Bacterial Community Structure Research Articles

Successive monoculture of Eucalyptus spp. alters the structure and network connectivity, rather than the assembly pattern of rhizosphere and bulk soil bacteria

Eucalyptus as a fast-growing timber tree plays a crucial role in maintaining wood supplication and ecosystem balance worldwide. Nonetheless, the management practices of Eucalyptus plantation in southern China have resulted in productivity decline and soil degradation due to high-intensity successive cultivation. Soil bacteria is a sensitive indicator of soil quality, how does the successive planting of Eucalyptus regulate the soil bacterial community structure for instance the abundance of oligotrophic bacteria, network complexity, and soil bacteria assembly remain ambiguity. To explicate the underlying influencing mechanisms of successive cultivation of Eucalyptus plantations on soil bacterial community structure. Four harvests of Eucalyptus plantations that underwent 0, 1, 2, and 3 times of harvesting were conducted to examine variations in the bacterial community between rhizosphere and bulk soils after successive planting of Eucalyptus. An adjacent evergreen broadleaf forest was employed as control. The present study revealed that successive planting of Eucalyptus increased and reduced the relative abundance of Chloroflexi (oligotrophic bacteria) and Proteobacteria (copiotrophic bacteria), respectively. Continuous planting of Eucalyptus did not modify the assembly pattern of soil bacterial communities, which was governed by stochastic processes. Successive planting of Eucalyptus decreased co-occurrence network complexity, and elevated the proportion of rare microorganisms in the keystone bacterial taxa. Soil particle size composition (clay, silt, sand) indirectly influenced the structure of soil bacterial communities by directly affecting pH, carbon, nutrients, and their stoichiometric ratios. Improving soil physical structure, increasing the input of soil carbon, nitrogen, and other nutrient resources, and maintaining a balanced resource allocation may be effective strategies for ensuring enhanced productivity and sustainable utilization of soil in successive Eucalyptus plantations.

Phosphogypsum with Rice Cultivation Driven Saline-Alkali Soil Remediation Alters the Microbial Community Structure.

The improvement of saline-alkali land plays a key role in ensuring food security and promoting agricultural development. Saline soils modifies the response of the soil microbial community, but research is still limited. The effects of applying phosphogypsum with rice cultivation (PRC) on soil physicochemical properties and bacterial community in soda saline-alkali paddy fields in Songnen Plain, China were studied. The results showed that the PRC significantly improved the physicochemical properties of soil, significantly reduced the salinity, increased the utilization efficiency of carbon, nitrogen, and phosphorus, and significantly increased the activities of urease and phosphatase. The activities of urease and phosphatase were significantly correlated with the contents of total organic carbon and total carbon. A redundancy analysis showed that pH, AP, ESP, HCO3-, and Na+ were dominant factors in determining the bacterial community structure. The results showed that PRC could improve soil quality and enhance the ecosystem functionality of soda saline-alkali paddy fields by increasing nutrient content, stimulating soil enzyme activity, and regulating bacterial community improvement. After many years of PRC, the soda-alkali soil paddy field still develops continuously and healthily, which will provide a new idea for sustainable land use management and agricultural development.

Positive Effect of Camelina Intercropping with Legumes on Soil Microbial Diversity by Applying NGS Analysis and Mobile Fluorescence Spectroscopy

