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Abstract Microbial necromass carbon (MNC) can reflect soil carbon (C) sequestration capacity. However, changes in the reserves of MNC in response to warming in alpine grasslands across the Tibetan Plateau are currently unclear. Based on large-scale sampling and published observations, we divided eco-clusters based on dominant phylotypes, calculated their relative abundance, and found that their averaged importance to MNC was higher than most other environmental variables. With a deep learning model based on stacked autoencoder, we proved that using eco-cluster relative abundance as the input variable of the model can accurately predict the overall distribution of MNC under current and warming conditions. It implied that warming could lead to an overall increase in the MNC in grassland topsoil across the Tibetan Plateau, with an average increase of 7.49 mg/g, a 68.3% increase. Collectively, this study concludes that alpine grassland has the tendency to increase soil C sequestration capacity on the Tibetan Plateau under future warming.

Taste and odor (T&O) compounds have emerged as crucial parameters for assessing water quality. Therefore, identifying effective methodologies for the removal of these compounds is imperative. In this study, an effective approach utilizing laccase assisted by a micro-electric field was developed for the degradation of 2-methylisoborneol (2-MIB). For this purpose, the optimal conditions for the laccase-catalyzed degradation of 2-MIB were determined, and they were pH 4.0, 25 °C, 150 rpm, 0.1 U/mL of laccase, and 200 ng/L of 2-MIB. Under these specified conditions, the degradation efficiency of 2-MIB was approximately 78% after a 4 h reaction period. Subsequently, the introduction of an electric field yielded a synergistic effect with the enzyme for 2-MIB degradation. At an electric current intensity of 0.04 A over a 4 h duration, the degradation efficiency increased to 90.78%. An analysis using SPME-GC/MS provided information on the degradation intermediates of 2-MIB resulting from laccase-catalyzed degradation, electrocatalytic degradation, and micro-electric-assisted laccase degradation. The potential degradation pathways of 2-MIB illustrated that these three methods result in common degradation products, such as capric aldehyde, nonylaldehyde, and 2-ethylhexanol, and their final products include 3-pentanone, acetone, and 2-butanone. This study provides an enzyme–electrochemical method for the efficient and rapid degradation and removal of 2-MIB. The strategy of laccase catalysis assisted by a micro-electric field has good potential for the removal of pollutants from the natural environment.

Despite the fact that physical and chemical processes have been widely proposed to explicate the stabilization mechanisms of soil organic carbon (SOC), thebioavailability of SOC linked to soil physical structure, microbial community structure, and functional genes remains poorly understood. This study aims to investigate the SOC division based on bioavailability differences formed by physical isolation, and to clarify the relationships of SOC bioavailability with soil elements, pore characteristics, and microbial activity. Results revealed that soil element abundances such as SOC, TN, and DOC ranked in the same order as the soil porosity as clay > silt ≥ coarse sand > fine sand in both top and sub soil. In contrast to silt and clay, which had reduced SOC bioavailability, fine sand and coarse sand had dramatically enhanced SOC bioavailability compared to the bulk soil. The bacterial and fungal community structure was significantly influenced by particle size, porosity, and soil elements. Copiotrophic bacteria and functional genes were more prevalent in fine sand than clay, which also contained more oligotrophic bacteria. The SOC bioavailability was positively correlated with abundances of functional genes, C degradation genes, and copiotrophic bacteria, but negatively correlated with abundances of soil elements, porosity, oligotrophic bacteria, and microbial biomass (p

The augmented prevalence of Se (Se) pollution can be attributed to various human activities, such as mining, coal combustion, oil extraction and refining, and agricultural irrigation. Although Se is vital for animals, humans, and microorganisms, excessive concentrations of this element can give rise to potential hazards. Consequently, numerous approaches have been devised to mitigate Se pollution, encompassing physicochemical techniques and bioremediation. The recognition of Se volatilization as a potential strategy for mitigating Se pollution in contaminated environments is underscored in this review. This study delves into the volatilization mechanisms in various organisms, including plants, microalgae, and microorganisms. By assessing the efficacy of Se removal and identifying the rate-limiting steps associated with volatilization, this paper provides insightful recommendations for Se mitigation. Constructed wetlands are a cost-effective and environmentally friendly alternative in the treatment of Se volatilization. The fate, behavior, bioavailability, and toxicity of Se within complex environmental systems are comprehensively reviewed. This knowledge forms the basis for developing management plans that aimed at mitigating Se contamination in wetlands and protecting the associated ecosystems.

