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To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg−1), electrical conductivity (8.22 mS·cm−1), urease (0.18 mg·g−1·d−1), and nitrate reductase (0.13 mg·g−1·d−1), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg−1), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices. [ABSTRACT FROM AUTHOR]

Tillage and straw returning are promising practices to improve soil quality, especially because of the unclear controlling effects on microbial communities and functions. A 5‐year field experiment in a winter wheat‐summer maize cropping system was implemented in the North China Plain to address this research gap. Management practices were deep tillage, rotary tillage, and no‐tillage, each with either wheat only or both wheat and maize straw returning. Shotgun metagenomic sequencing was performed to investigate the microbial community, diversity, co‐occurrence network, and function in the topsoil (0–20 cm). The associations between soil physiochemical properties and microbial community characteristics were also evaluated. Rotary tillage with only wheat straw returning (RTS) significantly increased Shannon's diversity index by 0.24%–1.71% compared to other treatments. No‐tillage with only wheat straw returning (NTS) showed the most stable microbial network with the highest betweenness centrality (199.09), average path distance (2.31), and modularity (0.50). NTS had the highest relative abundance of microbial carbon (C), nitrogen (N) metabolisms, and C fixation pathways. Among deep tillage practices, both wheat and maize straw returning (DTD) were more beneficial to the stability of microbial networks than only wheat straw returning (DTS), yet without improvement in microbial diversity and function. In conclusion, microbial community and function are practical predictors of variations in soil nutrient availability, and pH value in response to different tillage and residue management practices. In particular, our study provides a basis for the development of a sustainable crop residue management system. [ABSTRACT FROM AUTHOR]

The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0–20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms' carbon and nitrogen fixation capacities. [ABSTRACT FROM AUTHOR]

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology. [ABSTRACT FROM AUTHOR]

The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0–20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms’ carbon and nitrogen fixation capacities.

To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg−1), electrical conductivity (8.22 mS·cm−1), urease (0.18 mg·g−1·d−1), and nitrate reductase (0.13 mg·g−1·d−1), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg−1), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices.

The over-utilizing of nitrogen fertilizers in paddy wetlands potentially threatens to the surrounding waterbody, and a deep understanding of the community and function of microorganisms is crucial for paddy non-point source pollution control. In this study, top soil samples (0-15cm) of paddy wetlands under groundwater's irrigation at different depths (H1: 6.8m, H2: 13.7m, H3: 14.8m, H4: 15.6m, H5: 17.0m, and H6: 17.8m) were collected to investigate microbial community and function differences and their interrelation with soil properties. Results suggested some soil factor differences for groundwater's irrigation at different depths. Deep-groundwater's irrigation (H2-H6) was beneficial to the accumulation of various electron acceptors. Nitrifying-bacteria Ellin6067 had high abundance under deep groundwater irrigation, which was consistent with its diverse metabolic capacity. Meanwhile, denitrifying bacteria had diverse distribution patterns. Iron-reducing bacteria Geobacter was abundant in H1, and Anaeromyxobacter was abundant under deep groundwater irrigation; both species could participate in Fe-anammox. Furthermore, Geobacter could perform dissimilatory nitrate reduction to ammonia using divalent iron and provide substrate supply for anammox. Intrasporangium and norank_f_Gemmatimonadacea had good chromium- and vanadium-reducting potentials and could promote the occurrence of anammox. Low abundances of methanotrophsMethylocystis and norank_f_Methyloligellaceae were associated with the relatively anoxic environment of paddy wetlands, and the presence of aerobic methane oxidation was favorable for in-situ methane abatement. Moisture, pH, and TP had crucial effects onmicrobial community under phylum- and genus-levels. Microorganisms under shallow groundwater irrigation were highly sensitive to environmental changes, and Fe-anammox, nitrification, and methane oxidation were favorable under deep groundwater irrigation. This study highlights the importance of comprehensively revealing the microbial community and function of paddy wetlands under groundwater's irrigation and reveals the underlying function of indigenous microorganisms in agricultural non-point pollution control and greenhouse gas abatement. [ABSTRACT FROM AUTHOR]

