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Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change. [ABSTRACT FROM AUTHOR]

Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities. [ABSTRACT FROM AUTHOR]

There are various types of land use in the agricultural and pastoral areas of northern China, including natural grassland and artificial grassland, scrub land, forest land and farmland, may change the soil microbial community However, the soil microbial communities in these different land use types remain poorly understood. In this study, we compared soil microbial communities in these five land use types within the agro-pastoral ecotone of northern China. Our results showed that land use has had a considerable impact on soil bacterial and fungal community structures. Bacterial diversity was highest in shrubland and lowest in natural grassland; fungal diversity was highest in woodland. Microbial network structural complexity also differed significantly among land use types. The lower complexity of artificial grassland and farmland may be a result of the high intensity of anthropogenic activities in these two land-use types, while the higher structural complexity of the shrubland and woodland networks characterised by low-intensity management may be a result of low anthropogenic disturbance. Correlation analysis of soil properties (e.g., soil physicochemical properties, soil nutrients, and microbiomass carbon and nitrogen levels) and soil microbial communities demonstrated that although microbial taxa were correlated to some extent with soil environmental factors, these factors did not sufficiently explain the microbial community differences among land use types. Understanding variability among soil microbial communities within agropastoral areas of northern China is critical for determining the most effective land management strategies and conserving microbial diversity at the regional level. [ABSTRACT FROM AUTHOR]

Biofertilizers with phosphate-solubilizing microorganism (PSM) inoculations have been suggested to diminish the limitation of phosphorus (P) deficiency in plants. However, their applications in agriculture are restricted due to the inconstant effects of various PSMs. Proper carriers for the inoculations may overcome this shortcoming and improve PSMs' effectiveness. The objective of this study was to investigate whether straw compost, a type of organic material, can act as a carrier for improving the efficiencies of phosphate-solubilizing bacteria and fungi named Acinetobacter sp. and Aspergillus niger, respectively, in soils. We monitored the growth and cellular physiological responses of one type of model plants, named perennial ryegrass (Lolium perenne L.), under four soil treatments, including non-fertilization, PSM inoculation alone, straw compost addition alone, and the combined applications of both PSMs and straw compost. We found the combined treatments significantly improved the growth by 14.7% for shoot height and 79.7% for shoot weight, respectively, on average. P and potassium (K) uptakes of ryegrass were also increased by 102.5% and 65.3%, respectively, after the application of both PSMs and straw compost. Furthermore, physiological properties, such as photosynthetic efficiency and P-transportation capacity, of ryegrass were also significantly improved under combined treatments when compared to other treatments, regardless of the types of PSM included. The piecewise structural equation model further indicated that PSM inoculation and straw compost input are synergistically contributing to the nutrient uptake of ryegrass through many direct and indirect ways. We propose that straw compost is a good carrier material for PSMs' survival and would improve their plant growth promotion ability in soil. Our results provide valuable insights into the exploitation and utilization of P-biofertilizers in agriculture. [ABSTRACT FROM AUTHOR]

Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure. [ABSTRACT FROM AUTHOR]

In the present study, biological indicators were used to assess the impact of applying spent mushroom substrate and manure on the soil environment. The use of spent mushroom substrate had a varied effect on the microorganisms. Stimulation was recorded in the abundance of copiotrophic bacteria and fungi, but only in the first year of the study. In the case of cellulolytic bacteria, this effect was visible only in single plots. Similar observations were also noted regarding the relative DNA content (in relation to the control), which increased for both bacteria and fungi after applying spent mushroom substrate. In the soil fertilized with spent mushroom substrate, a decrease in DNA concentration was observed, but only in the first and second year. For enzymatic activity, the use of spent mushroom substrate alone proved to be more favorable, but this effect was again observed only in the first year of the study. The application of manure caused similar changes as observed with the use of spent mushroom substrate. These observations indicate a similar impact of spent mushroom substrate and manure on the parameters tested. The research presented suggests the use of both classical methods and methods based on the analysis of DNA extracted from soil to study the impact of spent mushroom substrate on the activity of soil microbial populations. [ABSTRACT FROM AUTHOR]

Sweet potato stem nematode disease is a devastating disease, which seriously affects the yield and quality of sweet potato (Ipomoea batatas (L.) Lam.). At present, soil treatment with pesticides is mainly used to prevent sweet potato stem nematode disease. In this study, Illumina MiSeq high‐throughput sequencing technology was used to analyze the diversity of soil bacterial and fungal communities treated with different pesticides. At the same time, high performance liquid chromatography was used to determine the pesticide residues in soil and sweet potato, and the impact on sweet potato yield was investigated. Kruskal–Wallis test was used to analyze the four α‐diversity indexes of soil under different pesticide treatments, and the differences were not significant (p > 0.05), indicating that there was no significant difference in the diversity and abundance of bacterial and fungal communities in soil under different pesticide treatments. The results of principal coordinate analysis showed that there was no significant difference in bacterial and fungal community structure among different pesticide treatments (p > 0.05). Pesticide residue analysis and yield statistics of sweet potato showed that the residual amount of three kinds of pesticides in sweet potato did not exceed the maximum limit stipulated by the current National Standards for Food safety (GB2763‐2021). When 5% chlorpyrifos phoxim particles were applied at 15.18 kg/acre, sweet potato was unaffected by pests and diseases basically, and the yield was the highest. [ABSTRACT FROM AUTHOR]