Abstract Closely related with microbial activities, soil developments along the glacier forelands are generally considered a carbon sink; however, those of continental glacier forelands remain unclear. Continental glaciers are characterized by dry conditions and low temperature that limit microbial growth. We investigated the carbon characteristics along a chronosequence of the Laohugou Glacier No. 12 foreland, a typical continental glacier on the Tibetan Plateau, by analyzing soil bacterial community structure and microbial carbon-related functional potentials. We found an unexpected carbon loss in which soil organic carbon decreased from 22.21 g kg−1 to 10.77 g kg−1 after receding 50 years. Structural equation modeling verified the important positive impacts from bacterial community. Lower carbon fixation efficiency along the chronosequence was supported by less autotrophic bacteria and carbon fixation genes relating to the reductive tricarboxylic acid cycle. Lower carbon availability and higher carbon requirements were identified by an increasing bacterial copy number and a shift of the dominant bacterial community from Proteobacteria and Bacteroidetes (r-strategists) to Actinobacteria and Acidobacteria (K-strategists). Our findings show that the carbon loss of continental glacier foreland was significantly affected by the changes of bacterial community, and can help to avoid overestimating the carbon sink characteristics of glacier forelands in climate models.

IntroductionBacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments.MethodsHere, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics.Results and discussionThe different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.

IntroductionThe functions of terrestrial ecosystems are mainly maintained by bacteria, as a key component of microorganisms, which actively participate in the nutrient cycling of ecosystems. Currently, there are few studies have been carried out on the bacteria contributing to the soil multi-nutrient cycling in responding to climate warming, which hampers our obtainment of a comprehensive understanding of the ecological function of ecosystems as a whole.MethodsIn this study, the main bacteria taxa contributing to the soil multi-nutrient cycling under the long-term warming in an alpine meadow was determined based onphysichemical properties measurement and high-throughput sequencing, and the potential reasons that warming altered the main bacteria contributing to the soil multi-nutrient cycling were further analyzed.ResultsThe results confirmed that the bacterial β-diversity was crucial to the soil multi-nutrient cycling. Furthermore, Gemmatimonadetes, Actinobacteria, and Proteobacteria were the main contributors to the soil multi-nutrient cycling, and played pivotal roles as keystone nodes and biomarkers throughout the entire soil profile. This suggested that warming altered and shifted the main bacteria contributing to the soil multi-nutrient cycling toward keystone taxa.DiscussionMeanwhile, their relative abundance was higher, which could make them have the advantage of seizing resources in the face of environmental pressures. In summary, the results demonstrated the crucial role of keystone bacteria in the multi-nutrient cycling under the climate warming in the alpine meadow. This has important implications for understanding and exploring the multi-nutrient cycling of alpine ecosystems under the global climate warming.

In recent years, taste and odor (T&O) compounds in drinking water are becoming a serious problem, which has brought many challenges to drinking water treatment plants. Due to global concerns about the emergence of T&O compounds, researchers have proposed various water treatment technologies to ensure the quality of drinking water. In this paper, abiotic and biotic methods for the treatment of T&O compounds are reviewed, including process parameters, advantages and disadvantages, removal efficiency and mechanism. Geosmin (GSM) and 2-methylisoborneol (2-MIB) are the most common odorous substances with earthy and musty smells. The chemical and biological methods for the possible degradation pathways of these two compounds are summarized. Furthermore, suggestions and approaches are provided for efficient and safe strategies for T&O compound treatments and their future applications.

