Diversity Of Bacterial Communities Research Articles

Mechanisms of heavy metal-induced rhizosphere changes and crop metabolic evolution: The role of carbon materials

To investigate the effects of modified carbon-based materials on soil environmental remediation and crop physiological regulation, this research relied on rice pots with lead (Pb) and cadmium (Cd) composite contamination. Dolomite, montmorillonite, attapulgite and sepiolite modified biochar with different doses have been developed to explore the mechanisms on heavy metal passivation, nutrient improvement, microbial activation, and crop growth. The results indicated that the modified materials effectively reduced heavy metal bioavailability and accumulation in plant tissues through adsorption complexation. Specifically, under montmorillonite and sepiolite modified treatments, the Grains-Pb content significantly decreased by 29.23–30.31% and 27.49–30.58%, compared to the control group (CK). Meantime, carbon-based materials increased available nutrient levels, providing a biological substrate for soil microorganisms metabolism. The content of ammonium nitrogen (NH4+-N) and available phosphorus (AP) in different proportions of montmorillonite modified biochar increased by 10.99–13.98% and 55.76–77.86%, respectively, compared to CK. Furthermore, sepiolite modified biochar enhanced bacterial community diversity, significantly improving the tolerance and resistance of bacterial communities such as Proteobacteria and Acidobacteria to heavy metals. Meanwhile, carbon-based materials enhanced community stability and network complexity, improving microbial stress resistance to adverse environments. In summary, montmorillonite and sepiolite modified biochar regulated microbial community interaction mechanisms by mitigating the physiological toxicity of heavy metals. This process enhanced soil available nutrients and ecological function stability, which had significant implications for improving crop growth and quality.

Similarities and differences in bacterial communities between the Pearl River (Guangzhou section) and its estuary.

The Pearl River and its estuary are highly exposed to anthropogenic disturbance. Because bacterial communities play an indispensable role in aquatic ecosystems, there has been an increased research focus on the statuses of these communities under human-induced perturbations. This study investigated the composition, diversity, and structure of bacterial communities across 29 sites from the Guangzhou section of the Pearl River (GZ) to the Pearl River Estuary (PRE) using 16S rRNA gene amplicons. The results revealed similar dominant phyla of bacteria in both GZ and PRE, as well as significant differences in bacterial community composition and diversity between the two sections. Proteobacteria and Cyanobacteria were identified as the primary drivers of compositional differences between GZ and PRE. The Cyanobacteria Dolichospermum_NIES41 and Cuspidothrix issatschenkoi were only present in GZ, whereas the marine Gram-negative bacteria of Porticoccus litoralis and Thalassolituus oleivorans were unique to PRE. Bacterial community composition and diversity exhibit both similarities and differences between GZ and PRE; Proteobacteria and Cyanobacteria are key factors underlying these variations. Bacterial communities in both GZ and PRE are strongly influenced by human activities, and salinity is an important factor in controlling their differences. This study provides a comprehensive analysis of the bacterial communities in GZ and PRE, establishing a foundation for better management of aquatic ecosystems impacted by anthropogenic activities.

Fertilization shapes microbial life strategies, carbon and nitrogen metabolic functions in Camellia oleifera soil

Mineral, organic and microbial fertilizers are crucial for maintaining and improving soil quality, ecosystem functions, and fruit yield in Camellia oleifera plantations. However, how the application of these fertilizers shapes the life strategies and functions of soil microbial communities is unclear. Here, we conducted a one-year field experiment with three types of fertilizers: mineral (NPK), manure (Man), and microbial (MicrF), and analyzed soil properties, bacterial and fungal communities to assess microbial life strategies, functional traits and their determinants. The application of MicrF strongly increased the diversity of both soil bacterial (by 6.4%) and fungal communities (by 23%). Organic matter inputs from Man and MicrF had greater effects on the life strategies of bacteria than fungi: the dominant r-strategy bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased with Man and MicrF, but K-strategists (Acidobacteria) decreased. Conversely, the abundance of r-strategy fungi (Ascomycota) decreased, but that of K-fungi (Basidiomycota) increased. Predictions of the functions indicated that microbial fertilization accelerated the bacterial carbohydrates, carbon and nitrogen metabolism, while also increasing the prevalence of wood saprotrophic fungi. The changes in the taxonomic and functional characteristics of the microbial communities induced co-metabolism priming effects, which were mainly regulated by soil organic carbon, available phosphorus, ammonium nitrogen contents, and carbon-nitrogen ratio. The application of MicrF is an effective approach to increase the diversity and multifunctionality of soil microbial communities in Camellia oleifera plantations, including organic matter decomposition, carbon and nitrogen metabolism. These findings provide valuable insights into the fertilizer regimes based on microbial ecological strategies and functional profiles in Camellia oleifera plantations.

