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•High removal efficiencies of COD, TN and TP in electrolysis-integrated constructed wetlands (E-CWs) were obtained.•Performance of MFC-CWs was slightly better than that of ...EC-CWs.•Higher microbial community diversity and richness in E-CWs driven higher pollutants removal.•Functional genes related to nitrogen transformation were greatly enriched in CWs by electrolysis.
The molecular mechanism of contaminant removal in different electrolysis -integrated constructed wetlands (CWs) was explored. Electrolysis (microbial fuel cells (MFC) and direct current (EC))-integrated CWs achieved high removal efficiencies for chemical oxygen demand (COD; 82.18% in MFC-CWs and 81.57% in EC-CWs), total nitrogen (TN; 75.08% in MFC-CWs and 69.19% in EC-CWs) and total phosphorus (TP; 92.56% in MFC-CWs and 92.86%), which was higher than that in CWs. Additionally, MFC-CWs had an average voltage of 384.56 ± 44.49 mV with the highest power density of 977 mW m−2. The pollutant removal performance of the MFC-CWs was better than that of the EC-CWs. Microorganisms in electrolysis-integrated CWs, especially in the MFC-CWs, gained higher diversity and richness than those in CWS. However, the effects between MFC and EC for CWs were different. In addition, nitrogen functional genes in electrolysis-integrated CWs were significantly more abundant than those in the CWs, and the electron transfer rate also increased. Combined analyses of microorganisms and functional genes revealed that the main contributors to nitrogen removal were anaerobic ammoxidation, ammonia oxidation, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) for CWs, anaerobic ammoxidation, ammonia oxidation, denitrification and DNRA for EC-CWs, anaerobic ammoxidation, ammonia oxidation and denitrification for MFC-CWs
Biochar can enhance organic carbon storage and mitigate the adverse effects of pesticides in the soil. However, the mechanisms by which field-aging affects the impacts of biochar on herbicide ...behavior and the composition of microbial communities in the soil remain unclear. This study aimed to investigate the influences of aged and fresh biochar on herbicide behavior and microbial community structure in the soil. Herein, with 14C-labeled technology, aged treatment (soil amended with field-aged biochar), fresh treatment (soil amended with fresh biochar), and control (soil without biochar) were installed to evaluate their treatment capacities. The results showed that the average leaching out and mineralization of simazine in the aged treatment were significantly higher by 4.8% and 1.66% (P < 0.05) compared with the fresh treatment. Relative to the control, the pesticide was significantly adsorbed (P < 0.05) in the aged treatment. The abundance of arbuscular mycorrhizal fungi (AMF) significantly increased by 1.03 and 1.16-fold, whereas fungi increased dramatically by 1.02-fold and decreased by 1.21-fold in the aged and fresh treatments, respectively (P < 0.05). In addition, eukaryotes were effectively reduced by 1.02 and 1.14-fold in these treatments, respectively (P < 0.05). This study suggests that field aging can undermine the impacts of biochar on pesticides and modify the microbial community structure in the soil environment.
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•The treatment performance of aged and fresh biochar in pesticide-polluted soil was evaluated.•Field-aging lowered the biochar adsorption capacity for simazine in the soil environment.•Fresh biochar increased arbuscular mycorrhizal fungi but reduced eukaryotes in the soil environment.•Fresh biochar significantly lessened the leaching and decomposition of simazine in the soil.
Fermented foods and beverages have been a key component of the human diet for thousands of years, and play an important nutritional, cultural, and economic role in most human societies. Differences ...in ingredients, local practices, and environmental conditions can impact microbial communities in fermented foods resulting in distinct flavors, textures, and nutritional properties. Despite their ancient roots, omnipresence, potential health benefits, recent hype, and the plethora of tools to study microbial diversity, the microbial and functional diversity of most fermented foods currently remain unknown, while changing lifestyle practices threaten the loss of some fermented foods, with dire implications for gastrointestinal health.
In this commentary we discuss the nutritional, cultural, and economic values of fermented foods and (i) introduce FermDB, the largest interoperable database and map of fermented foods to date (https://bokulich-lab.github.io/FermDB/), intended as an extensible community resource for documenting and studying food fermentations; (ii) provide a consistent fermented food ontology for classification of these foods; and (iii) estimate global production values and biomass of some of the most common fermented foods to contextualize the social and economic importance of microorganisms for human food production.
We provide a new perspective on global diversity of fermented foods and associated microbial communities as a resource for sustainable food production. Additionally, the introduced database and ontology can act as a roadmap to the path toward conserving microbial biodiversity of traditional foods and studying their associated health benefits.
•Fermented foods are key to human health and a global cultural and economic resource.•Traditional fermented foods and their biodiversity are threatened by industrialization.•We outline a roadmap to preserve and study traditional fermented foods.•FermDB is the most extensive curated and interoperable fermented foods catalog to date.
Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. Because cover cropping can form an agroecosystem ...distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Despite the growing number of primary literature sources investigating the relationship between cover cropping and the soil microbiome, there has not been a quantitative research synthesis that is sufficiently comprehensive and specific to this relationship. We conducted a meta-analysis by compiling the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome.