Highly chlorinated benzenes usually have a low efficient degradation in environment. Here we proposed a synergistic removal strategy of pentachlorobenzene (PeCB) using Pseudomonas sp. JS100 coupled with immobilized nanoscale zero-valent iron (NZVI). The structural and textural features of the synergistic system were characterized by X-ray powder diffraction, field emission scanning electron microscopy, and a specific surface area and pore size analysis. Nanoscale zero-valent iron particles were dispersed and attached to the biofilter, which increased the specific surface area to 34.5 m2 g−1. The batch experiment revealed that the removal efficiency of PeCB reached 80.2% in the synergistic system within 48 h. The degradation followed pseudo-first-order reaction kinetics, and the reaction rate constant was measured to be 0.0336 h−1. In the degradation mechanism, PeCB was degraded by NZVI to lower chlorobenzenes, which were utilized by Pseudomonas sp. JS100 as nutrients, thereby achieving rapid removal of PeCB.

Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria’s environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans, especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans, adding to our understanding of QS regulation in biofilm development.

Alpine ecosystem stability and biodiversity of the Tibetan plateau are facing threat from dry valley vegetation uplift expansion, a process which is highly connected to variations in the soil microbial community and soil nutrients. However, the variation of microbial community properties and their relationship to soil nutrients have scarcely been explored in Tibetan dry valleys, which is a gap that hampers understanding the dry valley ecosystem’s response to vegetation change. In this study, we sampled grasslands (G), a grass-shrub transition area (T), and shrublands (S) along an uplift expansion gradient and investigated the link between microbial community properties and soil nutrients. The results showed that shrub degradation by grass expansion in Tibetan dry valley was accompanied by increasing relative phosphorus (P) limitation, which was the main driver for bacterial and fungal composition variation as it offered highest total effect on PC1 (0.38 and 0.63, respectively). Total phosphorus (TP) was in the center module of bacterial and fungal network under shrub soil and even acted as key nodes in fungal networks. During the replacement by grass, TP was gradually marginalized from both bacterial and fungal center network module and finally disappeared in networks, with ammonia and nitrate gradually appearing in the bacterial network. However, TC and total nitrogen (TN) were always present in the center modules of both fungal and bacterial network. These support that a TP variation-induced compositional and network functional shift in the microbial community was a potential reason for vegetation uplift expansion in Tibetan dry valley. This study highlighted the effect of TP on microbial community properties during dry valley vegetation uplift expansion and offered basic information on Tibetan alpine dry valley ecosystem’s response to climate change.

In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.

Excessive ammonia (NH3) emitted from nitrogen fertilizer application in farmland have caused serious disturbance to global environment, including reduction of visibility, formation of regional haze, and increase of nitrogen deposition. Application of biofertilizer has been considered as an effective approach for soil improvement and agriculture sustainability. In this study, a field experiment was conducted to evaluate the potential of B. subtilis biofertilizer on mitigating NH3 volatilization and to investigate the underlying mechanisms. Compared with organic fertilizer, the incorporation of B. subtilis biofertilizer reduced NH3 volatilization by up to 44%. Moreover, the application of B. subtilis biofertilizer reduced the abundance of ureC gene, and increased the abundance of functional genes (bacterial amoA and comammox amoA) and ammonia-oxidizing bacteria (AOB). This indicated that the conversion of fertilizer nitrogen to NH4+-N was decreased and the nitrification process was increased. In brief, the application of B. subtilis biofertilizer reduced the “source” and increased the “sink” of NH4+-N, thus reducing the retention of NH4+-N in alkaline soil, and mitigating NH3 volatilization. These results indicated that B. subtilis biofertilizer is an effective control strategy for agricultural NH3 emission, maintaining high crop yield and mitigating environmental disturbance.