Abstract Straw returning has been demonstrated as a beneficial approach for the utilization of renewable biomass source, which contributes to reducing environmental pollution and strengthening the sustainability of agriculture. However, information on how microorganisms respond to different straw return modes (SRMs) at varying nitrogen fertilizer levels (NFLs) in the black soil is still limited. The community composition, network pattern, and modular function of bacteria and fungi are investigated under three SRMs, including straw removal (CK), crushed straw incorporation (SD), and biochar incorporation (BC) at three NFLs (0, 144, and 240 kg N ha−1, respectively) mainly using Illumina MiSeq technique based on a long‐term maize field experiment. Results showed that bacterial richness, diversity, and fungal richness decreased with NFL reduction. However, these decreases can be compensated by SD and BC, demonstrating superiority for BC at reduced NFLs. SD and BC differed in their effects on the bacterial and fungal abundances (showing increments only in SD) and fungal Shannon diversity (remaining stable only in BC irrespective of NFLs). Microbial communities were substantially affected by SRMs and interacted with NFLs, which were driven by soil NH4+‐N, available potassium, total nitrogen, and pH. In addition, SD induced a network characterized by its highly complex (average degree 10.259 vs. 3.364) and stable structure (average clustering coefficient 0.503 vs. 0.239), Ascomycota as predominating keystone taxa, and abundant N‐cycling related bacteria, while BC formed a network comprising a superior modular structure (modularity 2.599 vs. 0.912), dominant symbiotic fungi, and soil bulk density as specific shaping factor, indicating that network pattern, keystone taxa, modular function, and determining factors shifted between SD and BC co‐occurrence networks. These results deepen insights into the response divergence of bacteria and fungi to SRMs and NFLs, providing a scientific basis for selecting the suitable strategy for sustainable straw utilization in the black soil area.

Abstract Sweet potato stem nematode disease is a devastating disease, which seriously affects the yield and quality of sweet potato (Ipomoea batatas (L.) Lam.). At present, soil treatment with pesticides is mainly used to prevent sweet potato stem nematode disease. In this study, Illumina MiSeq high‐throughput sequencing technology was used to analyze the diversity of soil bacterial and fungal communities treated with different pesticides. At the same time, high performance liquid chromatography was used to determine the pesticide residues in soil and sweet potato, and the impact on sweet potato yield was investigated. Kruskal–Wallis test was used to analyze the four α‐diversity indexes of soil under different pesticide treatments, and the differences were not significant (p > 0.05), indicating that there was no significant difference in the diversity and abundance of bacterial and fungal communities in soil under different pesticide treatments. The results of principal coordinate analysis showed that there was no significant difference in bacterial and fungal community structure among different pesticide treatments (p > 0.05). Pesticide residue analysis and yield statistics of sweet potato showed that the residual amount of three kinds of pesticides in sweet potato did not exceed the maximum limit stipulated by the current National Standards for Food safety (GB2763‐2021). When 5% chlorpyrifos phoxim particles were applied at 15.18 kg/acre, sweet potato was unaffected by pests and diseases basically, and the yield was the highest.

Straw returning has been demonstrated as a beneficial approach for the utilization of renewable biomass source, which contributes to reducing environmental pollution and strengthening the sustainability of agriculture. However, information on how microorganisms respond to different straw return modes (SRMs) at varying nitrogen fertilizer levels (NFLs) in the black soil is still limited. The community composition, network pattern, and modular function of bacteria and fungi are investigated under three SRMs, including straw removal (CK), crushed straw incorporation (SD), and biochar incorporation (BC) at three NFLs (0, 144, and 240 kg N ha−1, respectively) mainly using Illumina MiSeq technique based on a long‐term maize field experiment. Results showed that bacterial richness, diversity, and fungal richness decreased with NFL reduction. However, these decreases can be compensated by SD and BC, demonstrating superiority for BC at reduced NFLs. SD and BC differed in their effects on the bacterial and fungal abundances (showing increments only in SD) and fungal Shannon diversity (remaining stable only in BC irrespective of NFLs). Microbial communities were substantially affected by SRMs and interacted with NFLs, which were driven by soil NH4+‐N, available potassium, total nitrogen, and pH. In addition, SD induced a network characterized by its highly complex (average degree 10.259 vs. 3.364) and stable structure (average clustering coefficient 0.503 vs. 0.239), Ascomycota as predominating keystone taxa, and abundant N‐cycling related bacteria, while BC formed a network comprising a superior modular structure (modularity 2.599 vs. 0.912), dominant symbiotic fungi, and soil bulk density as specific shaping factor, indicating that network pattern, keystone taxa, modular function, and determining factors shifted between SD and BC co‐occurrence networks. These results deepen insights into the response divergence of bacteria and fungi to SRMs and NFLs, providing a scientific basis for selecting the suitable strategy for sustainable straw utilization in the black soil area. [ABSTRACT FROM AUTHOR]

Biofertilizers with phosphate-solubilizing microorganism (PSM) inoculations have been suggested to diminish the limitation of phosphorus (P) deficiency in plants. However, their applications in agriculture are restricted due to the inconstant effects of various PSMs. Proper carriers for the inoculations may overcome this shortcoming and improve PSMs’ effectiveness. The objective of this study was to investigate whether straw compost, a type of organic material, can act as a carrier for improving the efficiencies of phosphate-solubilizing bacteria and fungi named Acinetobacter sp. and Aspergillus niger, respectively, in soils. We monitored the growth and cellular physiological responses of one type of model plants, named perennial ryegrass (Lolium perenne L.), under four soil treatments, including non-fertilization, PSM inoculation alone, straw compost addition alone, and the combined applications of both PSMs and straw compost. We found the combined treatments significantly improved the growth by 14.7% for shoot height and 79.7% for shoot weight, respectively, on average. P and potassium (K) uptakes of ryegrass were also increased by 102.5% and 65.3%, respectively, after the application of both PSMs and straw compost. Furthermore, physiological properties, such as photosynthetic efficiency and P-transportation capacity, of ryegrass were also significantly improved under combined treatments when compared to other treatments, regardless of the types of PSM included. The piecewise structural equation model further indicated that PSM inoculation and straw compost input are synergistically contributing to the nutrient uptake of ryegrass through many direct and indirect ways. We propose that straw compost is a good carrier material for PSMs’ survival and would improve their plant growth promotion ability in soil. Our results provide valuable insights into the exploitation and utilization of P-biofertilizers in agriculture.

Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure.

Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage (Brassica campestris) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil. [ABSTRACT FROM AUTHOR]

The photodynamic inactivation (PDI) is a novel and effective nonthermal inactivation technology. This review provides a comprehensive overview on the bactericidal ability of endogenous photosensitizers (PSs)‐mediated and exogenous PSs‐mediated PDI against planktonic bacteria and their biofilms, as well as fungi. In general, the PDI exhibited a broad‐spectrum ability in inactivating planktonic bacteria and fungi, but its potency was usually weakened in vivo and for eradicating biofilms. On this basis, new strategies have been proposed to strengthen the PDI potency in food system, mainly including the physical and chemical modification of PSs, the combination of PDI with multiple adjuvants, adjusting the working conditions of PDI, improving the targeting ability of PSs, and the emerging aggregation‐induced emission luminogens (AIEgens). Meanwhile, the mechanisms of PDI on eradicating mono‐/mixed‐species biofilms and preserving foods were also summarized. Notably, the PDI‐mediated antimicrobial packaging film was proposed and introduced. This review gives a new insight to develop the potent PDI system to combat microbial contamination and hazard in food industry. [ABSTRACT FROM AUTHOR]

Pine wilt disease (PWD) caused by the pine wood nematode (Bursaphelenchus xylophilus) is a serious threat to coniferous forests worldwide. However, little is known about how soil microbial diversity responds to PWD and associated management practices. We investigated the community composition and diversity of bacteria and fungi in bulk and rhizosphere soil of Masson pine (Pinus massoniana Lamb.) forests following 0, 1, and 5 year PWD, with the dead pine in a certain plot being either managed (logged and removed from the plot) or unmanaged (maintained as standing dead wood). Both bacterial and fungal alpha diversity decrease after 5 year PWD and logging, with response degree being different between site locations. Alpha diversity of rhizosphere fungi, rather than bacteria, significantly decreases with the disease and logging. We observe an increase in the relative amount of bacterial functional groups involved in carbohydrate and amino acid metabolism after PWD infection and logging practice. With the disease infection, the relative abundance of ectomycorrhizal fungi decreases, while the relative abundance of saprotrophic fungi increases. Compared with logging treatment, unmanaged practice had a weaker effect on soil microbial communities. Our findings provide new insights into the short-term responses of soil microbial diversity to management practices after PWD infection. [ABSTRACT FROM AUTHOR]

Introduction: Rhizosphere microbes perform critical functions for their hosts, and their structure is strongly influenced by vegetation type. Although studies on the effects of vegetation on rhizosphere microbial community structure have been conducted at large and global environment scales, studies at local environment scales would eliminate numerous external factors such as climate and soil type, while highlighting the potential influence of local vegetation type. Methods: Here, we compared rhizosphere microbial communities using 54 samples under three vegetation types (herb, shrubs, and arbors, with bulk soil as the control) at the campus of Henan University. 16S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing. Results and Discussion: Rhizosphere bacterial and fungal community structures were influenced considerably by vegetation type. Bacterial alpha diversity under herbs was significantly different from that under arbors and shrubs. The abundance of phyla such as Actinobacteria was extremely higher in bulk soil than in the rhizosphere soils. Herb rhizosphere harbored more unique species than other vegetation type soils. Furthermore, bacterial community assembly in bulk soil was more dominated by deterministic process, whereas the rhizosphere bacterial community assembly was dominated by stochasticity and the construction of fungal communities was all dominated by deterministic processes. In addition, rhizosphere microbial networks were less complex than bulk soil networks, and their keystone species differed based on vegetation type. Notably, bacterial community dissimilarities were strongly correlated with plant phylogenetic distance. Exploring rhizosphere microbial community patterns under different vegetation types could enhance our understanding of the role of rhizosphere microbes in ecosystem function and service provision, as well as basic information that could facilitate plant and microbial diversity conservation at the local environment scale. [ABSTRACT FROM AUTHOR]

Introduction: Soil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear. Methods: Here, a field experiment was conducted under ambient precipitation as a control, -20% and -40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the northwest of China. Moreover, 16S rRNA gene and ITS sequencing were used to detect bacterial and fungal communities, and the PICRUST and FUNGuild databases were used to predict bacterial and fungal functional groups. Results: Results showed drought stress substantially changes the community diversity of bacteria and fungi, among which the bacteria community is more sensitive to drought stress than fungi, indicating that the diversity or structure of soil bacteria community could serve as an indicator of alpine grasslands status. However, the fungal community still has difficulty maintaining resistance under excessive drought stress. Our paper also highlighted that soil moisture content, plant diversity (Shannon Wiener, Pieiou, and Simpson), and soil organic matter are the main drivers affecting soil bacterial and fungal community composition and predicted functional potential. Notably, the soil microbial functional potential could be predictable through taxonomic community profiles. Conclusions: Our research provides insight for exploring the mechanisms of microbial community composition and functional response to climate change (longer drought) in a semiarid alpine grassland. [ABSTRACT FROM AUTHOR]

