Diversity Of Bacterial Communities Research Articles

Long-term biochar-based fertilizer substitution promotes carbon, nitrogen, and phosphorus acquisition enzymes in dryland soils by affecting soil properties and regulating bacterial community

Biochar-based fertilizers have shown positive effects on soil function, an understanding of how long-term biochar-based fertilizers substitution affects soil properties, microbial communities, and enzyme activities in dryland is lacking. We investigated the impacts of seven years biochar-based fertilizer substitution on the soil properties, bacterial community, and carbon (C), nitrogen (N), and phosphorus (P) acquisition-related enzymes in a dryland cauliflower-maize rotation. Four fertilization strategies were set up: no fertilizer (CK), chemical fertilizer (CF), 30 % replacement of chemical N with biochar-based fertilizer (LBF), and 60 % replacement of chemical N with biochar-based fertilizer (HBF). Results elucidated that biochar-based fertilizer substitution treatments had higher soil organic C (SOC) and nutrients (N, P, and potassium (K)) than non-biochar-based fertilizer treatments. Biochar-based fertilizer substitution improved C-, N-, and P-acquiring enzyme activities and C:N enzyme ratio, but decreased C:P and N:P enzyme ratios. We further found that biochar-based fertilizer substitution altered the soil bacterial community diversity and composition. Soil properties and bacterial community explained most variations in C-, N-, and P-acquiring enzymes. Modeling analysis revealed that biochar-based fertilizer substitution had positive effects on soil properties and bacterial community, which further positively regulated soil C-, N-, and P-acquiring enzymes. Key factors driving enzyme variations included available P, SOC, available K, available N, total K, and total N, as well as soil bacterial community composition and diversity. In conclusion, biochar-based fertilizer substitution could enhance C-, N-, and P-acquiring enzyme activities by boosting soil nutrient levels and altering bacterial community in dryland fields.

Comparing sewage sludge vs. digested sludge for starting-up thermophilic two-stage anaerobic digesters: Operational and economic insights.

Despite advances in anaerobic digestion (AD), full-scale implementation faces significant challenges, particularly during the start-up phase, where inoculum selection is crucial. This study examines the impact of inoculum choice on the operational and economic performance of thermophilic digesters during the start-up phase. Methanogenic reactors R3 and R4 were inoculated with digested sludge (DiS) and diluted sewage sludge (DSS), respectively, and fed with hydrolyzed source-sorted organic fraction of municipal solid waste (SS-OFMSW) and thickened sewage sludge, which were processed in R1 and R2, serving as acidogenic reactors. A two-stage AD configuration was employed to mitigate inhibitory effects associated with the undigested inoculum (DSS). This approach enabled the establishment of methanogenic activity in R4 when the AD system is initiated with DSS. However, R3 outperformed R4, achieving 49 % of the feedstock's theoretical methane potential compared to 15 % in R4. Methane production and volatile solids (VS) processing costs in R4 were 18 and 3 times higher than in R3, respectively. R3's superior performance was attributed to DiS's diverse bacterial community, with over 66 % of genera involved in hydrolysis, volatile fatty acid production, and syntrophic methane production. In contrast, DSS was dominated by Trichococcus and Lactococcus (75.4 %), primarily involved in butyrate oxidation and lactate production. This study provides valuable insights into effective inoculum selection for the start-up of full-scale digesters.

Elevational patterns in the diversity and composition of soil archaeal and bacterial communities depend on climate, vegetation, and soil properties in an arid mountain ecosystem

Elevational patterns in the diversity and composition of soil archaeal and bacterial communities depend on climate, vegetation, and soil properties in an arid mountain ecosystem

Bacterial community composition and metabolic characteristics of three representative Marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Microbial recruitment and microbial ecological roles in soil nutrient cycling of Populus cathayana males and females