Camelina (Camelina sativa (L.) Crantz) is a valuable source of essential amino acids, especially sulphur-containing ones, which are generally lacking in leguminous crops, thus representing an alternative source of protein for both humans and farm animals. Rhizosphere soil samples from five experimental plots with mono- and mixed cultivations of three camelina cultivars, including two introduced varieties Cs1.Pro (Luna) and Cs2.Pro (Lenka) and one Bulgarian variety Cs3.Pro (local Bulgarian landrace) with variety 666 of vetch (Vicia sativa L.) (Cs3-Vs.Pro) and variety Mir of pea (Pisum sativum L.) (Cs3-Ps.Pro), were collected and analysed. The total DNA was isolated from the rhizosphere soils and the presence of the 16S rRNA gene was confirmed by amplification with the universal primer 16SV34. In the present study, the structure of the soil bacterial community in five different plots (Cs1.S.Pro, Cs2.S.Pro, Cs3.S.Pro, Cs3.Vs.S.Pro, and Cs3.Ps.S.Pro) where camelina was grown alone and by being intercropped with pea and vetch was analysed via a metagenomic approach. The number of observed species was highest in the local genotype of the camelina Cs3 grown alone, followed by soil from the intercropped variants Cs3-Vs and CsS-Ps. The soil bacterial communities differed between the sole cultivation of camelina and that grown with joint cultivation with vetch and peas, indicating that legumes considerably affected the growth and development of beneficial microorganisms by aspects such as nitrogen fixing, levels of nitrifying bacteria, and levels of phosphorus-dissolving bacteria, thus helping to provide better plant nutrition. The α-diversity indicated that bacterial communities in the rhizosphere were higher in soils intercropped with vetch and pea. The optical properties of cereals and legumes were determined by their energy structure, which includes both their occupied and free electronic energy levels and the energy levels of the atomic vibrations of the molecules or the crystal lattice.

Ecological practices increase soil fertility and microbial diversity under intensive farming

Intensive farming offers a potential solution to feed the growing population due to its high productivity. Conventional management (CO) based on inorganic fertilization practices degrades soil quality, but restorative practices including ecological intensification (EI) and organic management results in maintaining soil quality without compromising productivity. In this paper, two different management systems were evaluated: CO, based on inorganic fertilization, and EI, focused on providing organic nutrients to soils to support crops.EI increased soil fertility, together with higher alpha diversity indices, more differentially abundant amplicon sequence variant (ASVs) (247 EI vs. 165 CO) and indicator taxa (60 EI vs. 32 CO). Distinct bacterial taxa were associated with the different management systems, revealing their roles in soil processes and nutrient availability. In the CO treatment, indicator genera such as Nitrospira and Desulfarculaceae were linked to N fertilization and nitrite oxidation, while RB41 was associated with phosphorus availability. Ammoniphilus, PAUC26f, and BSV26 were also indicators of CO management. Conversely, EI treatment promoted bacteria involved in organic matter decomposition and nutrient cycling, such as Halomonas, Chryseolinea and Rhodobacteraceae. Gemmatimonas, Steroidobacter, Altererythrobacter, Acidibacter and Anseongella contribute to carbon and nitrogen cycling. Burkholderiaceae and Rhodopirellula play roles in phosphate solubilization and organic P mineralization, respectively. Numerous taxa with plant growth-promoting (PGP) attributes, such as BIrii41, Pseudomonas, and Lysobacter, were also identified as indicators of the EI treatment.EI associated bacteria were positively correlated with soil organic carbon contents, nitrates, and exchangeable bases, while negatively correlated with CO bacteria. A distance-based multivariate multiple regression (DistLM) demonstrated a strong relationship (r2 = 0.78) between soil physicochemical variables and bacterial community structure, with SOC explaining the most variations in the model. Other significant parameters included potassium (K), electrical conductivity (EC), and nitrates. The results suggest that EI promotes more sustainable soils in terms of fertility and microbial diversity.

Sex-Dependent Rhizosphere Microbial Dynamics and Function in Idesia polycarpa through Floral and Fruit Development

