Diversity Of Bacterial Communities Research Articles

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.

Influence of soil organic carbon fractions on the soil priming effect under different vegetation restoration modes

AbstractThe soil priming effect is a key mechanism influencing carbon (C) cycling processes between the forest soil organic carbon (SOC) pool and the atmosphere. Different vegetation restoration modes have different SOC pool compositions, and it is not clear whether such differences affect the soil priming effect. Therefore, we selected soil from six typical vegetation restoration modes Platycladus orientalis (PO), Pinus sylvestris (PS), Quercus acutissima (QA), shrub (SH) and wasteland (WL) in the soil and rocky mountainous areas of northern China and measured the soil properties, microbial communities, microbial necromass carbon (MNC), SOC fractions and the soil priming effect. The SOC content decreased in the order of PO (21.33 g kg−1), PS (22.00 g kg−1), QA (13.67 g kg−1), SH (13.33 g kg−1) and WL (10.33 g kg−1), and the trends of the mineral‐associated organic carbon (MAOC) and fungal necromass carbon (FNC) content were the same as those of the SOC content. The soil priming effect was greater in both forests and shrublands than in wastelands, with the greatest effect occurring in PO forests, where the soil priming effect reached 159.91 mg CO2‐C kg−1 soil after 30 days of incubation, which was 1.4 times greater than that in WL. The soil priming effect was mainly determined by the difference in MAOC content. In addition, the soil C/N ratio and bacterial community diversity also indirectly affected the soil priming effect by influencing the soil MNC and SOC fractions. Overall, afforestation increased the SOC content, fungal necromass contribution and mineral conservation, increasing the soil priming effect. This theoretical foundation supports the enhancement of SOC sequestration capacity by implementing various modes of vegetation restoration in the future.

How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP.

Enhancing compost quality through biochar and oyster shell amendments in the co-composting of seaweed and sugar residue

Aquaculture and agricultural production generate substantial amounts of waste, including seaweed (which has plant-stimulating properties), oyster shells, and sugar residues. Through composting and appropriate management, these wastes have the potential to be converted into beneficial soil amendments. However, there is a lack of research exploring the potential of composting in promoting the conversion of seaweed into more stable humified forms, as well as in assessing whether composted seaweed retains its beneficial effects on plant growth. Additionally, studies on using oyster shells as additives to reduce waste pressure and comparing their effectiveness with biochar are relatively scarce. This study examines the impact of incorporating 5% corn stover biochar (T1), 10% biochar (T2), and 10% oyster shell powder (T3) on key physicochemical properties, product quality, and microbial community dynamics during the co-composting of seaweed and sugar residues. Results indicate that organic matter (OM) loss in T1 and T2 increased by 31.2% and 26.4%, respectively, compared to the control (CK). Moreover, Excitation-emission matrix (EEM) fluorescence spectroscopy revealed that humic substances in T1 and T2 surged by 434% and 423%, respectively, far exceeding the 289% increase in CK. The 10% biochar treatment also improved alginate degradation and seed germination index, due to the presence of biostimulants in seaweed and an increased abundance of Cobetia. Microbial analysis post-composting showed that T2 and T3 significantly enhanced the diversity and richness of bacterial communities. Notably, although oyster shell powder did not improve the humification degree of compost as significantly as biochar, it achieved effective weight reduction of waste (OM loss of 43.57%, far exceeding CK's 35.34%) without hindering the composting process. All four compost treatments retained the plant-stimulating effects of seaweed and facilitated alginate degradation. These results underscore the potential of biochar to enhance composting efficiency and utilize composting to process large quantities of oyster shell waste.

Synergistic biodegradation of trichloroethylene-contaminated soil using Typha angustifolia L. and an anaerobic degrading bacterial consortium

Plant-microorganism combined bioremediation is a highly efficient and environmentally sustainable method for the remediation of contaminated soils. Despite its potential, the synergistic effects of wetland plants and anaerobic microbial consortium on the removal of chlorinated hydrocarbons (CAHs) from soil remain inadequately understood. In this study, an anaerobic bacterial consortium, capable of completely dechlorinating trichloroethylene (TCE), was enriched and screened from long-term CAH-contaminated soil. Subsequently, the combined effects of the wetland plant Typha angustifolia L. and the degrading bacterial consortium on the removal of TCE from soil were investigated, along with the underlying microbial mechanisms. The results demonstrated that the bacterial consortium was able to completely convert 0.5 mM TCE to vinyl chloride (VC) within 7 days, and subsequently degrade VC to ethylene within 48 days. The integration of Typha angustifolia L. with the degrading bacterial consortium significantly enhanced both the removal and complete dechlorination of TCE from the soil compared to either treatment alone. Furthermore, this combination substantially increased the diversity and richness of soil bacterial communities, enriched dechlorinating microorganisms, and elevated the relative abundance of dehalogenating enzymes and peroxidases involved in pollutant degradation. In addition, the combination resulted in a more complex soil bacterial community, closer microbial interactions, and a more stable microbial co-occurrence network. This study extends the scope of plant-microorganism combined bioremediation for CAH- contaminated soils.