Abstract Phyllosphere and rhizosphere are unique and wide‐ranging habitats that harbor various microbial communities, which influence plant growth and health, and the productivity of the ecosystems. In this study, we characterized the shared microbiome of the phyllosphere and rhizosphere among three plants (Ipomoea pes‐caprae, Wedelia chinensis, and Cocos nucifera), to obtain an insight into the relationships between bacteria (including diazotrophic bacteria) and fungi, present on these host plants. Quantitative PCR showed that the abundances of the microbiome in the soil samples were significantly higher than those in the phyllosphere samples, though there was an extremely low abundance of fungi in bulk soil. High‐throughput sequencing showed that the alpha‐diversity of bacteria and fungi was higher in the rhizosphere than the phyllosphere samples associated with the same plant, while there was no obvious shift in the alpha‐diversity of diazotrophic communities between all the tested phyllosphere and soil samples. Results of the microbial composition showed that sample‐specific bacteria and fungi were found among the phyllosphere and rhizosphere of the different host plants. About 10%–27% of bacteria, including diazotrophs, and fungi overlapped between the phyllosphere and the rhizosphere of these host plants. No significant difference in microbial community structure was found among the tested rhizosphere samples, and soil properties had a higher influence on the soil microbial community structures than the host plant species.

Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.

Chitin-char is obtained from fast pyrolysis of chitin. To obtain the maximum surface area, chitin-char is treated by nitric acid. Then, a kind of new arsenic removal bio-material is prepared by loading Ca(OH)2 on the char (called Ca(OH)2-char). IR spectroscopy before and after char treatment reveal at least three distinct patterns of peak changes. An adsorption study is performed at different doses, pHs, and coexisting ions in the batch mode. The adsorption kinetics follows two first-order equations. Kinetic studies yield an optimum equilibrium time of 2 h with an adsorbent dose of 0.4 g/L and concentration of 10 mg/L. Using only 0.4 g/L of carbon, the maximum removal capacity is about 99.8%. The result indicates that the Ca(OH)2-char has a high adsorption capacity in the process of removing arsenic (III).

In this study, magnetic Fe3O4 nanoparticles (NPs) were used as an effective enhancer to increase the biomass and total lipid production of Chlorella sp. UJ-3. It was found that the biomass of algal cells increased significantly when they were exposed to low concentrations of Fe3O4 NPs (20 mg/L), while the best total lipid content of algal cells was achieved when they were exposed to high concentrations of Fe3O4 NPs (100 mg/L). Therefore, we established a strategy to promote the growth and lipid accumulation of microalgae by initially exposing the algal cells to low concentrations of Fe3O4 NPs and then treating them with an increased concentration of Fe3O4 NPs after 12 days of culture. For this strategy, the biomass and total lipid production of algal cells increased by 50% and 108.7%, respectively, compared to the untreated control. The increase in lipid production and change in the fatty acid composition of Chlorella cells were found to help them to cope with the increased number of reactive oxygen species produced due to oxidative stress in alga cells after the addition of Fe3O4 NPs. This study provided a highly efficient way to improve the lipid production of microalgae using nanoparticles.

Abstract Methane fluxes, which are controlled by methanogens and methanotrophs, vary among wetland vegetation species. In this study, we investigated belowground methanogens and methanotrophs in two soils under two different dominant vegetation species with different methane fluxes in the Zoige wetland, which was slightly but significantly (p ≤ 0.05) higher in soils covered by Carex muliensis than that in soils covered by Eleocharis valleculosa. Real‐time quantitative PCR and Illumina MiSeq sequencing methods were used to elucidate the microbial communities based on the key genes involved in methane production and oxidation. The absolute abundances of methanogens and methanotrophs of samples from C. muliensis were 1.80 ± 0.07 × 106 and 4.03 ± 0.28 × 106 copies g‐soil−1, respectively, and which from E. valleculosa were 3.99 ± 0.19 × 105 and 2.53 ± 0.22 × 106 copies g‐soil−1 , respectively. The t‐test result showed that both the abundance of methanogens and methanotrophs from C. muliensis were significantly higher (p ≤ 0.05) than that of samples from E. valleculosa. However, the diversities and compositions of both methanogens and methanotrophs showed no significant differences (p ≥ 0.05) between vegetation species. The path analysis showed that the microbial abundance had a greater effect than the microbial diversity on methane production potentials and the regression analysis also showed that the methane emissions significantly (p ≤ 0.05) varied with the abundance of methane‐cycling microbes. These findings imply that abundance rather than diversity and composition of a methane‐cycling microbial community is the major contributor to the variations in methane emissions between vegetation types in the Zoige wetland.