The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent

BackgroundIn addition to their role as endosymbionts for plant roots, arbuscular mycorrhizal fungi (AMF) engage in complex interactions with various soil microorganisms, the rhizosphere, and the root endosphere of host plants. They also host diverse prokaryotic groups within their mycelia, contributing to what is termed multipartite symbiosis. In this study, we examined the impact of three AMF species—Rhizophagus irregularis, R. clarus, and R. cerebriforme—combined with microbial bioaugmentation on the diversity and composition of bacterial communities in the mycelia and hyphosphere. Using a microcosm design to separate the influence of host plant roots from AMF mycelia and Illumina MiSeq amplicon sequencing to analyze the bacterial communities.ResultsOur results revealed that, while AMF identity and microbial bioaugmentation did not affect the structure of bacterial communities in the hyphosphere soil, they significantly altered the communities associated with their mycelia. Although all three AMF species belong to the same genus, with R. irregularis and R. clarus being closely related compared to R. cerebriforme, we observed variations in the bacterial communities associated with their mycelia. Interestingly, the mycelial bacterial community of R. cerebriforme contained 60 bacteriome core taxa exclusive to it, while R. clarus and R. irregularis had 25 and 9 exclusive taxa, respectively.ConclusionThis study suggests that organismal phylogeny influences the bacterial communities associated with AMF mycelia. These findings provide new insights into AMF and bacterial interactions, which are crucial for the successful deployment of AMF inoculants. The taxonomic diversity of AMF inoculants is important for engineering the plant microbiome and enhancing ecosystem services.

Structure and Function of Soil Bacterial Communities in the Different Wetland Types of the Liaohe Estuary Wetland.

Soil bacterial communities play a crucial role in the functioning of estuarine wetlands. Investigating the structure and function of these communities across various wetland types, along with the key factors influencing them, is essential for understanding the relationship between bacteria and wetland ecosystems. The Liaohe Estuary Wetland formed this study's research area, and soil samples from four distinct wetland types were utilized: suaeda wetlands, reed wetlands, pond returning wetlands, and tidal flat wetlands. The structure and function of the soil bacterial communities were examined using Illumina MiSeq high-throughput sequencing technology in conjunction with the PICRUSt analysis method. The results indicate that different wetland types significantly affect the physical and chemical properties of soil, as well as the structure and function of bacterial communities. The abundance and diversity of soil bacterial communities were highest in the suaeda wetland and lowest in the tidal flat wetland. The dominant bacterial phyla identified were Proteobacteria and Bacteroidota. Furthermore, the dominant bacterial genera identified included RSA9, SZUA_442, and SP4260. The primary functional pathways associated with the bacterial communities involved the biosynthesis of valine, leucine, and isoleucine, as well as lipoic acid metabolism, which are crucial for the carbon and nitrogen cycles. This study enhances our understanding of the mutual feedback between river estuary wetland ecosystems and environmental changes, providing a theoretical foundation for the protection and management of wetlands.