Introduction: Maize (Zea mays L.)-soybean (Glycine max L.) intercropping has been widely utilized in agricultural production due to its effectiveness in improving crop yield and nutrient use efficiency. However, the responses of maize rhizosphere microbial communities and the plant pathogen relative abundance to maize growth traits in maize-soybean intercropping systems with different chemical nitrogen fertilizer application rates remain unclear. Methods: In this study, a field experiment was conducted, and the bacterial and fungal communities of maize rhizosphere soils in maize-soybean intercropping systems treated with different N fertilization rates were investigated using Illumina NovaSeq sequencing. Maize growth traits, soil physicochemical properties and soil enzyme activities were also examined. Results and discussion: We found that intercropping and N fertilizer treatments strongly influenced soil microbial diversity, structure and function. The PLSPM (partial least squares path modeling) confirmed that soil nutrients directly positively affected maize biomass and that intercropping practices indirectly positively affected maize biomass via soil nutrients, especially NH4 C-N. Intercropping agronomic approaches also improved maize growth traits by reducing the plant pathogen abundance, and the relative abundance of the plant pathogen Trichothecium roseum significantly decreased with intercropping treatments compared to monocropping treatments. These results confirmed the benefits of maize-soybean intercropping treatments for agricultural production. [ABSTRACT FROM AUTHOR]

Freeze–thaw has been proved to be a simple, cost-effective, and highly efficient manner to purify wastewater. However, it remains unclear how microbial compositions and functions in meltwater differentiate over progressive thawing and how such differences affect the end product water quality. In this study, wastewater was frozen, progressively thawed via microwave and collected at five intervals: 5 min, 3 min, 3 min, 3 min, and 3 min (termed as T1~T5). It only took 8 min of microwave and 38.8% of total water to remove more than 75% of the dissolved salt and typical pathogenic microbes, and merely 11 min to reach a removal rate greater than 90%. The Shannon index indicated that the α diversity of bacterial and fungal communities significantly reduced from T1 to T5, and the NMDS dissimilarities also illustrated significantly different β diversity between T1 and T2 and T3, T4, and T5. The OTU-based bacterial and fungal co-occurrence networks developed from T1, T5, and CK were significantly different from each other and clustered in distinct modules. Microbial functional profiles further showed that the meltwater preferentially discharged at T1 selectively removed pathogenic and symbiotic fungi and bacterial subsets associated with endocrine diseases, carbohydrate metabolism, and aging. Yet, other microbial subsets tended to be selectively enriched in the end product at T5, such as saprotrophic fungi and bacterial subsets related to drug resistance, infectious diseases, cancers, and xenobiotics' biodegradation and metabolism. Overall, the fast thawing facilitated by microwave and in turn the efficient removal of brines from ice crystals offered a new approach to overcome the prolonged time cost required by natural thawing. Selective discharge and enrichment of microbial subsets during progressive thawing alarmingly calls for in-depth investigations on the temporal fluxes of microbes when attempting to reuse wastewater in the regions suitable to apply freeze–thaw protocols. [ABSTRACT FROM AUTHOR]

Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system. [ABSTRACT FROM AUTHOR]

The microbial characteristics of water treated by tea polyphenols after the ultrafiltration process were studied based on the continuous disinfection performance of tea polyphenols. Metagenomics was carried out to investigate the microbial community distribution, functional characteristics, and variations after disinfection, to reveal the disinfection principle of tea polyphenols, and to provide the theoretical basis for using tea polyphenols as a disinfectant to better control the growth of microorganisms. The analysis of microbial diversity and community structure showed that the microbial diversity in water was significantly reduced after disinfection with tea polyphenols. The results of hierarchical clustering analysis showed that microbial metabolism, environmental information processing, and functional modules in genetic information processing were significantly inhibited after disinfection treatment using tea polyphenols. The tea polyphenols inhibit the growth and reproduction of microorganisms by selection on the microorganisms in the water, thus achieving the effect of bacterial inhibition. HIGHLIGHTS Tea polyphenols as disinfectants inhibit the regrowth of bacteria.; Tea polyphenols disinfection significantly reduces the diversity of microorganisms in water.; The gene function of many microorganisms in water is greatly changed after disinfection by tea polyphenols.; Tea polyphenols disinfection exerts a greater inhibitory effect on the metabolism of various nucleotides and related processes of microorganisms.;