Plants can alter microbial communities through root exudates, and change the characteristics of the soil. However, the relationship between soil microbial communities and environmental factors is not well understood. Here, we studied bacterial and fungal communities and their relationships with environmental factors. We integrated data of environmental factors, microbial composition, diversity, functional prediction, and co‐occurrence network from uncultivated, maize, cabbage, and cocozelle soils in a karst area of Southwest China. Soil bacterial and fungal community composition differed with plant types. Maize soil had more taxa and greater alpha diversity of bacteria and fungi than other soils. In maize soil, the relative abundance of Actinobacteria and Ascomycota was significantly lower than that in uncultivated soil, while its contents of soil organic matter (OM), alkali‐hydrolyzable nitrogen, and total nitrogen (TN) showed the opposite trend. These indicators were not significantly different between cabbage and cocozelle soils. The results of the Mantel test and the RDA analysis indicated that TN and OM were important drivers of bacterial and fungal communities. Functional prediction and network analysis showed that maize soil had a high nitrogen fixation capacity and a complex and stable network. To summarize, maize soil not had a low relative abundance of Ascomycota and high content of TN and OM, nitrogen fixation ability, and a rich microbial community. Therefore, cultivating maize is suitable for improving soil microbial community. These findings might help in formulating a reasonable cultivation management program to prevent land degradation in the karst areas. [ABSTRACT FROM AUTHOR]

In this study, a screening of the efficacy of a microbial consortium of bacteria and fungi isolated from activated sludge, river sediment, and compost for the degradation of LDPE/TPS was performed. According to the morphological and biochemical characterization, eight bacteria, Bacillus sonorensis, Bacillus subtilis, Lysinibacillus massiliensis, Bacillus licheniformis, Bacillus indicus, Bacillus megaterium, Bacillus cereus, and Pseudomonas alcaligenes, five molds, Aspergillus sp. 1, Aspergillus sp. 2, Trichoderma sp., Rhizopus sp., Penicillium sp., and Alternaria sp., and a yeast, Candida parapsilosis, were identified. The first experiment E1 was inoculated with microorganisms isolated from activated sludge and river sediment, and E2 with microorganisms isolated from compost. In both experiments, different types of polymeric materials, low density polyethylene (E1-1 and E2-1), thermoplastic starch (E1-2 and E2-2), low density polyethylene + thermoplastic starch (E1-3 and E2-3), low density polyethylene + thermoplastic starch + styrene-ethylene-styrene (E1-4 and E2-4) were added. The obtained results, weight loss, SEM, and FTIR analysis showed that the microorganisms in both experiments were able to degrade polymeric materials. The mixed culture of microorganisms in experiments E1-2 and E2-2 completely degraded TPS (thermoplastic starch). The percent weight losses of LDPE, LDPE+20% TPS, and LDPE+20% TPS+SEBS in experiment E1 were 3.3184%, 14.1152%, and 16.0062% and in experiment E2 were 3.9625%, 20.4520% and 21.9277%, respectively. SEM microscopy shows that the samples with a LDPE matrix exhibited moderate surface degradation and negligible oxidative degradation under the given conditions. FTIR/ATR data demonstrate that degradation was more intense in E2 than in E1. [ABSTRACT FROM AUTHOR]

• Microplastic (MP)-associated bacterial and fungal communities were uncovered. • The differentiation of microbial taxa depending on coastal systems was explored. • Degradation of MPs can influence on microbial colonization and biofilm formation. • Microbial functions can alter the properties of MPs in the coastal environment. • Enrichment of specific taxa on MPs may influence their impact on the ecosystem. Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem. [Display omitted] [ABSTRACT FROM AUTHOR]

Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (i.e., robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (i.e., cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (i.e., bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soi l communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterialfungal network. Infer community assembly mechanism by phylogenetic-binbased null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities' assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles. [ABSTRACT FROM AUTHOR]

Microbes like bacteria and fungi are crucial for host plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.). Herein, we evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sensi and Cherry Wine) and two fibers (American Victory and Unknown). The four hemp varieties showed significant variations in microbiome diversity. The roots had significantly abundant fungal and bacterial endophyte diversity indices, whereas the stem had higher fungal than bacterial diversity. Interestingly, the soil system showed no significant diversity variation across CBD vs. fiber genotypes. In fungal phyla, Ascomycota and Basidiomycota were significantly more abundant in roots and stems than leaves in CBD-rich genotypes compared to fiber-rich genotypes. The highly abundant bacterial phyla were Proteobacteria, Acidobacteria, and Actinobacteria. We found 16 and 11 core-microbiome bacterial and fungal species across genotypes. Sphingomonas, Pseudomonas, and Bacillus were the core bacteria of fiber genotypes with high abundance compared to CBD genotypes. Contrarily, Microbacterium, and Rhizobium were significantly higher in CBD than fiber. The Alternaria and Gibberella formed a core-fungal microbiome of fiber-genotype than CBD. Contrarily, Penicillium, and Nigrospora were significantly more abundant in CBD than fiber genotypes. In conclusion, specific hemp genotypes recruit specialized microbial communities in the rhizosphere and phyllosphere. Utilizing the core-microbiome species can help to maintain and improve the growth of hemp plants and to target specialized traits of the genotype., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Introduction: Transmission of bioaerosols through the air is known as an important route for a wide range of nosocomial infections. Therefore, in the present study, we aimed to evaluate the type and diversity of bioaerosols and antibiotic resistance of bacterial bioaerosols in the indoor environments of Sina Educational and Treatment Hospital, Tabriz, Iran. Methods and materials: Bioaerosol samples were collected from February to March (winter) and June to July (summer) 2020 in three periods of daytime (morning, noon and evening). After sampling, fungal and bacterial samples were incubated and the disk diffusion agar method (Kirby-Bauer) was used for assessing the antibiotic resistance. Results: the concentration of bioaerosols varied significantly in different wards. In addition, the concentration of bioaerosols in winter was observed to be higher than in summer. The highest and lowest airborne fungal concentrations were found in burns operating room and men's infectious ward (49 CFU/m3) and children's burns ward (28 CFU/m3), respectively. The predominantly isolated bacteria were Streptococcus spp. (38%) and Staphylococcus spp. (37%). Also, the main isolated fungi belonged to the genera Aspergillus (75.9%) and Penicillium (22.5%). The highest rates of antibiotic resistance were observed for colistin (100%) in Gram-negative and penicillin (84.2%) in Gram-positive. Conclusion: Timely and regular disinfection of hospital wards can affect the density of bioaerosols. Owing to the prevalence of COVID-19 epidemic in the world, the staff and patients often were wearing masks, gloves and special clothing as well as using disinfectants to prevent coronavirus infection in wards during the summer sampling.