Water system degradation has a severe impact on daily life, especially in developing countries. However, microbial changes associated with this degradation, especially changes in microbes related to sulfur (S) cycling, are poorly understood. In this study, the abundance, structure, and diversity of sulfate-reducing microorganisms (SRM) and sulfur-oxidizing microorganisms (SOM) in the sediments from the Ziya River Basin, which is polluted by various human interventions (urban and agricultural activities), were investigated. Quantitative real-time PCR showed that the S cycling-related (SCR) genes (dsrB and soxB) were significantly elevated, reaching 2.60 × 107 and 1.81 × 108 copies per gram of dry sediment, respectively, in the region polluted by human urban activities (RU), and the ratio of dsrB to soxB abundance was significantly elevated in the region polluted by human agricultural activities (RA) compared with those in the protected wildlife reserve (RP), indicating that the mechanisms underlying water system degradation differ between RU and RA. Based on a 16S rRNA gene analysis, human interventions had substantial effects on microbial communities, particularly for microbes involved in S cycling. Some SCR genera (i.e., Desulfatiglans and Geothermobacter) were enriched in the sediments from both RA and RU, while others (i.e., Desulfofustis and Desulfonatronobacter) were only enriched in the sediments from RA. A redundancy analysis indicated that NH4+-N and total organic carbon significantly influenced the abundance of SRM and SOM, and sulfate significantly influenced only the abundance of SRM. A network analysis showed high correlation between SCR microorganisms and other microbial groups for both RU and RA, including those involved in carbon and metal cycling. These findings indicated the different effects of different human interventions on the microbial community composition and water quality degradation.

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR.

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Farnesol, a quorum‐sensing molecule, was used successfully to improve laccase production in submerged cultures of Trametes versicolor. At the optimal farnesol concentration of 60 μM added at the beginning of the culture, the extracellular laccase activity reached 629.3 U L−1 after 6 days of cultivation, which represented a 1.92‐fold increase relative to the control without farnesol treatment. The addition of farnesol resulted in an increase in the accumulation of H2O2 and an increased expression of the laccase (lac) gene and the RhoA gene. The RhoA gene correlated with hyperbranched mycelia, which facilitated the secretion of the intracellular laccase. This study provides a basis for understanding the induction mechanism of farnesol for enhancing laccase production.

The biodiversity of fungi, which are extremely important in maintaining the ecosystem balance in alpine lakeside wetlands, has not been fully studied. In this study, we investigated the fungal communities of three lakeside wetlands from different altitudes in the Qinghai–Tibet Plateau and its edge. The results showed that the fungi of the alpine lakeside wetland had higher species diversity. Functional annotation of fungi by FUNGild software showed that saprophytic fungi were the most abundant type in all three wetlands. Further analysis of the microbial phylogenetic molecular ecological network (pMEN) showed that saprophytic fungi are important species in the three wetland fungal networks, while symbiotic fungi and pathotrophic fungi have different roles in the fungal networks in different wetlands. Community diversity was high in all three lakeside wetlands, but there were significant differences in the composition, function and network structure of the fungal communities. Contemporary environmental conditions (soil properties) and historical contingencies (geographic sampling location) jointly determine fungi community diversity in this study. These results expand our knowledge of fungal biodiversity in the alpine lakeside wetlands.

Recently, a new oxygenic pathway has been proposed based on the disproportionation of NO with putative NO dismutase (Nod). In addition to a new process in nitrogen cycling, this process provides ecological advantages for the degradation of substrates in anaerobic conditions, which is of great significance for wastewater treatment. However, the Nod distribution in aquatic environments is rarely investigated. In this study, we obtained the nod genes with an abundance of 2.38 ± 0.96 × 105 copies per gram of dry soil from the Zoige wetland and aligned the molecular characteristics in the corresponding Nod sequences. These Nod sequences were not only found existing in NC10 bacteria, but were also found forming some other clusters with Nod sequences from a WWTP reactor or contaminated aquifers. Moreover, a new subcluster in the aquifer-similar cluster was even dominant in the Zoige wetland and was named the Z-aquifer subcluster. Additionally, soils from the Zoige wetland showed a high potential rate (10.97 ± 1.42 nmol of CO2 per gram of dry soil per day) for nitrite-dependent anaerobic methane oxidation (N-DAMO) with low abundance of NC10 bacteria, which may suggest a potential activity of Nod in other clusters when considering the dominance of the Z-aquifer subcluster Nod. In conclusion, we verified the occurrence of Nod in an alpine wetland for the first time and found a new subcluster to be dominant in the Zoige wetland. Moreover, this new subcluster of Nod may even be active in the N-DAMO process in this alpine wetland, which needs further study to confirm.