Contamination of per- and polyfluoroalkyl substances (PFAS) poses a significant threat to soil ecosystem health, yet there remains a lack of understanding regarding the responses of soil microbial communities to prolonged PFAS exposure in field conditions. This study involved a three-year field investigation to track changes in microbial communities and functions in soil subjected to the contamination of a primary PFAS, perfluorooctanoic acid (PFOA). Results showed that PFOA exposure altered soil bacterial and fungal communities in terms of diversity, composition, and structure. Notably, certain bacterial communities with a delayed reaction to PFOA contamination showed the most significant response after one year of exposure. Fungal communities were sensitive to PFOA in soil, exhibiting significant responses within just four months of exposure. After two years, the impact of PFOA on both bacterial and fungal communities was lessened, likely due to the long-term adaptation of microbial communities to PFOA. Moreover, PFOA exposure notably inhibited alkaline phosphatase activity and reduced certain phosphorus cycling-related functional genes after three years of exposure, suggesting potential disruptions in soil fertility. These new insights advance our understanding of the long-term effects of PFOA on soil microbial communities and functions at a field scale. [Display omitted] • Bacterial community shows a delayed response to PFOA. • Fungal community exhibits a more immediate sensitivity to PFOA. • Long-term adaptation likely lessens PFOA impact on bacterial and fungal communities. • PFOA exposure reduced alkaline phosphatase activity and P cycling genes. [ABSTRACT FROM AUTHOR]

Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality. [ABSTRACT FROM AUTHOR]

Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system.

Maize-peanut intercropping (M//P) is widely used in the North China Plain, but little is known about the changes in soil microorganism and its interactions with soil nutrient availability. Based on 3 years of field experiment, this study systematically investigated the soil microorganisms and soil properties in the 0–10 cm, 10–20 cm and 20–40 cm soil layers. This study found that M//P changed the soil microbial community composition compared to monoculture modes in all the studied soil layers but had the most effects in the 10–20 cm soil layer. Soil organic carbon, available phosphorus and available potassium explained the most variation in the microbial composition, while Proteobacteria, Acidobacteria and Planctomycetes were the phyla that were most affected by environmental factors. Based on the correlations and microbial function analysis, we speculated that: 1) M//P increased the relative abundance of Chlorobi, Parcubacteria and Chlamydiae, which promoted carbon and nitrogen metabolism; 2) M//P increased the relative abundance of Chlamydiae, Saccharibacteria, and Parcubacteria and then enhanced phosphonate and phosphinate metabolism, providing more available phosphorus for crops; 3) some KEGG pathways related to immunity and disease were increased in M//P, which may be related to disease control. [ABSTRACT FROM AUTHOR]

Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality.

Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.

We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).

We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil). [ABSTRACT FROM AUTHOR]

Performic acid (PFA), a new generation of disinfectant, has shown outstanding performance for wastewater treatment. However, the effect of PFA on wastewater microbial community changes as well as the differences in comparison to the commonly disinfectants used are poorly documented. We provide an overview of the PFA effect and that of chlorine and UV, two commonly used disinfectants, on microbial community diversity and structure. The study was performed using wastewaters from three municipal wastewater treatment plants (WWTPs) processed by activated sludge, lagoon and reed beds, and biofilter. We focused on disinfection of pathogen microorganisms, identifying sensitive and resistant bacteria to disinfectants that can serve as biomarkers for evaluating the disinfectant performances. As well, we investigated the modifications of microbial functions after treatment by functional predictive analysis. The more efficient E. coli inactivation was obtained with initial concentration of 4 mg/L of PFA with 15 min disinfectant contact time that achieved 95.71–99.99% inactivation efficiency. Although the origin of wastewater was the main factor determining the microbial community diversity and composition, the microbial communities were specific to the disinfectant used. Linear discriminant analysis Effect Size (LEfSe) identified 18 and 10 biomarkers, including pathogenic microorganisms affiliated to Chromobacterium , Flavobacterium , Aeromonas , Enterobacteriaceae, Escherichia_Shigella and Fusobacteriaceae, which were sensitive to PFA, while being resistant to chlorine and/or UV. Consistently, the predicted bacterial functional patterns diverged according to the wastewater origin and the disinfectant used. Pathogen microorganisms were more sensitive to PFA than the other treatments, demonstrating its potential for implementing a safe reuse of wastewater. • PFA was an efficient disinfectant comparing to chlorine and UV. • Microbial communities from treated water were specific to the disinfectant used. • Biomarkers sensitive to PFA and resistant to chlorine and/or UV were identified. • Bacterial predicted functions diverge according to WWTP and disinfectants. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) broadly coexist with heavy metals (HMs) in soil, Cd and Cu are the main types of soil HMs contamination, in addition to polystyrene (PS), which is also widely present in the environment and prone to aging. However, differences in the effects of MPs and HMs on soil properties and microbial characteristics under alternating wetting and drying (AWD) remain unclear. Thus, this study investigated the effects of four conventional (0.2% (w/w)) and aged MPs in indoor incubation experiments on soil properties under desiccation (Dry) and AWD. We found that with the influence of the "enzyme lock" theory, the coexistence of MPs and HMs under Dry had a more pronounced effect on soil physicochemical properties, whereas the effects on soil enzyme activity under AWD were more significant. In addition, MPs decreased the available Cu by 4.27% and, conversely, increased the available Cd by 8.55%. Under Dry , MPs affected microbial function mainly through physicochemical properties, with a contribution of approximately 72.4%, whereas under AWD enzyme activity and HMs were significantly greater, with increases of 28.2% and 7.9%, respectively. These results indicate that the effects of MPs on environmental variation and microbial profiles under AWD conditions differed significantly from those under Dry. [Display omitted] • Microplastics (MPs) under Dry effect more on physicochemical properties. • More evident effects of MPs on soil enzyme activities/heavy metals (HMs) under AWD. • The effects of MPs on soil microbial structure were more significant under AWD. • Combined contamination of MPs and HMs under AWD effect more on microbial functions. • Greater impact of enzyme activity and HMs on microbial function under AWD. [ABSTRACT FROM AUTHOR]