Soil nitrogen (N) availability influences plant production and soil nutrient cycling. However, how it influences sex-specific microbial community composition and rhizosphere nutrient cycling in dioecious plant species is poorly understood. We examined the rhizospheric bacterial and fungal community assemble and their influences on soil nutrient cycling under different N backgrounds in 30-year-old experimental stands and a soil microbial reshaping-controlled experiment. In comparison to male trees, female trees increased fungal community diversity, and the relative abundance of taxa related to nutrient availability; elevated phosphorus (P) mobilization by increasing acidic phosphatase activity and carboxylic acid release; and decreased the counts of denitrification nirS, nirK, and nosZ genes at high N supply. Males increased the nifH gene counts related to microbial N fixation at high N supply. Low N supply increased N fixation nifH gene counts in the rhizosphere of females. Males decreased bacterial and fungal diversity, increased enzymatic activities related to organic N and P mineralization, and elevated soil nitrate-nitrogen levels at low N supply. Our results indicate that sex-specific responses to N availability are associated with rhizospheric bacterial and fungal community composition and diversity and their effects on rhizospheric nutrient cycling, which may explain sex-specific resource utilization and niche differentiation.

Effects of combined applications of S-nZVI and organic amendments on cadmium and arsenic accumulation in rice: Possible mechanisms and potential impacts on soil health

In situ remediation of cadmium (Cd) and arsenic (As) (Cd&As) contaminated soil using iron-based materials has been extensively investigated. Simultaneous immobilizing Cd&As with iron-based materials while maintaining soil health poses a significant challenge. This study examined the effects of sepiolite-supported nanoscale zero-valent iron (S-nZVI) combined with organic amendments (RS: Rice straw; PM: Pig manure) on Cd&As uptake by rice and soil quality. Grain Cd (0.134mgkg-1) and inorganic As (iAs) (0.099mgkg-1) levels in S-nZVI+PM treatment were reduced by 78.95% and 68.69% compared to CK (P<0.05), and decreased by 52.62% and 17.50% compared to S-nZVI treatment (P<0.05), significantly lower than the Chinese Food Safety Standard (<0.20mgkg-1). The elevated soil pH, increased amorphous iron (Feox), and PM complexation co-contributed to Cd immobilization in S-nZVI+PM treatment; concurrently, the higher Feox maintained lower available As levels in paddy soil. In addition, S-nZVI+PM improved soil fertility, functional enzyme activity, soil bacterial community diversity, and increased brown rice yield. However, S-nZVI+RS facilitated the reductive dissolution of Fe(oxy)(hydro) oxides and As methylation in paddy soil, significantly increasing the total As and organic As content in grains by 113.13% and 236.79%, respectively, compared to S-nZVI treatment. Caution should be exercised in the application of S-nZVI+RS in As-contaminated paddy soil. S-nZVI+PM proved more effective in immobilizing Cd&As and provided greater benefits to soil quality compared to S-nZVI+RS. Overall, S-nZVI+PM represents an eco-friendly approach for alleviating Cd&As accumulation in rice grains while concurrently improving soil health.

Algal organic matter triggers re-assembly of bacterial community in plumbing system

Algal bloom outbreaks in upstream drinking water reservoirs inevitably lead to algal organic matter (AOM) pollution in downstream drinking water plants and distribution systems. However, the responses of indoor piped drinking water quality and microbial community to AOM remain to be well studied. In this study, we investigated the effects of low and high concentrations of Chlorella organic matters on pipe-based drinking water. We found that AOM introduced nitrogen and phosphorus contamination into drinking water and promoted massive regeneration of bacteria during stagnation, along with increased bacterial metabolic activity. Compared to the Control group, the utilization capacity of alcohols, acids, esters, and amino acids increased under the influence of AOM. In addition, AOM intrusion reduced the bacterial community diversity in drinking water. The bacterial communities became more saturated, interspecific relationships became more complex, and interspecific competition increased. Bacteria with the ability to denitrification, such as Pseudomonas putida, Sphingobium amiense, Delftia tsuruhatensis, and Acidovorax temperans, were the most abundant. Residual chlorine, ammonium, nitrite, and iron had notable effects on the bacterial community under the influence of AOM. The results help elucidate the response mechanism of microbial community to AOM contamination in indoor drinking water pipes and provide a scientific basis for drinking water safety risk management.