Coastal wetlands are significant sources of nitrous oxide (N 2 O), a potent greenhouse gas and ozone depleting agent. Land reclamation is known to change N 2 O emissions from coastal wetlands, but the long-term impacts on N 2 O sources and emissions are not well-understood. Here, we performed respiration inhibition and molecular techniques to dissect the long-term effects of coastal reclamation on bacterial, fungal and overall N 2 O emissions across a 53-year chronosequence of paddy soils reclaimed from coastal wetlands. Our findings showed that reclamation of coastal wetlands to paddy soils generally promoted N 2 O emissions in the chronosequences, despite a significant reduction in uncultivated paddy soils. The observed increase in N 2 O emissions was primarily attributed to an imbalance between N 2 O production and consumption driven by bacterial denitrifiers. Additionally, reclamation of coastal wetlands to paddy soils shifted N 2 O emissions from fungal to bacterial predominance in the chronosequences, with denitrification mediated by bacterial denitrifiers dominating bacterial N 2 O emissions. By integrating the analysis of N 2 O emission rates with soil physicochemical and microbiological properties, we demonstrated that the reduced salinity following coastal reclamation diminished the relative abundance of key fungal denitrifiers (e.g., Paraconiothyrium, Penicillium and Trichoderma), thus lowering the fungal contribution to N 2 O emissions. This study provides novel insights into the long-term influences of coastal reclamation on the sources and emissions of N 2 O, and enhance our knowledge of the underlying mechanisms driving these impacts, thereby contributing to improving future models of N 2 O emissions from coastal ecosystems under global change. [Display omitted] • Long-term impacts of coastal reclamation on N 2 O source and emission were explored. • Influences of coastal reclamation on N 2 O emission depend on reclamation types. • Coastal reclamation shifted N 2 O emission from fungal to bacterial dominance. • Bacterial denitrifiers mediated denitrification dominated bacterial N 2 O emission. • Reduction in the abundance of key fungal denitrifiers led to shift in N 2 O source. [ABSTRACT FROM AUTHOR]

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes. [ABSTRACT FROM AUTHOR]

The Dry-Hot Valley is a unique geographical region in southwestern China, where steep-slope cultivation and accelerating changes in land-use have resulted in land degradation and have aggravated soil erosion, with profound impacts on soil fertility. Soil microbes play a key role in soil fertility, but the impact of land-use changes on soil microbes in the Dry-Hot Valley is not well known. Here, we compared characteristics and drivers of soil microbial community composition and soil fertility in typical Dry-Hot Valley land uses of sugarcane land (SL), forest land (FL), barren land (BL) converted from former maize land (ML), and ML control. Our results showed that BL and SL had reduced soil organic carbon (SOC), total nitrogen (TN), and total potassium (TK) compared to ML and FL. This indicated that conversion of ML to SL and abandonment of ML had the potential to decrease soil fertility. We also found that fungal phyla Zoopagomycota and Blastocladiomycota were absent in SL and BL, respectively, indicating that land-use change from ML to SL decreased the diversity of the bacterial community. Redundancy analysis indicated that the relative abundance of bacterial phyla was positively correlated with TN, SOC, and available potassium (AK) content, and that fungal phyla were positively correlated with AK. Land-use indirectly affected the relative abundance of bacterial phyla through effects on soil moisture, clay, and AK contents, and that of fungal phyla through effects on clay and AK contents. In addition, land-use effects on bacteria were greater than those on fungi, indicating that bacterial communities were more sensitive to land-use changes. Management regimes that incorporate soil carbon conservation, potassium addition, and judicious irrigation are expected to benefit the stability of the plant–soil system in the Dry-Hot Valley. [ABSTRACT FROM AUTHOR]

Atmospheric nitrogen (N) deposition is known to alter soil microbial communities, but how canopy and understory N addition affects soil bacterial and fungal communities in different soil layers remains poorly understood. Conducting a 6-year canopy and understory N addition experiment in a temperate forest, we showed that soil bacterial and fungal communities in the organic layer exhibited different responses to N addition. The main effect of N addition decreased soil bacterial diversity and altered bacterial community composition in the organic layer, but not changed fungal diversity and community composition in all layers. Soil pH was the main factor that regulated the responses of soil bacterial diversity and community composition to N addition, whereas soil fungal diversity and community composition were mainly controlled by soil moisture and nutrient availability. In addition, compared with canopy N addition, the understory N addition had stronger effects on soil bacterial Shannon diversity and community composition but had a weaker effect on soil bacteria richness in the organic soil layer. Our study demonstrates that the bacterial communities in the organic soil layer were more sensitive than the fungal communities to canopy and understory N addition, and the conventional method of understory N addition might have skewed the effects of natural atmospheric N deposition on soil bacterial communities. This further emphasizes the importance of considering canopy processes in future N addition studies and simultaneously evaluating soil bacterial and fungal communities in response to global environmental changes.

