct phyla. Our results indicate that despite significant sequencing effort, retrieved hydrogenase sequences are not in themselves adequate surrogates of H2 oxidation activity in these soils. In fact, land-use exerted a greater influence than H2 exposure on both hydrogenase gene distribution and expression though expression of certain genes responded to H2. We argue that approaches relying on PCR/RT-PCR amplicon sequencing or quantification combined with physicochemical parameters are currently the best option to infer the activity of H2-oxidizing bacteria and probably other specialist functional guilds with similar population size in soil

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

The enrichment of H2-oxidizing bacteria (HOB) by H2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H2 while enhancing community level carbon substrate utilization potential and lowering CH4 uptake activity in soil. We found that H2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H2 on soil microbial communities will lead to a better understanding of the H2 fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

The enrichment of H2-oxidizing bacteria (HOB) by H2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H2 while enhancing community level carbon substrate utilization potential and lowering CH4 uptake activity in soil. We found that H2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H2 on soil microbial communities will lead to a better understanding of the H2 fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB

The bacterial community structure of submerged membrane bioreactor treating synthetic hospital wastewater

International audienceThe pharmaceuticals are biologically active compounds used to prevent and treat diseases. These pharmaceutical compounds were not fully metabolized by the human body and thus excreted out in the wastewater stream. Thus, the study on the treatment of synthetic hospital wastewater containing pharmaceuticals (ibuprofen, carbamazepine, estradiol and venlafaxine) was conducted to understand the variation of the bacterial community in a submerged membrane bioreactor (SMBR) at varying hydraulic retention time (HRT) of 6, 12 and 18 h. The variation in bacterial community dynamics of SMBR was studied using high throughput sequencing. The removal of pharmaceuticals was uniform at varying HRT. The removal of both ibuprofen and estradiol was accounted for 90%, whereas a lower removal of venlafaxine (<10%) and carbamazepine (>5%) in SMBR was observed. The addition of pharmaceuticals alters the bacterial community structure and result in increased abundance of bacteria (e.g., Flavobacterium, Pedobacter, and Methylibium) reported to degrade toxic pollutant