Inoculum selection and hydraulic retention time impacts in a microbial fuel cell treating saline wastewater

Microbial fuel cell (MFC) technology has received increased interest as a suitable approach for treating wastewater while producing electricity. However, there remains a lack of studies investigating the impact of inoculum type and hydraulic retention time (HRT) on the efficiency of MFCs in treating industrial saline wastewater. The effect of three different inocula (activated sludge from a fish-canning industry and two domestic wastewater treatment plants, WWTPs) on electrochemical and physicochemical parameters and the anodic microbiome of a two-chambered continuous-flow MFC was studied. For each inoculum, three different HRTs were tested (1 day, 3 days, and 6 days). The inoculum from the fish canning industry significantly increased voltage production (with a maximum value of 802 mV), power density (with a maximum value of 78 mW m−2), coulombic efficiency (with a maximum value of 19.3%), and organic removal rate (ORR) compared to the inocula from domestic WWTPs. This effect was linked to greater absolute and relative abundances of electroactive microorganisms (e.g., Geobacter, Desulfovibrio, and Rhodobacter) and predicted electron transfer genes in the anode microbiome likely due to better adaption to salinity conditions. The ORR and current production were also enhanced at shorter HRTs (1 day vs. 3 and 6 days) across all inocula. This effect was related to a greater abundance and diversity of bacterial communities at HRT of 1 day compared to longer HRTs. Our findings have important bioengineering implications and can help improve the performance of MFCs treating saline effluents such as those from the seafood industry.Key points• Inoculum type and HRT impact organic matter removal and current production.• Changes in bioenergy generation were linked to the electroactive anodic microbiome.• Shorter HRT favored increases in the performance of the MFC.Graphical

Use of analytical strategies to understand spatial chemical variation in bacterial surface communities.

Not only do surface-growing microbes such as biofilms display specific traits compared to planktonic cells, but also they display many heterogeneous behaviors over many spatial and temporal contexts. While the application of molecular genetics tools to extract or visualize gene expression or regulatory function data is now common in studying surface growth, the use of analytical chemistry tools to visualize the spatiotemporal distribution of chemical products synthesized by these surface microbes is less common. Here, we review chemical imaging tools that have been used to inform our understanding of surface-growing microbes. We highlight the use of confocal Raman Microscopy, surface-enhanced Raman spectroscopy, matrix-assisted laser desorption/ionization, secondary ion mass spectrometry, desorption electrospray ionization, and electrochemical imaging that have been applied to assess two-dimensional chemical profiles of bacteria. We specifically discuss the use of these tools to study rhamnolipids, alkylquinolones, and phenazines of the bacterium Pseudomonas aeruginosa.

Fecal microbiota is more stable during degradation and more diverse for ex situ cheetahs in Namibia compared to the USA

The relationships between gut microbiota and animal health are an important consideration increasingly influential in the management of wild and ex situ endangered species, such as the cheetah (Acinonyx jubatus). To better understand these relationships, fresh fecal samples are currently required as a non-invasive alternative for the gut microbiome. Unfortunately, fresh samples are challenging to collect in the wild. This study had two aims: 1) to determine the optimal collection time point for cheetah feces after deposit in their native environment of Namibia as a guide for wild cheetah fecal microbiome studies; and 2) to compare the fecal microbiota of two ex situ cheetah populations (Front Royal, VA, USA and Otjiwarongo, Namibia), which also consume different diets. We collected eight fresh fecal samples from cheetahs in Namibia and allowed them to decompose for four days, taking subsamples each day. The fresh Namibian samples (n = 8) were also used in objective two for comparison to fresh USA cheetah samples (n = 8). All samples were analyzed for bacterial community diversity and composition using 16S rRNA gene amplicon sequencing. First, over a five-day sampling period in Namibia, subsamples 1-3 days post-fresh showed no changes in bacterial diversity or composition compared to fresh subsamples. Second, fresh ex situ cheetah samples under Namibian conditions had increased bacterial taxa, more phylogenetically diverse bacterial communities, and compositionally distinct microbiomes from cheetahs managed in human care in the USA. However, when bacterial ASVs were weighted by relative abundance, both populations shared 69% of their total bacterial sequences indicating a conserved cheetah microbiota between the two populations. We also found few differences in predictive functions of the fecal microbiota between the populations, where only one disease-related pathway was higher in the USA samples. Overall, our findings suggest that in dry season conditions (no recorded rainfall) in Namibia, fecals may be usable for up to three days after defecation for microbial ecology studies. There are significant differences between ex situ Namibian and USA populations, and we suggest further investigation into the influence of diet, host demographics, and environment on the gut microbiota and health of cheetahs.

Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community-Leishan County, Guizhou Province, Southwest China.

Camellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region's economic sustainability. This study selected tea plantations with different tea planting durations of 3-5 years (Y5), 12-16 years (Y15), 18-22 years (Y20), 40-42 years (Y40), and 48-50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0-20 cm and 20-40 cm soil layers, respectively. Compared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota, Chloroflexi, Proteobacteria, and Actinobacteriota in the tea garden. FAPROTAX analysis highlighted aerobic and anaerobic chemoheterotrophy, cellulolysis, and nitrogen fixation as key bacterial functions. POC and MBC significantly influenced bacterial community structure. In conclusion, tea plantation soil exhibited the highest organic carbon content at 40 years of tea planting, indicating strong carbon accumulation capacity. However, soil acidification in the tea plantation may affect changes in organic carbon and bacterial community. Therefore, in the tea planting process, it is necessary to improve the management system of tea plantations to ensure the maintenance of a good ecological environment in the tea plantation soil, thus achieving sustainable development of the tea industry in the region.

Dynamically induced spatial segregation in multispecies bacterial bioconvection

Active matter, from motile bacteria to animals, can exhibit striking collective and coherent behavior. Despite significant advances in understanding the behavior of homogeneous systems, little is known about the self-organization and dynamics of heterogeneous active matter, such as complex and diverse bacterial communities. Under oxygen gradients, many bacterial species swim towards air-liquid interfaces in auto-organized, directional bioconvective flows, whose spatial scales exceed the cell size by orders of magnitude. Here we show that multispecies bacterial suspensions undergoing oxytactic-driven bioconvection exhibit dynamically driven spatial segregation, despite the enhanced mixing of bioconvective flows, and the fact that these species coexist in their natural habitat. Segregation is observed as patterns of spatially interlocked domains, with local dominance of one of the constituent species in the suspension. Our findings suggest that segregation mechanisms are driven by species-specific motile behaviors under conditions of hydrodynamic flow, rather than biochemical repulsion. Thus, species with different motile characteristics in the same ecological context can enhance their access to limiting resources. This work provides novel insights on the role of heterogeneity in active matter, as well as on the dynamics of complex microbial communities, their spatial organization and their collective behavior.

P1344 Impaired health-related quality of life is associated with alterations in gut microbiota signatures in patients with Inflammatory Bowel Disease: baseline data from the Australian IBD Microbiome study

