The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H
). H
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 H
are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H
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 H
-oxidizing microbes are keystone species driving C cycling along O
concentration gradients found in H
-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H
-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H
on C cycling and the C-cycling potential of H
-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H
as a driver of biogeochemical processes.
Summary
Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM ...fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns.
This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database,
https://globalamfungi.com
) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies.
The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene.
The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.
With the rapid development and democratization of the internet and smart phone industry, online food delivery services have become increasingly popular all over the globe, namely in China. One of the ...unfortunate drawbacks of these delivery services is that they mainly use single-use plastics as food packaging, therefore generating large amounts of disposable food containers to meet demand. Such plastic containers reach the end of their service life after a single meal, and are then discarded as plastic waste. The sheer amount of plastic food containers discarded in this manner exacerbates various environmental issues, including one that is invisible to the naked eye: microplastic pollution. This minireview summarizes the history of food delivery services in China, from orders made face-to-face to digital orders, as well as the consequences introduced by the tremendous amounts of plastic waste generated by the food delivery services. Microplastic pollution could be mitigated to a certain extent by improving the classification, handling and management of single-use plastic containers in China. Furthermore, additional studies focusing on microplastic pollution caused by food delivery services are needed, especially as the use of these services is on the rise worldwide.
•AGS1 cultivated in SBR using real wastewater (WW) possessed high bacterial richness.•Less bacterial diversity and richness found in AGS2 cultivated using synthetic WW.•A high population of epistylis ...dwelled in the AGS1 favored granulation process.•Epistylis population achieved organics degradation and removal from WW in AGS1.•High bacterial and epistylis growth in AGS1 was due to particulate matters from WW.
Aerobic 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.
Forests represent the largest terrestrial ecosystem on Earth, covering about 30% of its surface, and their microbial inhabitants carry out crucial ecosystem processes. Forests comprise a wide variety ...of microhabitats including soil, litter, living trees and dead wood. Forest fungi can form hyphal networks within or across such microhabitats in search of nutrients, and translocate plant-derived carbon from roots to soil. Various drivers affect their occurrence, such as climate and the presence of competing species. Drivers and predictors of fungal diversity at the fine scale of a forest stand composed of a range of microhabitats are, however, much less clear than those operating at larger scales. The aim of this study is to determine what best captures the heterogeneity of fungal communities in a 5000 m2 mixed forest stand in the temperate natural forest Žofín using a metabarcoding survey of the ITS2 region of fungal rRNA across seven microhabitats: soil, litter, fine roots, senescent leaves, twigs, branches and dead trees. We assessed the impact of microhabitat patchiness as well as the predictive power of niche and neutral processes in shaping fungal diversity and community structure within and across microhabitats. Environmental filters such as phosphorus content, carbon/nitrogen ratio and pH were significant predictors of fungal community composition between microhabitats. Contrastingly, fungal communities displayed significant spatial patterns only in soil, litter and roots, i.e. continuous microhabitats. When focusing on pairs of samples collected at the same approximate location, continuous microhabitats displayed a higher similarity, on average, between themselves and other microhabitats, as opposed to semi-continuous and patchy microhabitats. As the ultimate sink of organic matter, soil harbored the highest number of recurrent fungal units from other microhabitats, emphasizing that not only does soil collect debris across the forest floor, but it also acts as a crossroad where locally abundant fungi collide.
•Extensive sampling in Žofín, a protected beech-dominated nature reserve.•Metabarcoding survey of 357 fungal communities from seven forest microhabitats.•Only continuous microhabitats exhibited significant spatial patterns.•Environmental filters were significant predictors in 5 out of 7 microhabitats.•Soil acts as a crossroad between continuous and patchy microhabitats.
While high-affinity H
-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H
, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main ...purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H
. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity NiFe-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H
oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.
The enrichment of H
-oxidizing bacteria (HOB) by H
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 H
, 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 H
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 H
exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H
while enhancing community level carbon substrate utilization potential and lowering CH
uptake activity in soil. We found that H
triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H
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 H
on soil microbial communities will lead to a better understanding of the H
fertilization effect and soil biogeochemical processes.
An innovative dynamic microcosm chamber system was used to demonstrate that H
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 CH
oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H
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.
•Synthetic hospital wastewater was treated in SMBR at varying HRT.•SMBR efficiently treated Ibuprofen and estradiol from influent wastewater.•Pharmaceutical addition and HRT variations altered ...bacterial community structure.•The phylum Bacteroidetes became dominant phyla after pharmaceutical addition.•Pharmaceuticals addition causes growth of Flavobacterium, Pedobacter &Methylibium.
The 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.
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•External conditioning with CaCl2 made effluent sludge quick aggregation.•Aggregate’s reintroduced into SBR sharply reduced granulation time by 17 days.•Thauera enriched between ...external conditioning and granulation for AGS rapid cultivation and pollutants degradation.
Aerobic granular sludge (AGS) technology has been limited by its long startup time in sequencing batch reactors (SBRs). The objective of this work is to determine if a new amendment of the AGS process improves sludge granulation rate and pollutants removal efficiency. This amendment consisted in an external conditioning step during which the effluent sludge was dried, supplemented with 0.1 g CaCl2 g−1 dried sludge (DS) and then gradually reintroduced into the SBR. Results have shown that this technique can reduce the granulation time by 17 days while ensuring the stability of AGS. Stable aerobic granules were obtained on day 20, i.e. a few days after reintroducing 1.75 g·L-1 Ca2+-conditioned sludge to the SBR for 5 consecutive days. Mixed liquor suspended solids (MLSS), sludge volume index ratio at 30 min and 5 min (SVI30/SVI5) and average granule size in the AGS reactor were maintained at 5.7 g·L−1, 1.0 and 3.5 mm, respectively. The external conditioning led to an increase in extracellular polymers (EPS) production, a decrease in moisture content, specific oxygen uptake rate (SOUR) and iron precipitation. Altogether, these impacts led to a faster aggregation of the effluent sludge compared to a control SBR. Furthermore, microbial community analyses have shown that the external conditioning process enriched specific Betaproteobacteria (e.g. Thauera genus) in aggregates and AGS. Such outcomes could be linked to the faster granulation rate and more efficient pollutants degradation.
•The microbiome of SMBR during acclimatization with HWW was investigated.•Pathogenic bacteria were abundant in phase 3 of acclimatization.•Shift in the micro-eukaryotes community at phase 3 of ...acclimatization was observed.
This study was performed to understand the dynamics of the microbial community of submerged membrane bioreactor during the acclimatization process to treat the hospital wastewater. In this regard, three acclimatization phases were examined using a mixture of synthetic wastewater (SWW) and real hospital wastewater (HWW) in the following proportions; In Phase 1: 75:25 v/v (SWW: HWW); Phase 2: 50:50 v/v (SWW: HWW); and Phase 3: 25:75 v/v (SWW: HWW) of wastewater. The microbial community was analyzed using Illumina high throughput sequencing to identify the bacterial and micro-eukaryotes community in SMBR. The acclimatization study clearly demonstrated that shift in microbial community composition with time. The dominance of pathogenic and degrading bacterial communities such as Mycobacterium, Pseudomonas, and Zoogloea was observed at the phase 3 of acclimatization. This study witnessed the major shift in the micro-eukaryotes community, and the proliferation of fungi Basidiomycota was observed in phase 3 of acclimatization.
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