Male Idesia polycarpa, which display distinct morphological and physiological traits, exhibit greater adaptability to stressful environments than females. However, the connection between this adaptability and rhizosphere processes remains unclear. Here, we investigate the differences in root bacterial community structures between male and female plants at different developmental stages, identifying bacterial strains associated with plant sex through functional predictions. This study aims to inform the optimal allocation of male and female plants during cultivation and provide a theoretical basis for sex identification and breeding. Samples from seven-year-old male and female plants were collected during the flowering (May) and fruit ripening (October) stages. Rhizosphere nutrient content and bacterial diversity were analyzed using Illumina high-throughput sequencing technology. The results demonstrate that total nitrogen (TN), total carbon (TC), and available potassium (AK) varied between sexes at different times. No significant differences between male and female plants were observed in the Shannon, Simpson, and Chao1 indexes during the flowering period. However, the Chao1 and Shannon indexes were significantly higher at fruit maturity in male rather than female plants. The predominant phyla of rhizosphere bacteria were Pseudomonadota, Acidobacteriota, and Actinomycetes. Interestingly, from flowering to fruit ripening, the dominant phyla in both male and female plants shifted from Actinomycetes to Pseudomonadota. A significant correlation was observed between pH and AK and rhizosphere bacteria (p < 0.05), with metabolism being the main functional difference. This study provides preliminary insights into the functional predictions and analyses of bacteria associated with Idesia polycarpa. The above findings lay the groundwork for further investigation into the sex-specific differences in microbial flora across different developmental stages, elucidating the mechanisms underlying flora changes and offering theoretical support for the high-quality management of Idesia polycarpa.

Insights into the critical roles of water-soluble organic matter and humic acid within kitchen compost in influencing cadmium bioavailability

Compost has demonstrated potential as a cadmium (Cd) remediation agent, while it still remains unclear about the core components in driving the bioactive transformation of Cd. To address this issue, this study isolated three components—kitchen compost powder (KC), humic acid (HA), and water-soluble organic matter (DOM)—from kitchen compost to regulate soil properties, bacterial community structures and functions, and Cd migration risks. The results revealed that the addition of 20% KC and HA reduced the bioavailability factor of Cd by 47.20% and 16.74%, respectively, with HA contributing 35.47% of the total reduction achieved with KC. Conversely, the application of DOM increased the Cd risk through a reduction in soil pH and an increase in the abundance of Cd-activating bacteria, which adversely affected the stability of Cd complexes. However, the porous structure and organic matter in KC and HA provided adsorption sites for Cd passivation and promoted the growth of Cd-fixing bacteria. This study effectively identifies both the positive and negative effects of key compost components on Cd migration and provides scientific guidance for applying kitchen compost in soil management.

Aeration treatment promotes transformation of soil phosphorus fractions to plant-available phosphorus by modulating rice rhizosphere microbiota

Microorganisms play an important role in affecting the content of available phosphorus (P) in plant rhizosphere soil. However, the effect of aeration on available P in rice rhizosphere soil and its microbial mechanism remain unclear. This study aimed to elucidate the effects of aeration strategies on available P and P-solubilizing microorganisms in rhizosphere soil, employing three different aeration methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)). We analyzed the bacterial and fungal community structures in rice rhizosphere soil via Illumina sequencing techniques and quantified the abundance of P transformation functional genes related to inorganic P solubilization (pqqC) and organic P mineralization (phoC, phoD, and appA) through quantitative PCR. Our findings revealed that the AWD treatment significantly increased soil pH and Eh; Both AWD and CFA treatments markedly increased soil Olsen-P content at the tillering and heading stages, as well as the microbial carbon-to-phosphorus ratio (MBC/MBP) at the heading and maturity stages. Cluster analysis showed distinct bacterial communities at the heading and maturity stages under AWD, which differed from those in other treatments. Fungal communities at the tillering and heading stages under CFA and AWD grouped together. AWD and CFA treatments consistently enhanced labile-P in the rhizosphere soil throughout the entire growth stages, while reducing moderately labile-P during the tillering and heading stages. Compared to CF, at the heading and maturity stages, the copy numbers of pqqC, phoD, phoC, and appA were higher under AWD compared to other treatments. In conclusion, this study posits that the increase in Olsen-P in paddy fields due to aeration results from improved oxygen conditions in the rhizosphere, alterations in pH and Eh, effects on microbial stoichiometry, and adjustments in the abundance and composition of P-solubilizing microorganisms, thereby promoting P transformation. This conclusion provides new insights into the conversion of soil P Fractions into plant-available forms.