Abstract Background Inflammatory Bowel Disease (IBD) activity as well as disease monitoring and management have a substantial impact on the health-related quality of life (HRQoL) of affected patients1. This study investigated the association between HRQoL and gut microbial composition in IBD patients using the 32-item Inflammatory Bowel Disease Questionnaire (IBDQ-32). Methods Paired faecal and oral samples alongside participant demographics, disease characteristics and the IBDQ-32 survey were collected at baseline from patients with Crohn’s disease (CD) or ulcerative colitis (UC) enrolled in the Australian IBD Microbiome (AIM) study2 from June 2019 to November 2023. IBDQ-32 scores range from 32 to 224, with a higher score indicating better HRQoL. Patients were divided into two groups: impaired HRQoL (cumulative score &amp;lt;170) and preserved HRQoL (&amp;gt;170). Faecal and oral samples were self-collected in DNA stabilising buffer, aliquoted and stored at -80oC until extraction. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Chao1) between groups were assessed using Mann-Whitney U tests. Linear discriminant analysis was performed between groups to identify significantly enriched bacterial taxa. Beta diversity (weighted UniFrac dissimilarity) in bacterial communities were shown using Principal Coordinate Analysis (PCoA), and significance of variance was tested using ADONIS in R. Results 446 participants (232 CD, 214 UC) returned baseline faecal (n = 403) and/or oral samples (n = 436) and were included in the analysis, with patient and HRQoL characteristics in Table 1. Most CD and UC patients were in clinical remission at baseline (77.4% and 65.2% respectively, Table 1). Despite this, impaired HRQoL was common in both CD (42%) and UC (41%). Patients with impaired HRQoL had lower faecal microbial alpha and beta diversity (Fig 1A,B). There were no differences in alpha or beta diversity in oral samples. Linear discriminant analysis showed 9 and 36 significantly altered genera enrichment in impaired and preserved HRQoL faecal samples respectively (Fig 1C). Conclusion Despite a high proportion of clinical and biochemical remission, impaired HRQoL was common amongst UC and CD patients within the AIM study. Lower faecal but not oral alpha diversity was associated with impaired HRQoL, indicating reduced microbial richness in the gut. A high number of bacterial taxa had differential enrichment according to HRQoL status. Identification of a distinct microbial signature associated with impaired HRQoL may help to identify patients that require both optimisation of disease control and greater psychosocial support.

P1327 Microbial signatures associated with Inflammatory Bowel Disease in Australia: baseline data from the Australian IBD Microbiome study

Abstract Background Microbial dysbiosis is associated with Crohn’s disease (CD) and ulcerative colitis (UC) onset and disease activity, however, large-scale data pertaining to Australian patients are limited1. This study aimed to describe the differences in gut microbiota composition between patients with IBD and healthy controls within the Australian IBD Microbiome (AIM) study2. Methods Paired faecal and oral samples alongside participant demographics and disease characteristics were collected at baseline from all healthy controls (HC) and IBD patients enrolled in the Australian IBD Microbiome (AIM) study from June 2019 to November 2023. Faecal and oral samples were self-collected in DNA stabilising buffer, aliquoted and stored at -80oC until extraction. Samples underwent 16S rRNA sequencing with annotation of DNA sequences to operational taxonomic units at the genus level. Differences in alpha diversity (Chao1) between groups were assessed using Mann-Whitney U tests. Beta diversity (weighted UniFrac dissimilarity) in bacterial communities were shown using Principal Coordinate Analysis (PCoA), and significance of variance was tested using ADONIS in R. Results 751 participants (305 HC, 232 CD, 214 UC) returned baseline faecal (n = 697) and/or oral samples (n = 737) and were included in the analysis, with patient group characteristics presented in Table 1. Most IBD patients were in clinical remission (Table 1). However, CD and UC patients had comparably lower faecal alpha diversity than the HC group (Figure 1A). Faecal beta diversity differed between CD, UC, and HC groups (Figure 1B). Five phyla were significantly different between the three groups in faecal samples (Figure 1C). No significant inter-group differences were seen with oral microbial analysis. Conclusion Compared to healthy adults, patients with IBD in Australia have distinct gut microbial profiles. Faecal rather than oral microbial sampling demonstrated a difference in community structure between IBD and healthy groups. Incorporating longitudinal microbial sampling and increasing sequencing resolution may elucidate a pathogenic relationship between gut microbiota and IBD.

Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce

Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.

Variations of microbiota and metabolites in rhizosphere soil of Carmona microphylla at the co-contaminated site with polycyclic aromatic hydrocarbons and heavy metals.