Soil microbes play an important role in terrestrial carbon (C) cycling, but their functional response to global warming remains yet unclear. Soil metaproteomics has the potential to contribute to a better understanding of warming effects on soil microbes as proteins specifically represent active microbes and their physiological functioning. To quantify warming effects on microbial proteins and their distribution among different functional and phylogenetic groups, we sampled forest soil that had been artificially warmed (+4 °C) during seven consecutive growing seasons and analyzed its metaproteomic fingerprint and linked to soil respiration as a fundamental ecosystem service. Bacterial protein abundances largely exceeded fungal abundances at the study site but protein abundances showed only subtle differences among control and warmed soil at the phylum and class level, i.e. a temperature-induced decrease in Firmicutes , an increase in Agaricomycetes and Actinobacteria , and a decrease in the Asco/Basidiomycota ratio. Community function in warmed soil showed a clear trend towards increased proteins involved in microbial energy production and conversion, related to the increased CO 2 efflux from warmed soil as a result of stress environmental conditions. The differences in community function could be related to specific phyla using metaproteomics, indicating that microbial adaptation to long-term soil warming mainly changed microbial functions, which is related to enhanced soil respiration. The response of soil respiration to warming (+35% soil CO 2 efflux during sampling) has not changed over time. Accordingly, potential long-term microbial adaptations to soil warming were too subtle to affect soil respiration rates or, were overlaid by other co-varying factors (e.g. substrate availability). [ABSTRACT FROM AUTHOR]

Soil salinization and heavy metal (HM) pollution are global environmental problems. Bioorganic fertilizers facilitate phytoremediation, but their roles and microbial mechanisms in natural HM-contaminated saline soils have not been explored. Therefore, greenhouse pot trials were conducted with three treatments: control (CK), manure bioorganic fertilizer (MOF), and lignite bioorganic fertilizer (LOF). The results showed that MOF and LOF significantly increased nutrient uptake, biomass, toxic ion accumulation in Puccinellia distans , soil available nutrients, SOC, and macroaggregates. More biomarkers were enriched in MOF and LOF. Network analysis confirmed that MOF and LOF increased the number of bacterial functional groups and fungal community stability and strengthened their positive association with plants; Bacteria have a more significant effect on phytoremediation. Most biomarkers and keystones play important roles in promoting plant growth and stress resistance in the MOF and LOF treatments. In summary, besides enrichment of soil nutrients, MOF and LOF can also improve the adaptability and phytoremediation efficiency of P. distans by regulating the soil microbial community, with LOF having a greater effect. [Display omitted] • Bioorganic fertilizers improved plant growth and phytoremediation efficiency. • Bioorganic fertilizers enhanced nutrients uptake and changed microbial community. • More beneficial biomarkers were enriched in the bioorganic fertilizer treatments. • Network showed an increased positive correlation between microbes and plant. • Key taxa play important roles in promoting plant growth and stress resistance. [ABSTRACT FROM AUTHOR]