How biochar curbs the negative impacts of plastic mulching on soil enzymes and microorganisms while elevating crop yields in ridge-furrow systems

Ridge-furrow tillage is an important tillage and yield enhancement method used in dry farming areas; however, the spatial characteristics of the soil microenvironment under ridge-furrow tillage and the response of crop yields to mulching and biochar addition are not known. In this study, we conducted a three-year field experiment in which mulch and biochar, alone or combined, were introduced into ridge-furrow tillage system to explore their interactive effects on soil enzyme activities, bacterial communities, functional genes, and crop yields. The findings reveal significant spatial differences in soil physicochemical composition, enzyme activity, microbial communities, and functional genes under ridge-furrow tillage, which are further exacerbated by the addition of mulching and biochar. Under the premise of ridge-furrow tillage, both mulching and biochar addition reduce the α diversity of bacterial communities. Mulching simplifies the bacterial network, while biochar addition has the opposite effect. Mulching and biochar addition increase the relative abundance of carbon, nitrogen, and phosphorus functional genes and accelerate nutrient cycling, especially on the ridges. Mulching significantly improves crop yield but is detrimental to alkaline phosphatase activity and the abundance of the gene function. The addition of biochar mitigates the harm of mulching and further increases alfalfa yield. These findings not only provide scientific support for optimizing ridge-furrow tillage but also deepen our comprehensive understanding of the soil biochemical environment after the addition of mulching and biochar, further revealing their positive effects on yield formation.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

The Effects of Acid-Modified Biochar and Biomass Power Plant Ash on the Physiochemical Properties and Bacterial Community Structure of Sandy Alkaline Soils in the Ancient Region of the Yellow River

The application of biochar can effectively enhance soil organic matter (SOM) and improve soil structure. Biomass power plant ash (BPPA) is also rich in essential nutrients for plants, with similar carbon content. Considering production cost and agricultural waste recycling, it is beneficial to apply BPPA to improve soil fertility and quality. However, it remains unclear whether its ameliorative effects surpass those of biochar in alkaline soils. In the study, we set up seven pot experiments of faba beans in sandy alkaline soils from the ancient region of the Yellow River, including the controls (CK), different amounts of acid-modified BPPA (A1, A2, A3), and the same amounts of acid-modified biochar (B1, B2, B3), to compare their effects on soil physiochemical properties and bacterial community structure. The results indicate that the application of both biochar and BPPA can improve soil physiochemical properties. At the same dosage, the biochar application outperformed BPPA treatment in terms of soil physical properties such as bulk density (BD), maximum water-holding capacity (FC), and soil capillary porosity (SP2). Conversely, BPPA treatment displayed advantages in chemical properties such as readily oxidizable organic carbon (ROOC), total nitrogen (TN), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), and electrical conductivity (EC). All the treatments enhanced the richness and diversity of bacterial communities, increasing the relative abundance of eutrophic groups such as Bacteroidota and Firmicutes while decreasing that of oligotrophic groups like Actinobacteriota. BPPA also increased the relative abundance of Proteobacteria, while the opposite was observed for biochar. Correlation analysis showed that the environmental factors such as soil pH, EC, TN, AK, SOM, and SP2 emerged as primary factors influencing the bacterial community structure of alkaline soils, significantly affecting their diversity and abundance. Among them, SP2 and SOM were the dominant physical and chemical factors, respectively. Overall, the application of both acid-modified BPPA and biochar can enhance the physiochemical properties of sandy alkaline soils, while the application of BPPA is superior for improving soil nutrient content and enhancing bacterial community structure. The study explores the potential mechanisms through which the application of acid-modified BPPA affects soil characteristics and microbial features, providing new insight into developing optimizing fertilization strategies for enhancing soil quality in the ancient region of the Yellow River.