Influence of long-term ecological reclamation on carbon and nitrogen cycling in soil aggregates: The role of bacterial community structure and function

Understanding the influence of microbial taxa and functions on soil carbon (C) and nitrogen (N) cycling, particularly concerning soil aggregate sizes, is crucial for ecosystem management. This study examines the taxonomic and functional dynamics of soil bacterial communities within different aggregate sizes over time. Soil samples from a reclamation forest on the Loess Plateau in North China were collected across reclamation ages of 0, 3, 18, and 28 years. Soil aggregates were categorized into large macro-aggregates (>2000 μm), small macro-aggregates (250–2000 μm), and micro-aggregates (<250 μm) using a modified dry-sieving method. Soil aggregate stability, C and N concentrations, newly derived plant C, enzyme activities, bacterial communities, and functional genes in each aggregate fraction were systematically analyzed. There was a notable increase in soil aggregate stability and a higher proportion of large aggregates was found with increasing forest age. There were significant differences in bacterial community structures, particularly between micro-aggregates and large macro-aggregates and across different forest ages. Reclamation led to an increased abundance of copiotrophic bacterial taxa. Decreases in N-acquiring enzyme activity in micro-aggregates were contrasted by an increase in C, N, and phosphorus (P) acquisition activities in larger aggregates over time. Larger aggregates showed a faster recovery of C and N cycling genes accompanied by a significant enhancement in acetyl-CoA and ammonia oxidation processes, underscoring their importance in soil nutrient cycling. These results highlight the critical role of aggregate size in shaping microbial community structures and functions that influence soil C and N cycling during reclamation and provide new perspectives highlighting the significance of incorporating aggregate size considerations into soil management and reclamation strategies.

Effects of ammonium sulfate on the degradation and metabolism of dinotefuran in soil: Evidence from soil physicochemical properties and bacterial community structure

Ammonium sulfate and dinotefuran are widely used in agricultural practices; however, limited knowledge exists regarding the potential risks associated with their co-exposure. In this study, the impact of ammonium sulfate on the degradation of dinotefuran in four soils was investigated, and the formation of the main metabolites UF, DN, MNG, and NG was also determined. The underlying mechanisms were explored by the impact of ammonium sulfate on soil physicochemical properties as well as soil microorganisms. The half-life of dinotefuran sole exposure in soils were determined between 27.47 and 60.05 days. Co-exposure of ammonium sulfate significantly impeded the degradation of dinotefuran, resulting in 1.70–5.05 times longer half-life, reduced the content of the metabolites and changed their composition. Ammonium sulfate induced significant alterations in the structure and dominance of bacterial communities in the soils. The reduced relative abundance of Bacteroidota, Proteobacteria and Chloroflexi phyla related to dinotefuran degradation. Ammonium sulfate also led to a decrease in soil pH and organic matter content, which were negatively correlated with the degradation. PLS-SEM analysis revealed soil microbial diversity had a significant impact on the degradation of dinotefuran. The findings serve as a cautionary note regarding the risks of co-exposure to fertilizers and pesticides.

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.

Mechanisms of microbial diversity modulation of mineral black clay to achieve ecological restoration of open-pit mine dump