Summary: Snow algae are predicted to expand in polar regions due to climate warming, which can accelerate snowmelt by reducing albedo. Green snow frequently occurs near penguin colonies, and red snow distributes widely along ocean shores. However, the mechanisms underpinning the assemblage of algae and heterotrophs in colored snow remain poorly characterized.We investigated algal, bacterial, and fungal communities and their interactions in red and green snows in the Antarctic Peninsula using a high‐throughput sequencing method.We found distinct algal community structure in red and green snows, and the relative abundance of dominant taxa varied, potentially due to nutrient status differences. Contrastingly, red and green snows exhibited similar heterotrophic communities (bacteria and fungi), whereas the relative abundance of fungal pathogens was substantially higher in red snow by 3.8‐fold. Red snow exhibited a higher network complexity, indicated by a higher number of nodes and edges. Red snow exhibited a higher proportion of negative correlations among heterotrophs (62.2% vs 3.4%) and stronger network stability, suggesting the red‐snow network is more resistant to external disturbance.Our study revealed that the red snow microbiome exhibits a more stable microbial network than the green snow microbiome. [ABSTRACT FROM AUTHOR]

The continuous wheat–maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe–microbe interactions in three rotations, including wheat–maize → spring maize (WMFS), wheat–soybean (WS) and continuous wheat–maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production. [ABSTRACT FROM AUTHOR]

In this study, a screening of the efficacy of a microbial consortium of bacteria and fungi isolated from activated sludge, river sediment, and compost for the degradation of LDPE/TPS was performed. According to the morphological and biochemical characterization, eight bacteria, Bacillus sonorensis, Bacillus subtilis, Lysinibacillus massiliensis, Bacillus licheniformis, Bacillus indicus, Bacillus megaterium, Bacillus cereus, and Pseudomonas alcaligenes, five molds, Aspergillus sp. 1, Aspergillus sp. 2, Trichoderma sp., Rhizopus sp., Penicillium sp., and Alternaria sp., and a yeast, Candida parapsilosis, were identified. The first experiment E1 was inoculated with microorganisms isolated from activated sludge and river sediment, and E2 with microorganisms isolated from compost. In both experiments, different types of polymeric materials, low density polyethylene (E1-1 and E2-1), thermoplastic starch (E1-2 and E2-2), low density polyethylene + thermoplastic starch (E1-3 and E2-3), low density polyethylene + thermoplastic starch + styrene-ethylene-styrene (E1-4 and E2-4) were added. The obtained results, weight loss, SEM, and FTIR analysis showed that the microorganisms in both experiments were able to degrade polymeric materials. The mixed culture of microorganisms in experiments E1-2 and E2-2 completely degraded TPS (thermoplastic starch). The percent weight losses of LDPE, LDPE+20% TPS, and LDPE+20% TPS+SEBS in experiment E1 were 3.3184%, 14.1152%, and 16.0062% and in experiment E2 were 3.9625%, 20.4520% and 21.9277%, respectively. SEM microscopy shows that the samples with a LDPE matrix exhibited moderate surface degradation and negligible oxidative degradation under the given conditions. FTIR/ATR data demonstrate that degradation was more intense in E2 than in E1.

Wildfires can either negatively impact soil carbon (C) stocks through combustion or increase soil carbon stocks through the production of pyrogenic organic matter (PyOM), which is highly persistent and can affect non-pyrogenic soil organic carbon (SOC) mineralization rates. In this study, we used fine-resolution 13CO 2 flux tracing to investigate PyOM-C mineralization, soil priming effects, and their impacts on soil microbial communities in a Californian mixed conifer forest Xerumbrept soil burned in the 2014 King Fire. We added PyOM produced from pine biomass at 350 °C and 550 °C to the soil and separately traced the mineralization of 13C-labeled water-extractable and non-water-extractable PyOM-C fractions in a short-term 30-day incubation. Our results indicate that at the end of the incubation period, the water-extractable fraction was 10-50x more mineralizable in both 350 °C and 550 °C PyOM treatments than the SOC or non-water-extractable PyOM fraction. The addition of 350 °C PyOM led to a short-term positive priming effect, likely due to co-metabolism of easily mineralizable PyOM-C and the SOC, whereas 550 °C PyOM addition induced negative priming, potentially due to physical protection of SOC. We observed significant shifts in bacterial community composition in response to both 350 °C and 550 °C PyOM, and identified positive PyOM responders that increased in relative abundance belonging to the genera Noviherbaspirillum , Pseudonocardia , and Gemmatimonas. In contrast, fungal communities were less responsive to PyOM additions. Our findings expand our understanding of the post-fire cycling of PyOM and SOC, providing insights into the microbial mineralization of different PyOM-C fractions and their influence on soil C dynamics in fire-affected ecosystems. • Water extractable PyOM-C was more mineralizable than non-water-extractable PyOM-C. • 350 °C PyOM addition led to net positive priming. • 550 °C PyOM addition led to net negative priming. • Positive responders to 350 °C PyOM included Noviherbaspirillum and Gemmatimonas sp. [ABSTRACT FROM AUTHOR]

The Dry-Hot Valley is a unique geographical region in southwestern China, where steep-slope cultivation and accelerating changes in land-use have resulted in land degradation and have aggravated soil erosion, with profound impacts on soil fertility. Soil microbes play a key role in soil fertility, but the impact of land-use changes on soil microbes in the Dry-Hot Valley is not well known. Here, we compared characteristics and drivers of soil microbial community composition and soil fertility in typical Dry-Hot Valley land uses of sugarcane land (SL), forest land (FL), barren land (BL) converted from former maize land (ML), and ML control. Our results showed that BL and SL had reduced soil organic carbon (SOC), total nitrogen (TN), and total potassium (TK) compared to ML and FL. This indicated that conversion of ML to SL and abandonment of ML had the potential to decrease soil fertility. We also found that fungal phyla Zoopagomycota and Blastocladiomycota were absent in SL and BL, respectively, indicating that land-use change from ML to SL decreased the diversity of the bacterial community. Redundancy analysis indicated that the relative abundance of bacterial phyla was positively correlated with TN, SOC, and available potassium (AK) content, and that fungal phyla were positively correlated with AK. Land-use indirectly affected the relative abundance of bacterial phyla through effects on soil moisture, clay, and AK contents, and that of fungal phyla through effects on clay and AK contents. In addition, land-use effects on bacteria were greater than those on fungi, indicating that bacterial communities were more sensitive to land-use changes. Management regimes that incorporate soil carbon conservation, potassium addition, and judicious irrigation are expected to benefit the stability of the plant–soil system in the Dry-Hot Valley.