Multi-omics analysis of soil microbiota and metabolites in dryland wheat fields under different tillage methods

No-tillage and subsoiling can improve soil aggregate structure and realize a synergistic effect of soil carbon and nitrogen retention compared with deep tillage. This study aimed to investigate the effects of different tillage methods on the microbiome and metabolites in wheat rhizosphere. Results indicated that no significant differences in the diversity of soil bacterial and fungal communities were observed among the tillage methods. Analysis revealed that no-tillage enriched specific genera such as Cryptosporangium, Crossiella, Rhodothermaceae, Leptothrix, Stilbella, Diutina, and Pyrenochaetopsis, while subsoiling was associated with Rubrobacter, Latescibacteraceae, Nitrospira, Rokubacteriales, and Ctenomyces. Deep tillage, on the other hand, showed significant associations with Nocardia, Aeromicrobium, Sphingopyxis, Cordyceps, and Subulicystidium. Metabolomic analysis identified differential metabolites involved in various pathways, including the biosynthesis of plant secondary metabolites, ABC transporters, and starch and sucrose metabolism. Correlation analysis revealed a significant interaction between microorganisms and metabolites in wheat rhizosphere. Bacteria at the genus level exhibited greater associations with differential metabolites. In conclusion, different tillage practices can alter the composition of microbial communities and metabolites in wheat rhizosphere, and their interactions may affect soil fertility and wheat growth.

Distinct bacterial and eukaryotic communities reflect the specificity of different coral reefs in the South China Sea

The microbial composition of surrounding waters is crucial for the health of coral reefs and holds significant value for understanding the complexity and environmental adaptability of coral reef ecosystems. This study reveals the spatial heterogeneity and diversity characteristics of bacterial and eukaryotic communities in different coral reef regions of the South China Sea. Chao and Shannon indices showed significant differences (p < 0.05) in diversity of bacterial and eukaryotic communities across different coral reefs. PCoA (principal coordinate analysis) indicates significant differences in community composition among regions, highlighting the crucial role of coral reef environmental heterogeneity on microbial community. NST (normalized stochasticity ratio) analysis indicates that community assembly in coral reef areas is more influenced by ecological stochastic processes. Major bacterial groups include Proteobacteria, Cyanobacteria, and Bacteroidota, while dominant eukaryotic groups include Dinophyceae, Apicomplexa, Bacillariophyta, Florideophyceae, Mamiellophyceae, Syndiniales, Prasino-Clade-VII, and Ascomycota, each showing significant abundance differences across coral reef regions (p < 0.05). High abundance of Rhodobacterales and Flavobacteriales are detected in all coral reef waters. Correlation analysis indicates that temperature, pH, and salinity are important factors affecting the bacterial and eukaryotic communities. This study reveals the spatial heterogeneity of microbial communities in coral reef regions of South China Sea and underscores the significant impact of marine environmental heterogeneity on community structure.

Novel mechanistic understanding that Lactiplantibacillus plantarum is more capable of improving the ensiling performance of wheat straw silage than xylanase by driving certain key metabolites

Microbial and enzyme additives can improve silage performance, but there is limited comparative research on the effects of microbial and enzyme additives on improving silage fermentation quality, and the underlying microbial and metabolic pathways remain unclear. This study investigated the effects without inoculants (CK treatment) or with Lactiplantibacillus plantarum (LP treatment), xylanase (XY treatment) and their combination (LPXY treatment) on the fermentation quality, as well as on the microbial communities and metabolite profiles of the wheat straw silage. The results demonstrated that the LP treatment has a better effect on improving the fermentation quality of wheat straw silage compared to other treatments, as evidenced by markedly (p < 0.05) decreased the pH (4.06), acid and neutral fiber (ANF, NDF, 23.43 and 31.69%DM), and increased the lactic acid (LA, 965.89 mg/L) and acetic acid (AA, 656.10 mg/L) concentrations. After the fermentation process, the LP treatment significantly (p < 0.05) enhanced the abundance of Lactobacillus, reduced bacterial Shannon (p < 0.05) and increased some key metabolites content. The structural equation models (SEMs) and Pearson’s correlation results proved that the LP treatment improved the wheat straw silage fermentation quality via increasing the abundance of Lactobacillus, decreasing the diversity of bacterial community and enriching the content of certain key metabolites. The present study provides mechanistic evidence that Lactiplantibacillus plantarum additive is superior to xylanase additive and their combination on improving fermentation quality of wheat straw silage, that is, by enriching certain key metabolites to increase AA and LA concentrations, providing a reference for the cross study of silage feed fermentation microbiome and metabolome.Graphical