Co-contamination with organic/inorganic compounds is common in industrial area and poses a great risk to local soil ecological environment. In this study, an operating ink factory site co-contaminated with polycyclic aromatic hydrocarbons (PAHs, mild to moderate pollution level) and heavy metals (HMs, heavy pollution level) was selected and screened for native vegetation, Carmona microphylla. High-throughput sequencing and metabolomics were mainly used to investigate the responses of soil bacteria and metabolites to the composite pollution and rhizosphere effect. As the results showed, among three pollution levels, a medium level of pollution was favorable to increase the richness and diversity of soil bacterial community, while high level of pollution greatly decreased special OTUs number. In addition, HMs were the most significant factors driving bacterial community structure, especially for Cd. The influence of medium molecular weight PAHs with 4 rings (MMW-PAHs) on dominant bacteria was greater than low molecular weight PAHs with 2-3 rings (LMW-PAHs) and high molecular weight PAHs with 5-6 rings (HMW-PAHs). Soil bacterial function was affected mainly by pollution level, but not rhizosphere effect, in which high pollution level changed α diversity and structure and composition of C- and N-cycling bacteria. Rhizosphere promoted network complexity by increasing the connection densities among bacterial communities, metabolites, soil properties and the involved number of metabolites. Compared to HMs, PAHs played a more important role in shaping bacterial community through affecting metabolites in non-rhizosphere soil, which was different from rhizosphere soil with a more significant effect of HMs than PAHs. Some key bacterial taxa have established resistance to HMs in rhizosphere soils, whereas they were sensitive to compound contamination in non-rhizosphere soils. Some key bacterial taxa are resistant to HMs in rhizosphere soils, whereas they are susceptible to complex contamination in non-rhizosphere soils, which could be a consequence of the rhizosphere by regulating soil metabolism. It also provides a valuable reference for how co-contaminants and rhizosphere effect shape together soil bacterial community through the changes of soil metabolites.

Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities.

Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on bacterial metabolism and the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active and inactive bacteriophages (phages) to soil DOM with original bacterial communities and incubated them at 18 or 23 °C for 35 days. Phages initially (1-4 days) reduced CO2 efflux rate by 13-21% at 18 °C and 3-30% at 23 °C but significantly (p < 0.05) increased by 4-29% at 18 °C and 9-41% at 23 °C after 6 days, raising cumulative CO2 emissions by 14% at 18 °C and 21% at 23 °C. Phages decreased dominant bacterial taxa and increased bacterial community diversity (consistent with a "cull-the-winner" dynamic), thus altering the predicted microbiome functions. Specifically, phages enriched some taxa (such as Pseudomonas, Anaerocolumna, and Caulobacter) involved in degrading complex compounds and consequently promoted functions related to C cycling. Higher temperature facilitated phage-bacteria interactions, increased bacterial diversity, and enzyme activities, boosting DOM mineralization by 16%. Collectively, phages impact soil DOM mineralization by shifting microbial communities and functions, with moderate temperature changes modulating the magnitude of these processes but not qualitatively altering their behavior.

From Young to Over-Mature: Long-Term Cultivation Effects on the Soil Nutrient Cycling Dynamics and Microbial Community Characteristics Across Age Chronosequence of Schima superba Plantations

Optimizing forest management requires a comprehensive understanding of how soil properties and microbial communities evolve across different plantation ages. This study examines variations in soil nutrient dynamics, enzyme activities, and bacterial communities in Schima superba Gardn. &amp; Champ plantations of 10, 15, 27, 55, and 64 years. By analyzing soil from depths of 0–20 cm, 20–40 cm, and 40–60 cm, we identified significant age-related trends in soil characteristics. Notably, nutrient contents, including total organic carbon (TOC), total phosphorus (TP), total carbon (TC), total nitrogen (TN), and nitrate nitrogen (NO3−-N), as well as soil water content (SWC), peaked in 55-year-old mature plantations and decreased in 64-year-old over-mature plantations. Enzyme activities, such as urease, sucrase, and acid phosphatase, decreased with soil depth and exhibited notable differences across stand ages. Microbial community analysis indicated the predominance of Acidobacteria, Chloroflexi, Proteobacteria, Actinobacteria, and Verrucomicrobiota in nutrient cycling, with their relative abundances varying significantly with age and depth. Mature and over-mature plantations exhibited higher absolute abundances of functional genes related to methane metabolism, nitrogen, phosphorus, and sulfur cycling. Reduced calcium ion levels were also linked to lower gene abundance in carbon degradation, carbon fixation, nitrogen, and phosphorus cycling, while increased TOC, NH4+-N, NO3−-N, and AP correlated with higher gene abundance in methane metabolism and phosphorus cycling. Our findings suggest that long-term cultivation of Schima superba enhances soil nutrient cycling. Calcium ion was identified as a significant factor in assessing soil properties and microbial dynamics across different stand ages, suggesting that extended plantation rotations can improve soil health and nutrient cycling.

