GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies.

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.

Microplastic Pollution in China, an Invisible Threat Exacerbated by Food Delivery Services.

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.

Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities.

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes.

The 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.

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.

Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.

While high-affinity H2-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H2, 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 H2. 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 H2 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.

Fast Granulation by Combining External Sludge Conditioning with FeCl3 Addition and Reintroducing into an SBR.

The separation of light and heavy sludge, as well as the aggregation rate of floccular sludge, are two critical aspects of the rapid granulation process in sequencing batch reactors (SBRs) in the early stages. In this study, we investigated the impact of a method to improve both sludge separation and granulation by coupling effluent sludge external conditioning with FeCl3 addition and then reintroducing it into the SBR. By supplementation with 0.1 g Fe3+ (g dried sludge (DS))-1, the concentration of extracellular polymeric substances (EPS) and sludge retention efficiency greatly increased, whereas the moisture content and specific oxygen uptake rate (SOUR) sharply decreased within 24 h external conditioning. Aggregates (1.75 ± 0.05 g·L-1) were reintroduced into the bioreactor once daily from day 13 to day 15. Afterwards, on day 17, aerobic granules with a concentration of mixed liquor suspended solids (MLSS) of 5.636 g/L, a sludge volume index (SVI30) of 45.5 mL/g and an average size of 2.5 mm in diameter were obtained. These results suggest that the external conditioning step with both air-drying and the addition of Fe3+ enhanced the production of EPS in the effluent sludge and improved rapid aggregation and high sludge retention efficiency. Consequently, the reintroduced aggregates with good traits shortened the time required to obtain mature aerobic granular sludge (AGS) and properly separate light and heavy sludge. Indeed, this method jump-started the aggregation, and rapid granulation processes were successful in this work. Additionally, while the removal efficiency of chemical oxygen demand (COD) and nitrogen from ammonium (NH4+-N) decreased when reintroducing the treated sludge into the SBR, such properties increased again as the AGS matured in the SBR, up to removal efficiencies of 96% and 95%, respectively.

Acclimatization of microbial community of submerged membrane bioreactor treating hospital wastewater.

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.

Author Correction: GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

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

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.

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.