The effect of urbanization on planktonic and biofilm bacterial communities in different water bodies of the Danube River in Hungary

Freshwaters play an essential role in providing ecosystem services worldwide, however, the water quality of different water bodies is strongly influenced by human activities such as urbanization, industry and agriculture. In this study, water and biofilm samples were collected from the main channel of the Danube River upstream and downstream of a metropolitan, from a regulated side arm within an urbanized area, and from two differently separated oxbow lakes located in nature conservation areas. The taxonomic diversity of bacterial communities was revealed by 16S rRNA gene-based amplicon sequencing using Illumina MiSeq platform. The results showed that all samples were dominated by phyla Pseudomonadota, Actinobacteriota and Bacteroidota. The bacterial community structures, however, clearly differentiated according to planktonic and epilithic or epiphytic habitats, as well as by riverine body types (main channel, side arm, oxbow lakes). The taxonomic diversity of biofilm communities was higher than that of planktonic ones in all studied habitats. Human impacts were mainly reflected in the slowly changing biofilm composition compared to the planktonic ones. Genera with pollution tolerance and/or degradation potential, such as Acinetobacter, Pseudomonas and Shewanella were mainly detected in biofilm communities of the highly urbanized section of the river side arm.

Characterisation of the bacteriomes harboured by major wireworm pest species in the Canadian Prairies.

Nearly all insects harbour bacterial communities that can have a profound effect on their life history, including regulating and shaping host metabolism, development, immunity and fitness. The bacteriomes of several coleopterans have been described; however, very little has been reported for wireworms. These long-lived larvae of click beetles (Coleoptera: Elateridae) are major agricultural pests of a variety of crops grown in the Canadian Prairies. Consequently, the goal of this study was to characterise the bacteriomes of five of the most significant pest species within the region: Limonius californicus, Hypnoidus abbreviatus, H. bicolor, Aeolus mellillus and Dalopius spp. To do this, we collected larvae from southern Manitoba fields (pre-seeding) and carried out 16S rRNA sequencing on individual specimens. Our results indicate wireworms have diverse and taxon-rich bacterial communities, with over 400 genera identified predominately from the phyla Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes. However, each species had nine or fewer genera comprising >80% of their bacteriome. Network analyses revealed some community structuring consistent among species, which may culminate in shaping/regulating host biology. Moreover, the microbial signatures were influenced by both ontogeny (early vs. late stage larvae) and reproductive strategy (sexual vs. parthenogenetic), with a myriad of other factors likely contributing to bacterial diversity that are impossible to resolve from our study. Overall, this metagenomics study represents the first to characterise the bacteriomes of wireworms in the Canadian Prairies and the findings could assist in the development of sustainable management strategies for these important agricultural pests.

Reclamation of co-pyrolyzed dredging sediment as soil cadmium and arsenic immobilization material: Immobilization efficiency, application safety, and underlying mechanisms

The safe management of toxic metal-polluted dredging sediment (DS) is imperative owing to its potential secondary hazards. Herein, the co-pyrolysis product (DS@BC) of polluted DS was creatively applied to immobilize soil Cd and As to achieve DS resource utilization, and the efficiency, safety, and mechanism were investigated. The results revealed that the DS@BC was more effective at reducing soil Cd bioavailability than the DS was (58.9–73.2% vs. 21.8–27.4%), except for the dilution effect, whereas the opposite phenomenon occurred for soil As (25.5–35.7% vs. 35.7–42.8%). The DS@BC immobilization efficiency was dose-dependent for both Cd and As. Soil labile Cd and As were transformed to more stable fractions after DS@BC immobilization. DS@BC immobilization inhibited the transfer of soil Cd and As to Brassica chinensis L. and did not cause excessive accumulation of other toxic metals in the plants. The appropriate addition of the DS@BC (8%) sufficiently alleviated the oxidative stress response of the plants and enhanced their growth. These findings indicate that the DS@BC was safe and effective for soil Cd and As immobilization. DS@BC immobilization decreased the diversity and richness of the rhizosphere soil bacterial community because of the dilution effect. The DS@BC immobilized soil Cd and As via direct adsorption, and indirect increasing soil pH, and regulating the abundance of specific beneficial bacteria (e.g., Bacillus). Therefore, the use of co-pyrolyzed DS as a soil Cd and As immobilization material is a promising resource utilization method for DS. Notably, to verify the long-term effects and safety of DS@BC immobilization, field trials should be conducted to explore the effectiveness and risk of harmful metal release from DS@BC immobilization under real-world conditions.