Diversity and Composition of Posidonia oceanica-Associated Bacterial and Fungal Communities: Effect of Boat-Induced Mechanical Stress in the Villefranche-sur-Mer Bay (France)

The anchoring and mooring of boats mechanically damage Posidonia oceanica plants; however, no information is available on the effect of this kind of damage on the plant holobiont, i.e., on the associated bacterial and fungal communities. Indeed, bacterial communities are known to change under different plant stress conditions but the dynamics of seagrass-associated fungi remain largely unexplored. We used DNA metabarcoding to profile the bacterial and fungal colonizers of two nearby P. oceanica patches in the Villefranche-sur-Mer bay (France) differing by the amount of exposure to mechanical stress due to boat transit and anchoring. Bacterial communities showed a significant reduction in diversity with an increase in Vibrio sp. in the rhizome and root samples from the impacted site, where the accumulation of dead organic material favors opportunistic heterotrophs. Conversely, fungal communities showed increased diversity in the leaf samples from the impacted site, where a reduction in the dominant P. oceanica host-specific mutualistic endosymbiont, Posidoniomyces atricolor, was found. This change was probably due to the opening up of new colonizable niches for several fungal species. Although this study represents a preliminary assessment of the effect of mechanical stresses on P. oceanica-associated microbial communities, it further supports their putative use as a seagrass descriptor.

Bacterial community and antibiotic resistance genes assembly processes were shaped by different mechanisms in the deep-sea basins of the Western Pacific Ocean.

As the intrinsic property of microorganisms, antibiotic resistance genes (ARGs) are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, human activities often obscure the natural distribution of ARGs through deterministic selective pressures. The deep-sea basin of the western Pacific Ocean is one of the least disturbed areas globally by human activities, providing a natural laboratory to investigate the intrinsic mechanisms governing ARGs in natural environments. In this study, we analyzed bacterial community and ARG diversity in 15 surface sediment samples from three deep-sea basins in the western Pacific Ocean. The relative abundance of ARGs in the surface sediments ranged from 3.10 × 10-3 to 5.37 × 10-2 copies/16S rRNA copies, with multidrug and β-lactam resistance genes dominated in all samples (49.06%-100%). The bacteria were mainly dominated by the Proteobacteria. The principal coordinate analysis (PCoA) showed significant spatial heterogeneity of ARGs and bacteria among the three basins. Null model, neutral community models (NCM), and normalized stochasticity ratio (NST) indicated that bacterial community was dominated by stochastic assembly, driven by geographic barriers leading to independent evolution. Conversely, the NST revealed that the ARGs profile was mainly shaped by deterministic processes. Environmental factors are more crucial than geographical factors and bacterial community for ARG occurrence among the selected factors. Meanwhile, we found that the spread of ARGs was mainly through vertical gene transfer in the pre-antibiotic era. The disparity between the assembly processes of bacterial community and ARGs may be attributed to the fact that ARG hosts were not the dominant bacteria in the community. This study first reported the distribution and assembly processes of ARGs and bacterial community in surface sediments of the western Pacific.

Pb pollution altered bacterial community assembly and predicted functions in aggregate-size fractions of agricultural soil near a smelter