•Meta-analysis up to 2019 on cover cropping effects on soil microbiome.•Cover cropping increased soil microbial abundance, activity, and diversity.•Effects are dependent on climate, termination methods, and tillage.
•Intercropping increased the soil nutrients and enzyme activities of proso millet.•The effect of intercropping on the soil bacterial diversity was larger than fungi.•Intercropping decreased the ...dominant bacterial abundance of Actinobacteria.•Intercropping did not markedly change the fungal community compositions.•The soil temperature and bulk density contribute more to the bacterial community.
Cereal-legume intercropping has been widely used to increase productivity and achieve sustainable development in modern agricultural systems. However, there has been few studies of intercropping in minor grain crops, and we therefore designed an experiment to monitor rhizosphere soil properties, enzyme activities, and the microbial community diversity of proso millet (Panicum miliaceum L.) under proso millet /mung bean intercropping systems on the Loess Plateau of China, and a sole planting was used as a control. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition. The results showed that the rhizosphere soil nutrient contents and enzyme activities were higher under intercropping patterns with significant correlations being observed. The physical properties were also changed, including the soil water content, bulk density, and soil temperature. The effect of intercropping patterns on bacterial diversity was larger than that on fungal diversity, especially alpha diversity, although both groups were markedly affected by intercropping patterns. Actinobacteria was the most abundant bacterial phylum, which was decreased by 32.37% under intercropping. Other phylum species, including Proteobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Firmicutes were also markedly affected by intercropping patterns. For the dominant fungal phyla, Ascomycota, Mortierellomycota, and Basidiomycota did not respond substantially to intercropping patterns. Binding spatial ordination analysis demonstrated that soil temperature and bulk density for bacteria and total nitrogen and nitrate contents for fungi contribute more to the microbial community than the other investigated soil parameters, whereas the soil enzyme activities played the same roles in bacteria and fungi. Overall, these results suggest that intercropping alters soil microbial community composition, and the soil bacteria reflect changes in soil properties and enzyme activities better than fungi. Meanwhile, these findings also provide insights into the mechanisms underlying the maintenance of biodiversity in the agro-ecosystems functioning.
Emerging contaminants such as microplastics and engineered nanoparticles (NPs) have become an environmental issue of global concern, but little is known about their joint effects in soil–plant ...systems. We studied the effects of two microplastics, conventional non-degradable high–density polyethylene (HDPE) and biodegradable polylactic acid (PLA), on maize growth and arbuscular mycorrhizal (AM) fungal communities in a soil spiked with or without ZnO NPs. HDPE and low–dose PLA promoted plant growth, while high–dose PLA significantly decreased maize shoot (by 16%–40%) and root biomass (by 28%–50%), indicating high-dose PLA may have strong phytotoxicity. ZnO NPs displayed non-significant effects on plant growth, but caused greater Zn accumulation in plants. Both HDPE and PLA further increased Zn concentrations in roots, while decreasing Zn translocation to aerial parts. High–throughput sequencing showed that microplastics and ZnO NPs singly and jointly influenced AM fungal community composition and diversity, particularly the relative abundance of dominant genera. The presence of ZnO NPs and microplastics generally increased soil pH. Overall, our findings imply increasing contamination by microplastics and NPs can have profound ecological impacts on plant fitness, plant quality, and soil microbial community composition and diversity, resulting in uncertain consequences for agroecosystems.
•Interactions of microplastics and nanoparticles on mycorrhizae were first studied.•Polylactic acid had low-dose stimulation and high-dose inhibition effects on plants.•Polyethylene antagonistically interacted with ZnO nanoparticles on plant growth.•Microplastics altered Zn accumulation and translocation in plants exposed to ZnO.•Microplastics and ZnO nanoparticles altered AMF community structure and diversity.
Establishment of the gastrointestinal microbiota during infancy affects immune system development and oral tolerance induction. Perturbations in the microbiome during this period can contribute to ...development of immune-mediated diseases. We monitored microbiota maturation and associations with subsequent development of allergies in infants and children.
We collected 1453 stool samples, at 5, 13, 21, and 31 weeks postpartum (infants), and once at school age (6–11 years), from 440 children (49.3% girls, 24.8% born by cesarean delivery; all children except for 6 were breastfed for varying durations; median 40 weeks; interquartile range, 30–53 weeks). Microbiota were analyzed by amplicon sequencing. Children were followed through 3 years of age for development of atopic dermatitis; data on allergic sensitization and asthma were collected when children were school age.