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time

BackgroundCereal diseases caused by insect-transmitted viruses are challenging to forecast and control because of their intermittent outbreak patterns, which are usually attributed to increased population densities of vector insects due to cereal crop rotations and indiscriminate use of pesticides, and lack of resistance in commercial varieties. Root microbiomes are known to significantly affect plant health, but there are significant knowledge gaps concerning epidemics of cereal virus diseases at the microbiome-wide scale under a variety of environmental and biological factors.ResultsHere, we characterize the diversity and composition of rice (Oryza sativa) root-associated bacterial communities after infection by an insect-transmitted reovirus, rice black-streaked dwarf virus (RBSDV, genus Fijivirus, family Spinareoviridae), by sequencing the bacterial 16S rRNA gene amplified fragments from 1240 samples collected at a consecutive 3-year field experiment. The disease incidences gradually decreased from 2017 to 2019 in both Langfang (LF) and Kaifeng (KF). BRSDV infection significantly impacted the bacterial community in the rice rhizosphere, but this effect was highly susceptible to both the rice-intrinsic and external conditions. A greater correlation between the bacterial community in the rice rhizosphere and those in the root endosphere was found after virus infection, implying a potential relationship between the rice-intrinsic conditions and the rhizosphere bacterial community. The discrepant metabolites in rhizosphere soil were strongly and significantly correlated with the variation of rhizosphere bacterial communities. Glycerophosphates, amino acids, steroid esters, and triterpenoids were the metabolites most closely associated with the bacterial communities, and they mainly linked to the taxa of Proteobacteria, especially Rhodocyclaceae, Burkholderiaceae, and Xanthomonadales. In addition, the greenhouse pot experiments demonstrated that bulk soil microbiota significantly influenced the rhizosphere and endosphere communities and also regulated the RBSDV-mediated variation of rhizosphere bacterial communities.ConclusionsOverall, this study reveals unprecedented spatiotemporal dynamics in rhizosphere bacterial communities triggered by RBSDV infection with potential implications for disease intermittent outbreaks. The finding has promising implications for future studies exploring virus-mediated plant-microbiome interactions.2AL1xEb7k2nunVBmbuNCsVVideo

Are bacterial communities and aggregation in fragile soils influenced by the management system?