Great attention has been paid to the potential of wastewater irrigation as a sustainable water source, particularly due to water scarcity and water pollution issues. However, few studies have focused on its adverse effects and on the health risks it may pose. In this study, the physicochemical properties of soils and plants irrigated with rural domestic wastewater and associated microbiological risks were investigated. The results showed that sewage irrigation could increase the production of vegetables and improve soil fertility. While the nitrate content of plants increased significantly, pathogens on plants and in soils increased after irrigation with raw wastewater. In particular, there was a wide range of pathogenic bacteria in the phyllosphere, which may indicate risks if contaminated vegetables are consumed directly. Treated wastewater irrigation was not significantly different from controls, which were irrigated by tap water; consequently, it can be used as an alternative water resource for agricultural irrigation. The presence of a wide spectrum pathogens in wastewater shows the necessity of long-term monitoring and further evaluation.

Removal of nitrogen (N) is a critical aspect in the functioning of constructed wetlands (CWs), and the N treatment in CWs depends largely on the presence and activity of macrophytes and microorganisms. However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha-1 d-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA) and denitrifying genes (nirS, nirK, and nosZ) were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold) and nirS genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera), nitrite-oxidizing bacteria (Nitrospira), and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments. The results of a canonical correspondence analysis and Mantle tests indicated that M. aquaticum may shift the sediment microbial community by changing the sediment chemical properties. The enriched nitrifiers and denitrifiers were distributed widely in the vegetated sediments, showing positive ecological associations among themselves and other bacteria based on phylogenetic molecular ecological networks.

Massively input and accumulated ammonium is one of the main causes of eutrophication in aquatic ecosystems, which severely deteriorates water quality. Previous studies showed that one of the commonly used macrophytes, Myriophyllum aquaticum, was capable of not only withstanding ammonium of high concentration, but also efficiently assimilating extracellular ammonium to constitutive amino acids and proteins. However, the genetic mechanism regulating such efficient nitrogen metabolism in M. aquaticum is still poorly understood. Therefore, RNA-based analysis was performed in this study to understand the ammonium regulatory mechanism in M. aquaticum in response to various concentrations of ammonium. A total of 7721 genes were differentially expressed, of which those related to nitrogen-transport, assimilation, and remobilization were highly-regulated in response to various concentrations of ammonium. We have also identified transcription factors and protein kinases that were rapidly induced in response to ammonium, which suggests their involvement in ammonium-mediated signalling. Meanwhile, secondary metabolism including phenolics and anthocyanins biosynthesis was also activated in response to various concentrations of ammonium, especially at high ammonium concentrations. These results proposed a complex physiological and genetic regulation network related to nitrogen, carbohydrate, transcription factors, and secondary metabolism for nitrogen use efficiency in M. aquaticum.