There are various types of land use in the agricultural and pastoral areas of northern China, including natural grassland and artificial grassland, scrub land, forest land and farmland, may change the soil microbial community However, the soil microbial communities in these different land use types remain poorly understood. In this study, we compared soil microbial communities in these five land use types within the agro-pastoral ecotone of northern China. Our results showed that land use has had a considerable impact on soil bacterial and fungal community structures. Bacterial diversity was highest in shrubland and lowest in natural grassland; fungal diversity was highest in woodland. Microbial network structural complexity also differed significantly among land use types. The lower complexity of artificial grassland and farmland may be a result of the high intensity of anthropogenic activities in these two land-use types, while the higher structural complexity of the shrubland and woodland networks characterised by low-intensity management may be a result of low anthropogenic disturbance. Correlation analysis of soil properties (e.g., soil physicochemical properties, soil nutrients, and microbiomass carbon and nitrogen levels) and soil microbial communities demonstrated that although microbial taxa were correlated to some extent with soil environmental factors, these factors did not sufficiently explain the microbial community differences among land use types. Understanding variability among soil microbial communities within agro-pastoral areas of northern China is critical for determining the most effective land management strategies and conserving microbial diversity at the regional level., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Sun, Sun, Zhang, Liu, Wang, Feng, Li, Tang and Jin.)

Climate change threatens the capacity of peatlands to continue storing carbon (C) belowground. Microorganisms are crucial in regulating the peatland C sink function, but how climate change affects the richness, biomass and functions of peatland microbiomes still remains uncertain. Here, we conducted a global meta-analysis of the response of peatland bacterial, fungal and micro-eukaryote communities to climate change by synthesizing data from 120 climate change experiments. We show that climate drivers such as warming, drought and warming-induced vegetation shift strongly affect microbial diversity, community composition, trophic structure and functions. Using meta-analytic structural equation modelling, we developed a causal understanding among the different strands of microbial properties. We found that climate drivers influenced microbial metabolic rates, such as CO 2 fixation and respiration, methane production and oxidation, directly through physiological effects, and indirectly, through microbial species turnover and shifts in the trophic structure of microbial communities. In particular, we found that the response of microbial CO 2 fixation increased for each degree in air temperature gained, while the response of microbial CO 2 respiration tended to decline. When extrapolated at the global peatland scale using the CMIP6 model under the SSP5-8.5 scenario, our findings suggest that the increasingly positive response of microbial CO 2 fixation to temperature anomalies in northern latitudes might compensate to some extent for the possible loss of C from microbial CO 2 respiration, possibly allowing peatlands to remain C sinks on long-term. Our findings have crucial implications for advancing our understanding of carbon-climate feedback from peatlands in a warming world. [Display omitted] • Responses of peatland microbes toclimate change drivers were studied by meta-analysis. • Warming and drought decrease microbial richness and shift community composition. • Warming and drought enhance the biomass of bacteria, fungi and intermediate microbial consumers. • Warming and drought enhance microbial metabolic rates, notably CO 2 fixation and emissions. • By yr 2100, the rise in microbial CO 2 fixation will continue to increase while that of microbial CO 2 emissions will stagnate. [ABSTRACT FROM AUTHOR]

Earthen sites are the important cultural heritage that carriers of human civilization and contains abundant history information. Microorganisms are one of important factors causing the deterioration of cultural heritage. However, little attention has been paid to the role of biological factors on the deterioration of earthen sites at present. In this study, microbial communities of Jinsha earthen site soils with different deterioration types and degrees as well as related to environmental factors were analyzed. The results showed that the concentrations of Mg2+ and SO 4 2− were higher in the severe deterioration degree soils than in the minor deterioration degree soils. The Chao1 richness and Shannon diversity indices of bacteria in different type deterioration were higher in the summer than in the winter; the Chao1 and Shannon indices of fungi were lower in the summer. The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. Based on both the relative abundances in amplicon sequencing and isolated strains, the bacterial phyla Actinobacteria, Firmicutes and Proteobacteria, and the Ascomycota genera Aspergillus , Cladosporium and Penicillium were common in all soils. The OTUs enriched in the severe deterioration degree soils were mostly assigned to Actinobacteria and Proteobacteria, whereas the Firmicutes OTUs differentially abundant in the severe deterioration degree were all depleted. All bacterial isolates produced alkali, implying that the deterioration on Jinsha earthen site may be accelerated through alkali production. The fungal isolates included both alkali and acid producing strains. The fungi with strong ability to produce acid were mainly from the severe deterioration degree samples and were likely to contribute to the deterioration. Taken together, the interaction between soil microbial communities and environment may affect the soil deterioration, accelerate the deterioration process and threaten the long-term preservation of Jinsha earthen site. • The microbial communities differed among deterioration types, degrees and seasons. • Mg2+ and SO 4 2− contents were highest in the severe deterioration degree soils. • The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. • Isolated bacteria and fungi produced acid or alkali that may accelerate deterioration. [ABSTRACT FROM AUTHOR]

The plant growth-promoting effects of biostimulants have been widely documented, while little is known about the intrinsic mechanism. In our study, a pot experiment was conducted to investigate the effects of biostimulants on maize, and the maize root transcriptome and rhizosphere microbiome were assessed. The physicochemical properties of the soil were significantly altered with various trends, and the growth and yield of maize were promoted by biostimulants. Sampling time and maize strain were the strongest factors that altered the rhizosphere microorganisms. Rhizosphere microbiota with biostimulant application exhibited high community robustness. Root transcriptome analysis suggested an altered expression profile induced by biostimulants and maize strains. An integrated correlation analysis demonstrated that phosphate and nitrate metabolism genes are tightly associated with some rhizosphere microbiota. These results implied the plant growth-promoting effects of biostimulants might act in a rhizosphere microorganism-dependent manner and help to expand the use of biostimulants in sustainable agriculture.

Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage ( Brassica campestris ) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wei, Fu, He, Zhong, Yang, Lou and He.)

The microbial diversity in Bactrian camel milk and naturally fermented camel milk with unique nutritional properties and medicinal value in Alxa, Inner Mongolia, has been little reported. The results of this study showed that the dominant bacterial phyla in Bactrian camel milk and naturally fermented camel milk were Firmicutes and Proteobacteria, and dominant fungal phyla were Ascomycota and Basidiomycota. During the natural fermentation process of Bactrian camel milk, dominant bacterial genus changed from Lactococcus to Lactobacillus , while dominant fungal genera changed from Apiotrichum , Cutaneotrichosporon and Candida to Kazachstania and Kluyveromyces. Therefore, the diversity and flora structure of bacteria and fungi in Bactrian camel milk and naturally fermented camel milk were significantly different (P < 0.05). The predicted gene functions by PICRUSt2 software showed that the main metabolic genes of bacteria were global and overview maps, carbohydrate metabolism and amino acid metabolism, etc.; the main metabolic genes of fungi were glyoxylate cycle, aerobic respiration I and II, etc. And the relative abundance of bacteria related to food-borne pathogenicity and environmental pollution such as Enterobacter , Enterococcus and Raoultella , etc. suddenly decreased, which provides a reference for the safety evaluation of camel milk and camel milk products and a basis for the study of probiotics. • The microbial diversity of Bactrian camel milk and fermented camel milk was revealed. • Changes of microbial communities in Bactrian camel milk during natural fermentation. • Changes in genera of food-borne pathogenicity and environmental bacteria. • KEGG analysis showed the main metabolic pathways of bacteria and fungi. • To provide reference for safety evaluation of camel milk and camel milk products. [ABSTRACT FROM AUTHOR]

Introduction: Soil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear., Methods: Here, a field experiment was conducted under ambient precipitation as a control, -20% and -40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the northwest of China. Moreover, 16S rRNA gene and ITS sequencing were used to detect bacterial and fungal communities, and the PICRUST and FUNGuild databases were used to predict bacterial and fungal functional groups., Results: Results showed drought stress substantially changes the community diversity of bacteria and fungi, among which the bacteria community is more sensitive to drought stress than fungi, indicating that the diversity or structure of soil bacteria community could serve as an indicator of alpine grasslands status. However, the fungal community still has difficulty maintaining resistance under excessive drought stress. Our paper also highlighted that soil moisture content, plant diversity (Shannon Wiener, Pieiou, and Simpson), and soil organic matter are the main drivers affecting soil bacterial and fungal community composition and predicted functional potential. Notably, the soil microbial functional potential could be predictable through taxonomic community profiles., Conclusion: Our research provides insight for exploring the mechanisms of microbial community composition and functional response to climate change (longer drought) in a semiarid alpine grassland., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wan, Li, Liu, Zhang, Liu and Xie.)

Introduction: Rhizosphere microbes perform critical functions for their hosts, and their structure is strongly influenced by vegetation type. Although studies on the effects of vegetation on rhizosphere microbial community structure have been conducted at large and global environment scales, studies at local environment scales would eliminate numerous external factors such as climate and soil type, while highlighting the potential influence of local vegetation type., Methods: Here, we compared rhizosphere microbial communities using 54 samples under three vegetation types (herb, shrubs, and arbors, with bulk soil as the control) at the campus of Henan University. 16S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing., Results and Discussion: Rhizosphere bacterial and fungal community structures were influenced considerably by vegetation type. Bacterial alpha diversity under herbs was significantly different from that under arbors and shrubs. The abundance of phyla such as Actinobacteria was extremely higher in bulk soil than in the rhizosphere soils. Herb rhizosphere harbored more unique species than other vegetation type soils. Furthermore, bacterial community assembly in bulk soil was more dominated by deterministic process, whereas the rhizosphere bacterial community assembly was dominated by stochasticity and the construction of fungal communities was all dominated by deterministic processes. In addition, rhizosphere microbial networks were less complex than bulk soil networks, and their keystone species differed based on vegetation type. Notably, bacterial community dissimilarities were strongly correlated with plant phylogenetic distance. Exploring rhizosphere microbial community patterns under different vegetation types could enhance our understanding of the role of rhizosphere microbes in ecosystem function and service provision, as well as basic information that could facilitate plant and microbial diversity conservation at the local environment scale., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Liu, Ma, Zhu, Liu, Liu and Shi.)

Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability ( i.e. , robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity ( i.e. , cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities ( i.e. , bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities' assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Gu, Xiong, Tan, Deng, Du, Yang and Hu.)

Nitrapyrin is a nitrification inhibitor used to retain ammonia-N in soil to improve crop yields and quality. Nitrapyrin targets specifically the ammonia oxidizers, but it is not known if it has non-target effects on the soil microbial communities. Here, we tested the hypothesis that nitrapyrin also leads to large shifts in soil microbial community structure, composition, diversity and functions. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH 4 NO 3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice (at grain filling and harvest), the 16S rRNA gene and ITS region were amplified and sequenced to follow the changes in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR, and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. Sampling dates and soil compartments had overwhelming effects on the microbial communities. However, nitrapyrin still significantly affected the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with the sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling dates significantly influenced the profiles observed. Our results show that nitrapyrin influences non-target soil- and plant-associated microbial communities. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions. • Nitrapyrin significantly altered bacterial, archaeal and fungal taxonomic abundance. • Nitrapyrin had an interact effect with time on N-cycle gene abundance and VOCs. • We showed an overriding impact of time on soil microbial structure and function. • An exceptional nitrapyrin effect on soil microbiome beyond ammonia-oxidizers. [ABSTRACT FROM AUTHOR]