Light-textured soils are widely distributed globally and, despite their limitations, have been integrated into agricultural production systems. This study aimed to assess how management systems—conventional tillage (CT) and no-till (NT)—affect aggregate formation pathways (physicogenic and biogenic) and bacterial communities. Two management systems (NT and CT) and three cover crops were evaluated: CJ: Crotalária (Crotalaria juncea (40 ​kg ​ha−1); M: Millet (Pennisetum glaucum - 60 ​kg ​ha−1); and C: Cocktail (Crotalária - Crotalaria juncea - 10 ​kg ​ha−1, Jack bean - Canavalia ensiformis - 75 ​kg ​ha−1, and Millet - Pennisetum glaucum - 30 ​kg ​ha−1). Undisturbed soil samples were collected from the crop row at a depth of 0.00–0.10 ​m. Aggregates with diameters between 9.7 and 8.0 ​mm were classified as biogenic or physicogenic. In addition to the chemical attributes of the aggregates, total organic carbon (TOC) and its fractions (mineral-associated organic carbon, MAOC; particulate organic carbon, POC; and free light fraction carbon, FLFC) were quantified. The structure and bacterial composition of the aggregates were also characterized. A higher proportion of biogenic aggregates (53–64%) was observed compared to physicogenic aggregates (36–47%). Cover crops exhibited significant differences in pH, calcium (Ca2+), base saturation, phosphorous (P), and percentage of base saturation. The management systems differed significantly for Ca2+ and P, with CT showing higher values than NT. The management system influenced organic matter accumulation and stabilization in the aggregates, with MAOC content being significantly lower in CT. POC and TOC were also significantly lower in physicogenic aggregates under CT. Bacterial community richness, diversity, and structure were significantly influenced by the management system, with greater richness and diversity in NT compared to CT. Network analysis revealed NT had more nodes and edges (65 and 406, respectively) than CT (52 and 357, respectively. Phyla abundance differed between the systems, with Firmicutes and Entotheonellaeota more abundant in CT, while WPS_2, GAL15, Bdellovibrionota, and Myxococcota were more abundant in NT. Despite the relatively short period of NT implementation (5 years), it had a positive effect on the bacterial community, which may subsequently influence nutrient and carbon content and their fractions in the aggregates.

Effects of calcium phosphate and phosphorus-dissolving bacteria on microbial structure and function during Torreya Grandis branch waste composting

Background Burkholderiais a phosphorus solubilizing microorganism discovered in recent years, which can dissolve insoluble phosphorus compounds into soluble phosphorus. To investigate the effects of Burkholderia and calcium phosphate on the composting of Torreya grandis branches and leaves, as well as to explain the nutritional and metabolic markers related to the composting process.MethodsIn this study, we employed amplicon sequencing and untargeted metabolomics analysis to examine the interplay among phosphorus (P) components, microbial communities, and metabolites during T. grandis branch and leaf waste composting that underwent treatment with calcium phosphate and phosphate-solubilizing bacteria (Burkholderia). There were four composting treatments, 10% calcium phosphate (CaP) or 5 ml/kg (1 × 108/ml Burkholderia) microbial inoculum (WJP) or both (CaP + WJP), and the control group (CK).ResultsThe results indicated that Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, pH, EC, and nitrogen content. Furthermore, these treatments significantly affected the diversity and structure of bacterial and fungal communities, altering microbial and metabolite interactions. The differential metabolites associated with lipids and organic acids and derivatives treated with calcium phosphate treatment are twice as high as those treated with Burkholderia in both 21d and 42d. The results suggest that calcium phosphate treatment alters the formation of some biological macromolecules.ConclusionBoth Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, nitrogen content and metabolites of T. grandis branch and leaf waste compost.These results extend our comprehension of the coupling of matter transformation and community succession in composting with the addition of calcium phosphate and phosphate-solubilizing bacteria.

Microplastics stimulated soil bacterial alpha diversity and nitrogen cycle: A global hierarchical meta-analysis

Microplastics (MPs) pollution is recognized as a global emerging threat with serious potential impacts on ecosystems. Our meta-analysis was conducted based on 117 carefully selected publications, from which 2160 datasets were extracted. These publications described experiments in which MPs were added to soil (in laboratory or greenhouse experiments or in the field) after which the soil microbial community was analyzed and compared to a control group. From these publications, we extracted 1315 observations on soil bacterial alpha diversity and richness indices and 845 datasets on gene abundance of bacterial genes related to the soil nitrogen cycle. These data were analyzed using a multiple hierarchical mixed effects meta-analysis. The mean effect of microplastic exposure was a significant decrease of soil bacterial community diversity and richness. We explored these responses for different regulators, namely MPs addition rates, particle size and plastic type, soil texture and land use, and study type. Of the bacterial processes involved in the soil nitrogen cycle, MPs addition significantly promoted assimilation of ammonium, nitrogen fixation and urea decomposition, but significantly inhibited nitrification. These results suggest that MPs contamination may have considerable impacts on soil bacterial community structure and function as well as on the soil nitrogen cycle.