In order to investigate the impact of Pb smelter pollution on bacterial community structure, diversity and function at the microenvironment scale, the maize rhizosphere soils subjected to long-term (over 20 years) Pb smelter pollution were collected, and bacterial communities and putative functions associated with different aggregate-size fractions were identified by 16S rRNA sequencing, KEGG and FAPROTAX. The results showed that Pb pollution significantly diminished bacterial diversity, and prompted a shift in the bacterial communities toward more oligotrophic taxa, including Firmicutes, Chloroflexi, and Gemmatimonadetes. Furthermore, the functional subcategories related to cell motility and energy metabolism, as well as the functional groups involved in carbon (C), nitrogen (N), and sulfur (S) cycles, exhibited a marked decline under Pb pollution. At the aggregate scale, distinct differences were observed in the composition of bacterial communities across silt and clay (<250 μm), micro-aggregates (250∼1000 μm), and macro-aggregates (1000∼2000 μm and >2000 μm) in uncontaminated soils. However, Pb pollution disrupted these original distinctions among bacterial communities in various aggregate-size fractions, with a decreased abundance of dominant Proteobacteria and an increased abundance of Firmicutes in large aggregates. While the differences in bacterial functional groups in aggregate-size fractions were also detected. The functional groups associated with carbon (C) and nitrogen (N) cycles were significantly enriched in the macro-aggregates (1000∼2000 μm) in uncontaminated soils. However, similar with the change of bacterial community structure, most functional groups (except for chemoheterotrophy) in aggregate-size fractions exhibited no significant differences under Pb exposure. Our results suggested that Pb pollution altered bacterial community structure and predicted functions at the aggregate level, and showed greater negative effects on bacterial functions in macro-aggregates (1000∼2000 μm). This study can provide a new perspective for the influence of Pb smelter pollution on soil aggregate microenvironment.

Hyperthermophilic composting coupled with vermicomposting stimulates transformation of organic matter by altering bacterial community

Hyperthermophilic composting (HTC) has been proven to be an effective strategy to recycle organic wastes, while vermicomposting (VC) has been widely applied to produce humic fertilizer. The combination of HTC with VC (HVC) is expected to integrate the advantages of both. This study showed that HTC pre-fermentation provided plentiful substances such as dissolved organic matter (DOM) for the subsequent VC enriching humic acid (HA). Compared to thermophilic composting (TC), HVC significantly stimulated the degradation of organic matter (OM) and the production of N-rich HA, and incubated higher diversity of bacterial community. SHapley Additive exPlanations (SHAP), correlation network, Mantel test and PLS-LM model were constructed to identify the potential roles of the key bacterial groups contributing to OM transformation. Firmicutes (e.g., Bacillus and Tuberibacillus) dominant in HTC may mineralize and mobilize OM, providing affluent bioavailable nutrients as part of DOM for microbial metabolism and abundant precursors for HA formation in the further VC. Actinobacteriota (e.g., Microbacterium) and Bacteroidota (e.g., Flavobacterium and Parapedobacter) prominent in VC metabolized DOM, mineralized OM and produced HA probably by enhancing the metabolic activity involved in OM degradation and amino acid generation. However, when DOM was exhausted, some members especially Proteobacteria (e.g., Ochrobactrum, Devosia and Cellvibrio) would change their roles from promoter to inhibitor of mineralization and humification. Altering the nutrient bioavailability and the composition of bacterial community can regulate the mineralization, mobilization and humification of OM. Overall, this study provides new insights into the roles of bacteria participating in transforming organic wastes into HA-rich composts.

Hydroxyapatite self-doped biochar with MgO modification immobilizes heavy metal and alters soil microbial community

Functionalized biochars are highly effective in the remediation of heavy metals and the improvement of soil properties. In this study, we prepared a hydroxyapatite self-doped biochar (FB) using fish scales as raw material, and impreged FB with MgCl2 following by pyrolysis to obtain MgO-loaded FB (MFB). A soil incubation experiment was conducted to explore the influence of MFB on the immobilization of Cu, Cd, and Pb, alongside the impact on the soil properties and bacterial community. The results demonstrated that the nano-hydroxyapatite components and MgO micro-nanoparticles on MFB promoted the immobilization of heavy metals in soils through dissolution-precipitation and ion-exchange. The availability of Cu, Cd, and Pb in soils amended with MFB was significantly decreased by 69.1 %, 63.5 %, and 53.7 %, respectively, compared to CK. Furthermore, the MFB amendment significantly increased soil organic carbon and available P, as well as enhanced enzyme activities related to the C-, N-, and P-cycles. Notably, the MgO loaded on biochar played a crucial role in altering the diversity and composition of soil bacterial communities. The complexity and stability of the co-occurrence networks of bacterial communities increased following MgO-loaded biochar addition, and there were more frequent positive interactions among bacterial taxa within the network. The effects of MFB on immobilizing heavy metals and shaping bacterial communities were conducive to the restoration of soil ecological functions. These findings provide a promising strategy for the remediation of heavy metal contaminated soils.

Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China.

The bacterial community performs an essential ecological role in maintaining agriculture systems. The roles of bacteria in the forest, marine, and agricultural systems have been studied extensively and intensively. However, similar studies in the areas irrigated by the Yellow River remain limited. In this study, we used Illumina sequencing analysis with the 16S rRNA method to analyze the bacterial diversity, community structure, and influencing factors in soil samples from eight regions of the Yellow River irrigation area in northwestern China. The bacterial community structure and diversity varied among samples from the eight regions. The samples differed significantly in terms of the bacterial community composition. Proteobacteria (approximately 12.4%-55.7%) accounted for the largest proportion and was the dominant bacteria, followed by Actinobacteria (approximately 9.2%-39.7%), Bacteroidetes (approximately 1.8%-21.5%), and Chloroflexi (approximately 2.7%-12.6%). Among the physicochemical variables, the soil pH in the eight regions was mildly alkaline, and the total nitrogen, total phosphorus, and total potassium contents in the soils differed significantly. However, the trend in the variations of the above variables was essentially similar. Soil bacteria in Yongning county had greater Chao1, Shannon-Wiener, and Simpson indices than those in the other regions. Notably, soil moisture, organic matter, and total nitrogen were recognized as the primary factors influencing the bacterial community in the Yellow River irrigation area. Our results revealed the laws of variation in soil bacterial diversity and community composition in the Yellow River irrigation area. Our findings could be beneficial for maintaining sustainable ecological practices in the Yellow River irrigation area.

Impact of Organic Fertilization Strategies on Soil Bacterial Community and Honey Pomelo (Citrus maxima) Properties

Soil health is a critical factor in sustainable agriculture, particularly in fruit production, where fertilization strategies play a vital role in maintaining the soil quality and enhancing fruit production and quality. This study investigates the effects of different fertilization strategies on soil bacterial communities and honey pomelo (Citrus maxima) properties in Ji’an City, Jiangxi Province, China. Three fertilization treatments were compared: conventional fertilization (CF: botanical organic plus chemical compound fertilizers), organic material fermented fertilization (OF: organic material including duck manure fermented fertilizer plus chemical compound fertilizer), and a special honey pomelo fertilizer (SF: organic material fermented fertilizer only during the whole honey pomelo growing season). Soil samples were collected at two depths (0–20 cm and 20–40 cm) from nine plots (three treatments × three replicates) and analyzed for their soil properties, bacterial community diversity and composition, and fruit characteristics. The results indicate that the OF and SF significantly improved the soil pH, soil organic matter (SOM), and nutrient availability compared to the CF. Additionally, the OF and SF treatments led to a 13.6% and 16.6% increase in fruit weight, respectively, and higher bacterial diversity, although no significant differences were observed in fruit quality parameters such as vitamin C, soluble sugar, and titratable acid. Acidobacteriota, Proteobacteria, Actinobacteria, and Chloroflexi were the dominant bacterial phyla. The soil bacterial composition structures were significantly different among the different fertilization strategies, and were well explained by soil properties such as the pH, SOM, total phosphorus, and available nutrients. Our study suggests that applying fermented organic fertilizers which use duck manure as part of the raw materials, either alone or in combination with chemical compound fertilizers, increases honey pomelo fruit production and improves soil health, contributing to the sustainable development of orchards.

Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era

BackgroundThe Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.ResultsStatistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.ConclusionThis characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

Characterizing the soil microbial community associated with the fungal pathogen Coccidioides immitis.

Coccidioidomycosis is a fungal disease affecting humans and other mammals, caused by environmental pathogens of the genus Coccidioides . Understanding the ecological factors that shape the distribution of Coccidioides in soils is important for minimizing the risk of human exposure, though this remains challenging due to the pathogen's highly variable spatial distribution. Here, we examined associations between the soil microbial community and Coccidioides immitis presence within the Carrizo Plain National Monument-a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows on C. immitis presence in soils. Using internal transcribed spacer 2 (ITS2) and 16S sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred with Coccidioides more frequently than expected by chance. Coccidioides -positive samples were significantly higher in microbial diversity than negative samples, an association partly driven by higher Coccidioides presence within rodent burrows compared to surface soils. Soil source ( i.e., rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher microbial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding associations between Coccidioides and microbial diversity, our study suggests that favorable microhabitats such as rodent burrows can lead to a positive association between soil diversity and Coccidioides presence, particularly in otherwise resource-limited natural environments.