[Display omitted] • Broadleaf species identity significantly affected microbial community composition in mixed litter. • Higher bacterial diversity was observed in decomposing mixed litter. • The fungal diversity was no different between single- and mixed-species litter. • Saprotrophic fungi increased in mixed litter and accelerated decomposition. • pH, lignin, air temperature, and soil moisture significantly influenced decomposers. Converting coniferous plantations to mixed plantations influences the microbial community composition and potential functions during litter decomposition. However, it is unclear how litter decomposition and associated microbial communities are interactively affected by litter mixing and environmental factors. Here, an in situ litter decomposition experiment was conducted to investigate the dynamics of microbial diversity in mixed litter (at a mass ratio of 1:1) from coniferous (Pinus massoniana) and broadleaf tree, including Bretschneidera sinensis, Manglietia chingii, Cercidiphyllum japonicum, Michelia maudiae, and Camellia oleifera. We found that the mass loss from mixed litter was higher than that of monospecific litter. The chemical characteristics of the broadleaf tree species included in the mixed litter significantly affected the microbial community composition and diversity, and those effects increased over time. Compared to the monospecific litter, the mixed litter had a higher relative abundance of saprotrophs and microbial functional groups related to carbon and nitrogen cycling. Moreover, litter chemistry (i.e., pH, lignin and cellulose content) and environmental factors (i.e., air temperature and soil moisture content) were the most crucial factors affecting the microbial decomposer community. Our results suggest that introducing broadleaf tree species with high litter quality to coniferous plantations changes the composition and function of microbial communities related to litter decomposition, which is conducive to accelerating litter decomposition in subtropical plantations. [ABSTRACT FROM AUTHOR]

The Critical Zone is defined as the thin, permeable layer from the tops of the trees to the bottom of the bedrock that sustains terrestrial life on Earth. The geometry and shape of the various weathering zones are known as the critical zone architecture. At the centre of the Critical Zone are soils and the microorganisms that inhabit them. In Western Australia, the million-year-old stable weathering history and more recent lateral erosion during the past hundreds of thousands of years have created a geomorphic setting where deep weathering zones are now exposed on the surface along the flanks of many lateritic hills. These old weathering zones provide diverse physical and chemical properties that influence near surface pedologic conditions and thus likely shape current surface microbiology. Here, we present data derived from a small lateritic hill on the UWA Farm Ridgefield. Spatial soil sampling revealed the contrasting distribution patterns of simple soil parameters such as pH (CaCl 2 ) and electric conductivity. These are clearly linked with underlying changes of the critical zone architecture and show a strong contrast with low values of pH 3.3 at the top of the hill to pH 5.3 at the bottom. These parameters were identified as major drivers of microbial spatial variability in terms of bacterial and archaeal community composition but not abundance. In addition, we used sensitive 14 C labelling to assess turnover of three model organic nitrogen compounds — an important biogeochemical functional trait relating to nutrient availability. Though generally rapid and in the order of rates reported elsewhere (t ½ < 5 h), some points in the sampling area showed greatly reduced turnover rates (t ½ > 10 h). In conclusion, we have shown that the weathering and erosion history of ancient Western Australia affects the surface pedology and has consequences for microbial community structure and function. [ABSTRACT FROM AUTHOR]

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4–50.4% and 63.7–74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic ( l -leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. [ABSTRACT FROM AUTHOR]

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes , Acidobacteria , Planctomycetes increased as alternatives to the reducing Firmicutes . For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota . Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota . Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil. [ABSTRACT FROM AUTHOR]

• Effects of microbial types and diversity on chalcopyrite bioleaching were studied. • Community with more sulfur oxidizers and high diversity showed high Cu recovery. • Microbial types showed greater influences on mineral dissolution than biodiversity. • A. caldus enhanced CuFeS 2 extraction greatly by regulating physicochemical factors. Six artificial communities with different function or biodiversity were reconstructed by six typical bioleaching species for chalcopyrite leaching. Absence of sulfur oxidizers in communities significantly reduced copper extraction rates, and low diversity communities also exhibited slightly poor bioleaching performances. The variations of pH, redox potential, ferrous and copper ions indicated that the community with both sulfur oxidizers and high diversity showed fast adaptation to the environment and rapid dissolution of chalcopyrite. Integrated analysis of mineralogical and microbial parameters demonstrated that functional types of microorganisms made more contributions in mediating chalcopyrite dissolution than microbial diversity. Further correlation analysis between microbial types and chalcopyrite dissolution performances showed that sulfur oxidizers, especially Acidithiobacillus caldus , could greatly accelerate chalcopyrite dissolution by regulating solution physicochemical factors, such as redox potential and pH. This study provided a theoretical basis for improving bioleaching efficiency by balancing microbial functional types and biodiversity. [ABSTRACT FROM AUTHOR]

Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size. [ABSTRACT FROM AUTHOR]