The harsh climatic conditions and severe scarcity of surface soil present significant challenges to ecological restoration in open-pit mine dumps within China's type II plant cold resistance zone. To address the topsoil shortage, mineral black clay was used to create synthetic soil. This study explored the application of an ecological restoration bacteria (ERB) consortium to accelerate the ecological restoration of synthetic soil-covered areas by enhancing soil ecosystem construction. The results demonstrated that ERB significantly influenced the native bacterial community structure in mixed black clay. Specifically, ERB disrupted the inhibitory effects of the Actinobacterota phylum on the development of native bacterial diversity, leading to an increase in unclassified_o_Solirubrobacterales sp., norank_f_norank_o_norank_c_KD4-96 sp., Sphingomonas sp., Luteitalea sp., norank_f_Vicinamibacteraceae sp., and other aerobic and anaerobic bacteria. These alterations in soil microbial structure directly impacted soil composition and vegetation diversity. The plant diversity survey and metabolomics analysis revealed that the reduction of harmful substances, such as HPED, HODE, and HOME, in black clay soil improved the growth and distribution of Salsola collina Pall. and Medicago sativa L. This increase facilitated the cycling of key nutrients, such as nitrogen (N) and phosphorus (P), and promoted the establishment of symbiotic relationships between plants, microorganisms, and soil. Ultimately, the ecological remediation of the synthetic soil was achieved through the synergistic effects of ERB, which included the degradation of inhibitory soil components, enhanced nutrient consumption by microbiota and plants, and the overall promotion of ecosystem stability in the reclamation area.

The rhizosphere bacterial community of water yam (Dioscorea alata L.) under limited water conditions

AbstractIntroductionYam cultivation in West Africa, the largest yam production area, has expanded to the northern Guinea savanna, which receives an annual rainfall of 800–1000 mm. However, variations in rainfall are problematic for the stable productivity of yams. Integrated soil fertility management is urgently needed to improve and stabilise yam productivity. Plants have complex interactions with bacterial communities, influencing their health and environmental adaptability. Although the growth of water yams (Dioscorea alata L.) at various rainfall levels might be related to their interaction with the bacterial community, their structure under water limitation is yet to be elucidated. Here, we evaluated the bacterial community structure in the rhizosphere (Rh) and roots of ‘A‐19’ under water limitation conditions.Materials and MethodsPlants were grown under normal conditions, and watering was reduced to less than 70% for 1 month. Rh and root samples were collected for DNA extraction, and downstream amplicon sequencing analyses were performed.ResultsThe dry weight of the shoots, particularly the leaves, decreased under water limitation. Bacterial diversity in the rhizocompartments was significantly reduced. However, bacterial community composition was not affected by water limitation. Despite water‐limited conditions, bacterial community structure was robust in the Burkholderia‐Caballeronia‐Paraburkholderia and Streptomyces clades. These taxa accounted for approximately 60% of the relative abundance in the roots under water limitation.Conclusionidentifying bacterial community composition of ‘A‐19’ under water‐limited conditions provides fundamental information for developing integrated soil fertility management strategies across rainfall gradients in West Africa. Our study indicates that ‘A‐19’ has a robust bacterial community structure for beneficial interactions with bacteria despite soil water conditions.

Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

AbstractMicrobes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession.

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.

Efficiency comparison of DNA extraction kits for analysing the cockle gut bacteriome

Cockles play a vital ecological role and provide valuable ecosystem services globally. However, the performance, production, and safe consumption of cockles are significantly influenced by their gut-associated bacteriome. Accurate understanding of gut-bacteriome interactions, and surveillance of pathogenic bacteria loads in cockles, rely on efficient DNA extraction methods that yield high-quality and representative bacterial DNA. Despite this importance, reliable extraction methods for cockles are currently overlooked. Therefore, we evaluated the performance of five DNA extraction kits (E.Z.N.A.® Soil DNA; FastDNA® Spin; DNeasy PowerSoil Pro; QIAamp PowerFecal DNA; ZymoBIOMICS™DNA Miniprep) in terms of DNA quality, yield, bacterial community structure (analysed by using denaturating gradient gel electrophoresis; DGGE), and bacteriome composition (analysed by 16S rRNA gene sequencing) in Cerastoderma edule gut. The DNeasy kit provided the highest purity and quantity of bacterial DNA, while the PowerFecal and Zymo kits exhibited reduced extraction efficiency. DGGE profiles revealed significant variability between the tested kits (R = 0.512; mean P = 0.011), but the FastDNA kit under-represented the bacterial community in cockles’ gut. Based on alpha diversity, the DNeasy kit outperformed the others and successfully detected all abundant genera found with the alternative kits. Our findings indicate that the DNeasy kit is an efficient DNA extraction method, enabling a molecular representation of the gut-associated bacteriome in C. edule. These results contribute to the development of effective techniques for studying the cockle gut bacteriome and its ecological implications.