Diversity of fecal microbiota, assessed by Shannon index, did not differ significantly among children from 5 through 13 weeks after birth, but thereafter gradually increased to 21 and 31 weeks. Most bacteria within the Bacteroidetes and Proteobacteria phyla were already present at 5 weeks after birth, whereas many bacteria of the Firmicutes phylum were acquired at later times in infancy. At school age, many new Actinobacteria, Firmicutes, and Bacteroidetes bacterial taxa emerged. The largest increase in microbial diversity occurred after 31 weeks. Vaginal, compared with cesarean delivery, was most strongly associated with an enrichment of Bacteroides species at 5 weeks through 31 weeks. From 13 weeks onward, diet became the most important determinant of microbiota composition; cessation of breastfeeding, rather than solid food introduction, was associated with changes. For example, Bifidobacteria, staphylococci, and streptococci significantly decreased on cessation of breastfeeding, whereas bacteria within the Lachnospiraceae family (Pseudobutyrivibrio, Lachnobacterium, Roseburia, and Blautia) increased. When we adjusted for confounding factors, we found fecal microbiota composition to be associated with development of atopic dermatitis, allergic sensitization, and asthma. Members of the Lachnospiraceae family, as well as the genera Faecalibacterium and Dialister, were associated with a reduced risk of atopy.
In a longitudinal study of fecal microbiota of children from 5 weeks through 6 to 11 years, we tracked changes in diversity and composition associated with the development of allergies and asthma.
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Soil microbial communities play an essential role in driving multiple functions (i.e., multifunctionality) that are central to the global biogeochemical cycles. Long-term fertilization has been ...reported to reduce the soil microbial diversity, however, the impact of fertilization on multifunctionality and its relationship with soil microbial diversity remains poorly understood. We used amplicon sequencing and high-throughput quantitative-PCR array to characterize the microbial community compositions and 70 functional genes in a long-term experimental field station with multiple inorganic and organic fertilization treatments. Compared with inorganic fertilization, the application of organic fertilizer improved the soil multifunctionality, which positively correlated with the both bacterial and fungal diversity. Random Forest regression analysis indicated that rare microbial taxa (e.g. Cyanobacteria and Glomeromycota) rather than the dominant taxa (e.g. Proteobacteria and Ascomycota) were the major drivers of multifunctionality, suggesting that rare taxa had an over-proportional role in biological processes. Therefore, preserving the diversity of soil microbial communities especially the rare microbial taxa could be crucial to the sustainable provision of ecosystem functions in the future.
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•Inorganic fertilization decreased soil multifunctionality.•Organic fertilization increased microbial diversity and multifunctionality.•Rare microbial taxa had an over-proportional role in multifunctionality.
The emission of nutrients and pesticides from agricultural soils endangers natural habitats. Here, we review to which extent carbon-rich organic amendments help to retain nutrients and pesticides in ...agricultural soils and to reduce the contamination of surrounding areas and groundwater. We compare straw, compost, and biochar to see whether biochar outperforms the other two more traditional and cheaper materials. We present a list of criteria to evaluate the suitability of organic materials to be used as soil amendments and discuss differences in elemental compositions of straw, compost, and biochar to understand, how soil microorganisms utilize those materials. We review their effects on physical and chemical soil characteristics, soil microbial communities, as well as effects on the transformation and retention of nutrients and pesticides in detail.
It becomes clear that for all three amendments their effects can vary greatly depending on numerous aspects, such as the type of soil, application rate, and production procedure of the organic material. Biochar is most effective in increasing the sorption capacity of soils but does not outperform straw and compost with regards to the other aspects investigated. Nevertheless, the possibility to design biochar properties makes it a very promising material. Finally, we provide critical comments about how to make studies about organic amendments more comparable (comprehensive provision of material properties), how to improve concepts of future work (meta-analysis, long-term field studies, use of deep-insight microbial DNA sequencing), and what needs to be further investigated (the link between structural and functional microbial parameters, the impact of biochar on pesticide efficiency).
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•Organic amendments have multiple beneficial effects in soils structure and function.•Biochar outperforms straw and compost only with regards to sorption.•Comparability criteria for experimental studies are recommended (C, N, H, pH, etc.).•Constant laboratory conditions often mask amendment effects in soils.•DNA sequencing methods are needed to better understand microbial communities.
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•Co-culture with S. vineae and C. butyricum enhanced hydrogen production and yield.•Hydrogen, acetate, and butyrate enhance with S. vineae supplementation.•Only lactate was produced ...at the monoculture of S. vineae.•Predicted gene expression implied C. butyricum converted lactate to butyrate/H2.
Dark fermentation has emerged as a promising method for converting waste into biohydrogen, a clean and sustainable energy source. However, the interaction between biohydrogen production performance and its microbial community has not been investigated sufficiently. This study investigated the effect of S. vineae on hydrogen production using defined cultures. Co-cultures of Clostridium butyricum (C. butyricum) with Sporolactobacillus vineae (S. vineae) increased the hydrogen production from 1.57 to 1.84 mol H2/mol glucoseadded, whereas lactic acid production did not increase in comparison with single culture of C. butyricum. At all the examined co-culture conditions, C. butyricum occupied more than 90% of the microbial composition; therefore, the microbial community analysis alone could not explain the difference in hydrogen production according to S. vineae addition. PICRUSt analysis showed that co-culture with S. vineae enhanced the expression of genes relating lactate to butyrate and H2 pathway, although S. vineae did not produce butyrate. Co-cultures of Clostridium sp. and Sporolactobacillus sp. could be beneficial for H2 production from the viewpoint of acidogenic pathway regulation. This study is expected to contribute to the understanding of the synergistic mechanisms of both the strains to obtain optimal biohydrogen production.
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