Shotgun metagenomic analysis reveals the diversity of PHA producer bacterial community and PHA synthase gene in Addis Ababa municipal solid waste disposal area ‘Qoshe’

BackgroundPolyhydroxyalkanoates (PHAs) are naturally produced biopolymers with significant scientific and biotechnological potential. This study aimed to investigate the diversity of the PHA-producing bacterial community and PhaC genes in soil samples collected from a municipal solid waste disposal site known as “Qoshe” in Addis Ababa, Ethiopia, using a shotgun metagenomics approach. The SqueezeMeta pipeline was used to analyze the microbial community in the waste samples. A CD search against the TIGRFAM protein family database was performed to identify the complete-length multidomain sequences of PhaC genes and classify them into their respective classes. Statistical analysis and data visualization were performed using RStudio with R version 4.2.3.ResultsThe findings of this study suggest that known and unknown taxa likely contribute to the phaC genes of municipal solid waste. Taxonomic profiling of the metagenomic data revealed that the majority of the PHA-producing taxa belonged to the phylum Proteobacteria (80%), followed by Actinomycetota (16.5%). Furthermore, this study identified Thiomonas and unclassified Mycobacterium as the main contributors to class I PhaC genes. Class II PhaC genes are predominantly associated with the Pseudomonadaceae family, followed by unclassified Hyphomicrobials and Acidimicrobiales. Class III PhaC genes are abundantly related to the Methylococcaceae family, specifically the Methylocaldum genus. The analysis of PhaC gene sequences revealed high level of diversity, with a significant proportion of putative PhaC genes exhibiting low sequence identity with each other and PhaC gene in the database. Notably, the sequence variation observed within the same PhaC gene classes suggests the potential presence of previously unidentified PhaC gene variants.ConclusionsOverall, this research improves our understanding of the diversity of PHA-producing taxa and PhaC genes in municipal solid waste environments, providing opportunities for sustainable PHA production and waste management strategies. However, additional studies, including the isolation and characterization of specific strains, are necessary to confirm the PHA production capabilities of these strains and explore their biotechnological potential.

Effect of inoculation with different Eurotium cristatum strains on the microbial communities and volatile organic compounds of Fu brick tea

Eurotium cristatum is the primary fungus in Fu brick tea (FBT) and plays a crucial role in its special flavor. This study investigated the effect of inoculation with different E. cristatum strains (i.e., ZJ, GX, GZ, HN, and SX) on the microbial communities and volatile organic compounds (VOCs) of FBT. A total of 113 VOCs were identified in all samples, with the concentration of VOCs (alcohols, aldehydes, and ketones) significantly higher in GXE FBT than in other samples. The core VOCs of GXE (19), GZE (16), HNE (19), SXE (15), and ZJE (13) FBT were identified using orthogonal partial least squares discriminant analysis and relative odor activity value (ROAV) analysis. Methional (a27), butanal (a41), 1-octen-3-one (a69), and ethyl acetate (a77) were key markers for inoculated FBTs, and 1-octen-3-ol, dimethyl disulfide, and acetoin-M were the specific markers of HNE. Linalool and (E)-2-octenal were particularly prominent in GXE, and isoamyl acetate-D was an important aroma component of GZE. Differences in microbial diversity were observed among the different inoculated fermented FBTs, and E. cristatum inoculation remarkably influenced the richness and diversity of bacterial communities. The VOCs were closely associated with fungi and bacteria, and 19 potentially dominant microorganisms (10 fungal and 9 bacterial genera) correlated with VOCs were identified. Among them, Aspergillus (fungi) and Pseudomonas (bacteria) exerted the greatest role. The FBT inoculated with E. cristatum from ZJ had the highest content of theaflavins and theabrownins, which intensified the red and yellow colors of the tea. E. cristatum greatly decreased the free amino acids and fatty acids, contributing to the aroma formation of FBT. Therefore, inoculating FBT with E. cristatum remarkably influenced the microbial communities and improved its flavor profile. This work provides a theoretical foundation on the role of E. cristatum in the formation and regulation of FBT flavor.