Influences of plant maternal effects, chemotype, and environment on the leaf bacterial community.

Plant individuals within a species can differ markedly in their leaf chemical composition, forming so-called chemotypes. Little is known about whether such differences impact the microbial communities associated with leaves and how different environmental conditions may shape these relationships. We used Tanacetum vulgare as a model plant to study the impacts of maternal effects, leaf terpenoid chemotype, and the environment on the leaf bacterial community by growing plant clones in the field and a greenhouse. We hypothesized that all three factors affect the bacterial community of the leaves and that terpenoid and bacterial profiles as well as chemodiversity and microbial diversity are correlated. The results revealed that the leaf microbial community was significantly influenced by plant maternal effects and environmental conditions (field vs. greenhouse), but not by the leaf terpenoid profile. There was also no evidence for a correlation between terpenoid profiles and bacterial community composition and diversity. Overall, a higher number of unique amplicon sequence variants were found in the leaves of clones grown under field conditions than in those grown in the greenhouse. We also identified interactions between individual terpenoids and specific members of the leaf bacterial community. Our study suggests that terpenoid chemodiversity has, overall, little effect on the leaf bacterial community, but some terpenoids might affect specific beneficial species. While more studies are needed to investigate the relationship between plant chemodiversity and plant microbiomes, our results highlight the importance of integrating plant maternal effects, chemodiversity, and environment in understanding plant-microbiome interactions.

Diversity of lake bacteria promotes human echovirus inactivation.

Human enteric viruses can remain infective in surface waters for extended periods of time, posing a public health risk. Microbial activity contributes to the inactivation of waterborne enteric viruses, but while individual bacteria-virus interactions have been characterized, the importance of microbial diversity remains unknown. Here, we experimentally manipulated the diversity of bacterial communities from Lake Geneva across three seasons using a dilution-to-extinction approach and monitored the inactivation and genome decay of echovirus 11, a member of the Enterovirus genus. Long-read sequencing of the 16S rRNA gene revealed diversity gradients ranging between 373 and 2,722 bacterial species. Compared to sterile controls, echovirus 11 inactivation was enhanced by the presence of active bacteria and depended both on season and sample dilution. Throughout all seasons, the highest inactivation (between 3.0 and 7.9 log10 fold reduction in infectivity over 96 h) was observed in the least diluted incubations (i.e., the highest bacterial richness). Genome decay exhibited a 24-h lag and was less pronounced than the corresponding infectivity loss (ranging between 2.3 and 3.8 log10 fold over 96 h), indicating that microbial inactivation primarily targets the echovirus 11 capsid. We found a positive-saturating relationship between bacterial species richness and viral inactivation, suggesting functional redundancy and pointing toward the importance of rare species for viral inactivation. Biomarker analysis revealed several clades of bacteria, particularly members of Chitinophagaceae, to be significantly associated with echovirus 11 inactivation. Overall, these findings suggest that high microbial diversity enhances the capacity of surface waters to rid themselves of contamination by enteric viruses and hence protects public health.IMPORTANCEHuman enteric viruses in natural waterbodies pose a public health risk. Microorganisms, particularly bacteria, contribute to the inactivation of enteroviruses, thereby mitigating this risk. We use experimental manipulations of lake water bacterial diversity to unravel the importance of diversity for the inactivation of echovirus 11, a model human pathogen. Our findings suggest that bacterial diversity is important for echovirus 11 inactivation and that specific, but numerically rare, bacteria present in the surface water of Lake Geneva across different seasons contribute to viral inactivation. These findings contribute to our understanding of the inactivation of human enteric viruses in natural waterbodies-a hitherto understudied ecosystem service.