Carvacrol acts on the larval midgut of Spodoptera frugiperda by destroying the tissue structure and altering the bacterial community

The fall armyworm, Spodoptera frugiperda, has become a global invasive pest in recent years, threatening agricultural production. Carvacrol (CAR) is a multifunctional plant-derived compound and exhibited significant bioactivities against many pests. Our previous study found that CAR inhibited growth and development in S. frugiperda. However, the effects of CAR on the midgut of this pest remain unknown. In this study, the actions of CAR on the larval midgut of S. frugiperda were investigated. The results found that 1.0 and 2.0 g/kg CAR treatments destroyed the structure of the larval midgut based on hematoxylin-eosin staining and transmission electron microscope observation. In addition, 2.0 g/kg CAR exposure significantly altered the larval midgut bacterial community composition and structure. The results of the linear discriminant analysis effect size (LEfSe) analysis suggest that six bacterial genera contributed to the different structures of the larval bacterial community. Furthermore, PICRUSt2 analysis found that 16 bacterial function categories were altered by CAR treatment, of which 8 were significantly increased. Our results provided new insight into the toxicological mechanisms of CAR against S. frugiperda larvae and laid the foundation for the field application of S. frugiperda control.

The mango bacterial black spot altered the endophyte community structure and diversity

Mango bacterial black spot is a major disease limiting mango production, which is now causing increasingly severe economic losses. In this study, we analyzed the differences in the composition and structure of bacterial and fungal communities in the pulp and leaves between the healthy mangoes of variety Kate and those affected by bacterial black spot, and attempted to explore potential biocontrol microorganisms for mangoes. The results showed there existed significant differences in microbial communities, the bacterial Stenotrophomonas, Curtobacterium, Massilia and fungous Penicillium, Alternaria, Aureobasidiu showed great abundance both in pulps and leaves. Some potential pathogenic bacteria, such as Pseudomonas, Xanthomonas, and Burkholderia, were also significantly enriched in the infected groups. In both the infected and healthy groups, the overall community structure of endophytic bacteria and fungi within the same organs was more similar, indicating that the composition of endophytes is organ-specific. After infection, the abundance of the potential probiotic bacterium class Paenibacillus was significantly increased both in leaves and pulp, suggesting that the pathogen invasion stimulated the defense systems of endophytes. Presumably, these Paenibacillus might be developed as defense bacteria for black spot as well as other plant diseases.

Machine learning models reveal how polycyclic aromatic hydrocarbons influence environmental bacterial communities

Polycyclic aromatic hydrocarbons (PAHs) are harmful and widespread pollutants in the environment, posing an ecological threat. However, exploring the influence of PAHs on environmental bacterial communities in different habitats (soil, water, and sediment) remains a major challenge. We collected and reanalyzed 1924 16S rRNA sequencing samples to determine the effects of PAHs on bacterial communities in different habitats and used machine learning to predict potential degrading bacteria. It was found that PAHs had substantial effects on the bacterial community, and that the bacterial community structure changed differently in different habitats. PAH contamination decreased the relative abundance of Proteobacteria in the soil (16.3 %) and sediment (10.1 %), whereas the abundance of Proteobacteria in water increased by 20.2 %. Among the tested models, the random forest model best identified the effects of PAHs on bacterial groups, with an accuracy of 99.51 % for soil, 97.72 % for sediment, and 100 % for water at the genus level. Using the random forest model, we identified 70 biomarkers that respond to PAHs, including potentially degrading microorganisms such as A4b, Bacillus, Flavobacterium and Polynucleobacter. Furthermore, PAH contamination did not significantly alter the functions of bacterial communities in the environment. This study provides a candidate strain set for future screening of PAH-degrading bacteria and contributes to the study of the adaptability of engineered PAH-degrading bacteria to the environment.