Many Gram-negative plant pathogenic bacteria employ a N-acylhomoserine lactone (AHL)-based quorum sensing (QS) system to regulate their virulence traits. A sustainable biocontrol strategy has been developed using quorum quenching (QQ) bacteria to interfere with QS and protect plants from pathogens. Here, the prevalence and the diversity of QQ strains inhabiting tobacco leaf surfaces were explored. A total of 1177 leaf-associated isolates were screened for their ability to disrupt AHL-mediated QS, using the biosensor Chromobacterium violaceum CV026. One hundred and sixty-eight strains (14%) are capable of interfering with AHL activity. Among these, 106 strains (63%) of the culturable quenchers can enzymatically degrade AHL molecules, while the remaining strains might use other QS inhibitors to interrupt the chemical communication. Moreover, almost 79% of the QQ strains capable of inactivating AHLs enzymatically have lactonase activity. Further phylogenetic analysis based on 16S rDNA revealed that the leaf-associated QQ bacteria can be classified as Bacillus sp., Acinetobacter sp., Lysinibacillus sp., Serratia sp., Pseudomonas sp., and Myroides sp. The naturally occurring diversity of bacterial quenchers might provide opportunities to use them as effective biocontrol reagents for suppressing plant pathogen in situ.

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses.

It is possible to improve cellulase production by controlling fungal morphology. Farnesol, the first quorum-sensing molecule found in eukaryotic organisms, is reported to influence the morphology of fungi. In this work, farnesol was investigated for its effect on morphology and cellulase production of Penicillium decumbens. Scanning electron microscopy (SEM) revealed that farnesol promoted the growth of hyphae, making possible and facilitating a higher yield of cellulase secretion. Enhanced interaction with the substrate in fermentation led to greater cellulase production. These findings are associated with the subsequent cellulase production of the fungus. Compared with a control medium, exogenously added 1 mM farnesol resulted in 1.32-fold increase in maximal filter paper activity with no significant change in the activity per unit of protein. These results provide a novel way to improve the cellulase production, promoting the commercial application of cellulase.

Water pollution caused by various eutrophic nutrients such as nitrogen (N) and phosphorus (P), such as outbreaks of eutrophication in rivers and lakes, has become a serious environmental problem in China. Such problems have spurred extensive studies aiming at finding environmentally friendly solutions. Various constructed wetlands (CWs), planted with different macrophytes, have been considered as environmentally safe technologies to treat various wastewaters for several decades. Due to their low energy and operational requirements, CWs are promising alternative solutions to water eutrophication problems. Within the CWs, macrophytes, sediments, and the microbial community are indispensable constituents of such an ecosystem. In this study, a laboratory-scale surface flow CW (LSCW) was constructed to investigate the effects of two different plants, Eichhornia (E.) crassipes (Mart.) Solms and Myriophyllum (M.) aquaticum, on the removal of eutrophic N and P. The results showed that both plants could significantly reduce these nutrients, especially ammonium (NH4+), and LSCW planted with M. aquaticum performed better (82.1% NH4+ removal) than that with E. crassipes (66.4% NH4+ removal). A Monod model with a plug flow pattern was used to simulate the relationship of influent and effluent concentrations with the kinetic parameters of this LSCW. Based on the model, a pilot-scale surface flow CW (PSCW) was designed, aiming to further enhance N and P removal. The treatment with M. aquaticum and polyethylene materials showed the best removal efficiency on NH4+ as well as on total nitrogen and phosphorus. In general, the enlarged PSCW can be a promising solution to the eutrophication problems occurring in aquatic environments.

Land-use conversion from woodlands to tea fields in subtropical areas of central China leads to increased nitrous oxide (N2O) emissions, partly due to increased nitrogen fertilizer use. A field investigation of N2O using a static closed chamber-gas chromatography revealed that the average N2O fluxes in tea fields with 225 kg N ha−1 yr−1 fertilizer application were 9.4 ± 6.2 times higher than those of woodlands. Accordingly, it is urgent to develop practices for mitigating N2O emissions from tea fields. By liquid-state fermentation of sweet potato starch wastewater and solid-state fermentation of paddy straw with application of Trichoderma viride, we provided the tea plantation with biofertilizer containing 2.4 t C ha−1 and 58.7 kg N ha−1. Compared to use of synthetic N fertilizer, use of biofertilizer at 225 kg N ha−1 yr−1 significantly reduced N2O emissions by 33.3%–71.8% and increased the tea yield by 16.2%–62.2%. Therefore, the process of bioconversion/bioaugmentation tested in this study was found to be a cost-effective and feasible approach to reducing N2O emissions and can be considered the best management practice for tea fields.

This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested.