Microbial Community Properties Research Articles

Antibiotic resistance of microorganisms isolated from the urine of patients before surgical treatment for benign prostatic hyperplasia: results from a 7-year single-center study

Introduction. The tendency of microorganisms to develop resistance mechanisms is a widely discussed and significant problem worldwide. Studying regional differences in the qualitative characteristics of microorganisms provides valuable information for empirically preventing and treating infectious complications, as well as providing an enhanced understanding of the variability in microbial community properties within the clinical context of diseases and patients' comorbidity status.Objective. To assess the antibiotic resistance of microorganisms isolated in high titers from the urine samples of patients with benign prostate hyperplasia (BPH) prior to surgery.Materials & Methods. This single-center, retrospective study conducted from March 2016 to February 2023 included 59 suprapubic-draining BPH-patients (Group I), 46 drainage-free BPH-patients with leukocyturia (Group II), and 44 drainage-free BPH-patients and no leukocyturia (Group III). Inclusion criteria: indications for BPH surgery, no history of sexually transmitted diseases, no symptoms of urinary tract infection, and no prostate cancer. The patient's voluntary informed consents to participate were also obtained.Results. The rates of resistance to ciprofloxacin in patients of Group I were statistically significantly higher compared to Group II (85.7% vs 55.6%, p = 0.002). Resistance of gram-negative microorganisms to meropenem and imipenem was higher in Group III compared to Group I (31.1% vs 13.7%, p = 0.006 for meropenem and 44.5% vs 9.8%, p = 0.001 for imipenem, respectively). Resistance of Gram-positive microorganisms to ampicillin in Groups I to III was 13.6%,6.3% and 20.0%, respectively with no significant difference between groups (p > 0.05). However, there was extremely high resistance among verified Gram-positive organisms to all the drugs in the fluoroquinolone class (ciprofloxacin, norfloxacin, levofloxacin) ranged from 63.6% to 80.0%.Conclusion. The present study demonstrates that the isolation frequency of antibiotic-resistant microorganisms from the urine sample of drainage-free BPH-patients or no clinical and laboratory signs of inflammation in the urinary tract is high. The presence of antibiotic resistance provides risks for developing difficult-to-control infectious complications. Currently, assessment of urine-derived microbial antibiotic resistance should be considered in every BPH-patient with indications for surgical management of bladder outlet obstruction, regardless of the presence of risk factors.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis.

As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.

Effects of Conventional Non-Biodegradable Film-Derived Microplastics and New Biodegradable Film-Derived Microplastics on Soil Properties and Microorganisms after Entering Sub-Surface Soil

Plastic film mulching, widely used in agriculture, leads to microplastic (MP) pollution in soils. While biodegradable polybutylene adipate terephthalate (PBAT) films may offer a solution, their impacts on subsurface soils and microorganisms remain unclear. To investigate the effects of conventional non-biodegradable polyethylene (PE) and biodegradable PBAT MPs on the properties of sub-surface soils and microbial communities, MPs were added at varying doses in a field experiment and incubated for 160 days. Physicochemical characteristics, nutrient dynamics, and microbial composition, diversity, and networks of soils were analyzed using standard techniques and 16S rRNA/ITS gene sequencing. Correlations between soil properties and microbes were assessed. Both MP types significantly altered soil characteristics, with PBAT-MP elevating pH and the levels of available phosphorus and potassium more than PE-MP. Microbial composition shifts occurred, with low-addition PBAT-MP promoting plastic-degrading genera. The assessment of α/β-diversity indicated that PBAT-MP predominantly influenced fungi while PE-MP impacted bacteria. An examination of microbial co-occurrence networks highlighted that PE-MP primarily disrupted fungal interactions, whereas PBAT-MP streamlined network complexity. Correlation analyses revealed that PBAT-MP promoted fungal diversity/network resilience correlating to nutrients. PE-MP and PBAT-MP significantly altered native soil/microbe relationships. PBAT-MP may exert greater, yet unknown, impacts over time through its biodegradation into newer and smaller fragments. Future research needs to integrate multi-omics and stable isotope science to elucidate the deep mechanistic impacts of degraded film-derived MPs on microbial ecological functions and biogeochemical cycles. Attention should also be paid to the long-term accumulation/transport of MPs in agricultural soils. Overall, this work deepens the impact and understanding of MPs from plastic film on sub-surface soil ecology. Furthermore, it provides a theoretical foundation for managing ‘white pollution’ in the film-covered farmlands of arid and semi-arid regions in China.

Delving into the Impacts of Different Easily Degradable Carbon Sources on the Degradation Characteristics of 2,4,6-Trichlorophenol and Microbial Community Properties

In chlorophenol wastewater treatment, adding easily degradable carbon sources, such as methanol, ethanol, sodium acetate, and sodium propionate, significantly improves the chlorophenol removal efficiency. This study systematically compares these conventional carbon sources in different sequencing batch reactors to understand their specific effects on both 2,4,6-trichlorophenol (2,4,6-TCP) degradation efficiency and microbial abundance. In a 35-day experiment, as a carbon source, ethanol exhibited a lower 2,4,6-TCP degradation concentration (77.56 mg/L) than those of methanol, sodium acetate, and sodium propionate, which achieved higher degradation concentrations: 123.89 mg/L, 170.96 mg/L, and 151.79 mg/L, respectively. As a carbon source, sodium acetate enhanced extracellular polymeric substance production (200.80 mg/g·VSS) by microorganisms, providing protection against the toxicity of chlorophenol and resulting in a higher 2,4,6-TCP removal concentration. Metagenomics identified crucial metabolic genes, including PcpA, chqB, Mal-r, pcaI, pcaF, and fadA. The abundance of genera containing the chqB gene correlated positively with the metabolic capacity for 2,4,6-TCP. Moreover, small molecular carbon sources such as methanol, sodium acetate, and sodium propionate promoted the enrichment of genera with functional genes.

Changes in temperature sensitivity of forest litter during decomposition along an altitudinal gradient in temperate mountains – A reciprocal litter transplantation study

The aim of this study was to assess the effects of the factors controlling the temperature sensitivity of litter decomposition, which is essential for predicting the rate of soil carbon loss in in the context of global climate changes. It based on the translocation of forest litter in a field experiment conducted in the Western Carpathians. Litterbags were used to expose litter originating from different altitudes (i.e., 600, 900, and 1200 m a.s.l.) at the altitude where it was collected and at two other altitudes on five different mountains. Litterbags were collected after 6, 10, and 24 months of exposure. The respiration rate of litter was measured in the laboratory, and Q10 coefficients were evaluated for two temperature ranges: lower (Q10L; 5 °C–15 °C) and higher (Q10H; 15 °C–25 °C). We tested whether litter Q10 values correlated with experimental factors, as well as soil and microbial community properties. After 24 months of exposure, the litter mass decreased to half of its initial mass. The general linear model (GLM) constructed for Q10 (R2adj = 77.3 %; p < 0.0001) indicated, that Q10L values were higher than Q10H values (2.19 ± 0.58 and 1.52 ± 0.31, respectively) and increased strongly with time (1.56 ± 0.36, 1.73 ± 0.45, and 2.36 ± 0.60, consecutively). There was a significant interaction between the temperature range and time, indicating that Q10L increased more over time than Q10H. Other interaction between temperature range and litter origin indicated that Q10L increased with the altitude of the litter origin, whereas Q10H did not change. The proportion of fungi in the microbial biomass correlated positively with Q10. Our results were consistent with the kinetic theory of higher temperature sensitivity for more decomposed organic matter. The conclusion that litter Q10L is more responsive to environmental conditions than Q10H has important implications for estimating soil carbon emissions.

Unravelling the correlations among the microbial community, physicochemical properties, and volatile compounds of traditional mung bean sour liquid

Sour liquid noodles are a characteristic traditional food in Luoyang, China. Mung bean sour liquid (MBSL) is fermented from mung beans and used to cook noodles (instead of using water). However, the microbial community, volatile compounds, and physicochemical properties of MBSL are still unclear. Here, a comprehensive study was conducted using a combination of Illumina HiSeq sequencing, gas chromatography‒mass spectrometry detection, and physicochemical analysis methods. Eight phyla and 59 genera of bacteria were identified in MBSL, of which 4 genera were dominant, namely, Lactobacillus, Lactococcus, Leuconostoc, and Lelliottia. Six phyla and 123 genera of fungi were detected, with 11 genera being dominant. The protein content, total acid content, and pH mainly influenced the microbial community. Myroides, Aeromonas, Flavobacterium, and Lactobacillus, etc. May play important roles in balancing MBSL ecosystems. There were 40 volatile compounds in MBSL, with 1-hexanol, eugenol, acetic acid, and hexanoic acid being considered key volatile compounds. Lactobacillus, Algoriella, Lelliottia, and Leuconostoc were significantly correlated with the volatile compounds found in MBSL. The complex correlation between microbial communities, volatile compounds, and physicochemical properties may be elucidated through these findings. Controlling environmental factors and increasing the number of selected microbial cultures may improve the quality of MBSL.

Biotic and abiotic factors interplay in structuring the dynamics of microbial co-occurrence patterns in tropical mountainsides

Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO43--P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient.

Chemical structure of hydrocarbons significantly affects removal performance and microbial responses in gas biotrickling filters

The control of emissions of short-chain hydrocarbons with different structures is critical for the petrochemical industry. Herein, three two-carbon-containing (C2) hydrocarbons, ethane, ethylene, and acetylene, were chosen as pollutants to study the effects of chemical structure of hydrocarbons on removal performance and microbial responses in biotrickling filters. Results showed that the removal efficiency (RE) of C2 hydrocarbons followed the sequence of acetylene > ethane > ethylene. When the inlet loading rate was 30 g/(m3·h) and the empty bed residence time was 60 s, the RE of ethane, ethylene, and acetylene was 57 ± 4.0 %, 49 ± 1.0 %, and 84 ± 2.7 %, respectively. The high water solubility resulted in the high removal of C2 hydrocarbons, while a low surface tension enhanced the removal of C2 hydrocarbons. Additionally, the microbial community, enzyme activity, and extracellular properties of microorganisms also contributed to the difference in C2 hydrocarbon removal. These results could be referred for the effective control of light hydrocarbon emissions.

Response of microbial communities to the changes in grazing intensity and season in a typical steppe

Livestock grazing is an influencing factor playing a key role in shaping the plant community, microbial community, and soil properties in grassland ecosystems. Northern China's Loess Plateau has been used for livestock grazing for centuries and is a vulnerable ecosystem. In this study, the fates of bacterial and fungal communities of the typical steppe of the Loess Plateau were investigated under increasing grazing intensities practiced in summer and winter seasons. The results revealed changes in soil physiochemical properties, plant community properties, and microbial diversity in response to alterations in the grazing intensity. The alpha diversity of microbial communities (including bacteria and fungi) exhibited an uneven trend during summer grazing due to an increase in grazing intensity, but it decreased during winter grazing; however, the observed changes were not significant. The beta diversity of the bacterial community was highly influenced by grazing intensity, the summer community clustered near nongrazing, and the winter community presented significantly different results. The beta diversity of the fungal community was not influenced by grazing intensity or season. Grazing induced the growth of fast-growing bacteria (such as Actinobacteria and Firmicutes) and saprophytic fungi and a reduction in overall pathogenic traits. Co-occurrence network analysis and a structural equation model revealed changes in soil and plant properties (such as soil nitrogen level, soil organic carbon level, aboveground biomass, and litter biomass), with an increase in grazing intensity contributing to alterations in bacterial and fungal diversities. This finding demonstrates that grazing intensity can directly affect soil microbes and play an indirect role by modifying soil nutrients and reducing plant biomass, which eventually contributes to changes in microbial communities. Overall, implementing low grazing intensity is suggested for maintaining the microbial community structure the same as that of the native microbiome (ungrazed) in the steppe ecosystems.

Soil multifunctionality predicted by bacterial network complexity explains differences in wheat productivity induced by fertilization management

Fertilization will cause changes in crop growth, soil microbial community and multiple ecosystem functions, but it is unclear whether and how the optimal productivity obtained by manure application and optimizing nitrogen is driven by microbial community and ecosystem multifunctionality. We explore this mechanism based on a field fertilization experiment using a split-plot design that began in 2014 with five N rates (N0, N75, N150, N225, N300) as main plots and two manure rates (M0, NPK group; M1, MNPK group) as subplots, respectively. In general, (1) grain yield was parabolically related to the N application rate. The N rates that obtained the highest yield were 150 kg ha−1 and 225 kg ha−1 for the MNPK and NPK groups, respectively. The average yield of the MNPK group was 10.5% higher than that of the NPK group. (2) Long-term fertilization management resulted in regular changes in soil multifunctionality (SMF) and the properties of various microbial communities. The richness, network complexity and soil multifunctionality of bacterial and fungal communities also increased initially and then decreased as the N rate. On average, the response ratio of soil multifunctionality to N75, N150, N225, N300 (control is N0) and M1 (control is M0) were 0.11, 0.41, 0.53, 0.44 and 1.19, respectively. The soil multifunctionality of MNPK was 260%, 722% and 101% higher than that of NPK at the tillering, jointing and harvest stages, respectively. (3) Soil multifunctionality not only always had a significant positive effect on aboveground biomass at all growth stages, but also had significant positive correlations with bacterial richness and network complexity. Based on the existing framework, we further demonstrated that high microbial richness supports multifunctionality by ensuring strong associative complexity among microorganisms. However, only bacterial network complexity always positively drove soil multifunctionality and indirectly influenced wheat growth at all growth stages in SEMs where multiple drivers were considered simultaneously (i.e., pH, SOC and biological factors). Random forest regression analysis showed that rare bacterial taxa had stronger predictive effects on soil multifunctionality than abundant taxa. Our results validate that M1N150 can ensure high yield in the study area while maintaining a high level of ecosystem function in the soil, which also contributes to the reduction of adverse environmental risks caused by fertilizer application. Importantly, the potential of microbial network complexity, especially bacterial network complexity, to influence crop growth by driving farmland ecosystem functions deserves to be explored under different crop types, cropping systems, and irrigation conditions, compared to previous microbial richness that has been simply quantified.

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions.

While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under high-pressure conditions, we established methanogenic and sulfate-reducing enrichment cultures under high-pressure conditions using production water from the Jilin Oilfield in China. We utilized a metagenomics approach to analyze the microbial community after a 90-day incubation period. Under methanogenic conditions, Firmicutes, Deferribacteres, Ignavibacteriae, Thermotogae, and Nitrospirae, in association with the hydrogenotrophic methanogen Archaeoglobaceae and acetoclastic Methanosaeta, were highly represented. Genomes for Ca. Odinarchaeota and the hydrogen-dependent methylotrophic Ca. Methanosuratus were also recovered from the methanogenic culture. The sulfate-reducing community was dominated by Firmicutes, Thermotogae, Nitrospirae, Archaeoglobus, and several candidate taxa including Ca. Bipolaricaulota, Ca. Aminicenantes, and Candidate division WOR-3. These candidate taxa were key pantothenate producers for other community members. The study expands present knowledge of the metabolic roles of petroleum-degrading microbial communities under high-pressure conditions. Our results also indicate that microbial community interactions were shaped by syntrophic metabolism and the exchange of amino acids and cofactors among members. Furthermore, incubation under in situ pressure conditions has the potential to reveal the roles of microbial dark matter.

Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.

In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.

Seasonal purification efficiency, greenhouse gas emissions and microbial community characteristics of a field-scale surface-flow constructed wetland treating agricultural runoff

Controlling nonpoint source pollution (NPSP) is very important for protecting the water environment, and surface-flow constructed wetlands (SFCWs) have been widely established to mitigate NPSP loads. In this study, the pollutant removal efficiencies, greenhouse gas (GHG) emissions, and chemical and microbial community properties of the sediment in a large-scale SFCW established beside a plateau lake (Qilu Lake) in southwestern China to treat agricultural runoff were evaluated over a year. The SFCW performed best in terms of nitrogen removal in autumn (average efficiency of 63.5% at influent concentrations of 9.3–35.4 mg L−1) and demonstrated comparable efficiency in other seasons (23.7–40.0%). The removal rates of total phosphorus (TP) and chemical oxygen demand (COD) were limited (18.6% and 12.4% at influent concentrations of 1.1 and 45.5 mg L−1 on average, respectively). The SFCW was a hotspot of CH4 emissions, with an average flux of 31.6 mg m−2·h−1; moreover, CH4 emissions contributed the most to the global warming potential (GWP) of the SFCW. Higher CH4 and N2O fluxes were detected in winter and in the front-end section of the SFCW with high pollutant concentrations, and plant presence increased CH4 emissions. Significant positive relationships between nutrient and heavy metal contents in the SFCW sediment were detected. The microbial community compositions were similar in autumn and winter, with Thiobacillus, Lysobacter, Acinetobacter and Pseudomonas dominating, and this distribution pattern was clearly distinct from those in spring and summer, with high proportions of Spirochaeta_2 and Denitratisoma. The microbial co-occurrence network in spring was more complex with stronger positive correlations than those in winter and autumn, while it was more stable in autumn with more keystone taxa. Optimization of the construction, operation and management of SFCWs treating NPSP in lake watersheds is necessary to promote their environmental benefits.

Integrating microbial community properties, biomass and necromass to predict cropland soil organic carbon

Manipulating microorganisms to increase soil organic carbon (SOC) in croplands remains a challenge. Soil microbes are important drivers of SOC sequestration, especially via their necromass accumulation. However, microbial parameters are rarely used to predict cropland SOC stocks, possibly due to uncertainties regarding the relationships between microbial carbon pools, community properties and SOC. Herein we evaluated the microbial community properties (diversity and network complexity), microbial carbon pools (biomass and necromass carbon) and SOC in 468 cropland soils across northeast China. We found that not only microbial necromass carbon but also microbial community properties (diversity and network complexity) and biomass carbon were correlated with SOC. Microbial biomass carbon and diversity played more important role in predicting SOC for maize, while microbial network complexity was more important for rice. Models to predict SOC performed better when the microbial community and microbial carbon pools were included simultaneously. Taken together our results suggest that microbial carbon pools and community properties influence SOC accumulation in croplands, and management practices that improve these microbial parameters may increase cropland SOC levels.

Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth

Droplet evaporation is a general process in unsaturated environments that results in micro-scale hydrodynamic flows which in turn determine the spatial distributions of microbial cells across surfaces. These spatial distributions can have significant effects on the development and functioning of surface-associated microbial communities, with consequences for important processes such as the spread of plasmids. Here, we experimentally quantified how evaporation-induced hydrodynamic processes modulate the initial deposition patterns of microbial cells (via the coffee ring effect and Marangoni convection) and how these patterns control the spread of an antibiotic resistance-encoding plasmid during surface-associated growth. We found that plasmid spread is a function of the initial density of cells deposited along the droplet periphery, which is a manifestation of the coffee ring effect. Using an individual-based model, we systematically linked how the different initial cell deposition patterns caused by the relative strengths of the coffee ring effect and Marangoni convection determine the extent of plasmid transfer during surface-associated growth. Our study demonstrates that evaporation-induced hydrodynamic processes that are common in nature can alter crucial ecological properties of surface-associated microbial communities and control the proliferation of plasmids, with consequences on the spread of antibiotic resistance and other plasmid-encoded traits.

Mosses stimulate soil carbon and nitrogen accumulation during vegetation restoration in a humid subtropical area

Mosses form a ground layer with a thickness of nearly 1 cm during the first decade of vegetation restoration, but their effects on the belowground microbial community and soil properties and the associated soil carbon (C) and nitrogen (N) accumulation in subtropical areas are unclear. Here, we measured soil C and N variables (soil organic C [SOC], total N [TN], dissolved organic C, ammonium [NH4+-N] and nitrate [NO3−-N]), soil microbial community and soil properties (soil water content [SWC] and pH) under four treatments (bare soil [BS], bare soil with transplanted moss, moss-covered soil [MS] and moss-covered soil with moss removed) in three vegetation types (forest plantations, forage grasslands and mixed plantations and forage grasslands) in a subtropical climate. We analyzed the effects of native mosses, moss transplantation and removal using BS and MS as references. One year post-treatment, moss transplantation increased NO3−-N and NH4+-N in the 0–5 cm and 2–5 cm soil layers, respectively. Conversely, moss removal decreased SOC and TN in the 0–2 cm soil layer and SWC in the 0–5 cm soil layer. Compared to BS and MS, native moss presence, moss transplantation and removal decreased the total microbial, bacterial and fungal biomass and altered the soil microbial community composition (ratios of fungi and bacteria and Gram-positive bacteria to Gram-negative bacteria) to varying degrees. Moss properties (biomass, C and N concentrations, C:N ratio and saturated water absorption content), as well as SWC, soil microbial biomass and community composition regulated by mosses affected soil C and N. These findings underscore the crucial role of mosses in facilitating soil C and N accumulation during vegetation restoration.

Heterogeneity of microbiome and flavor profiles of industrial-scale Laotan Suancai: Fermentation craft plays important roles

Laotan Suancai is a well-known Chinese traditional fermented vegetable with a unique flavor. However, there are significant differences in the quality of Laotan Suancai pickled by jars (LTSC-J) and pools (LTSC-P) on an industrial scale. To reveal the effect of fermentation craft on Laotan Suancai quality, the microbial community, flavor metabolites, and physicochemical properties of the two types of Laotan Suancai, as well as their interrelationship were investigated. LTSC-P had higher salinity, glucose content, and histidine content, while LTSC-J had higher TA, lactic acid content, and isobutyric acid content. Nine differential aroma-active compounds were found between the two types of Laotan Suancai: anethole, eucalyptol, diallyl sulfide, estragole, diallyl disulfide, eugenol, linalool, nonanal, and ethyl butyrate. LTSC-P showed a higher relative abundance of Weissella, Acinetobacter, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Inhella, and Leuconostoc compared to LTSC-J. Co-occurrence analysis indicated the distinct differences in the co-occurrence patterns of the microbial network across the two types of Laotan Suancai. RDA analysis indicated that glucose, salinity, TA, maltose, and nitrite were the main drivers for the differences in bacterial communities between the two types of Laotan Suancai. Spearman correlation analysis revealed strong correlations between 18 bacteria and 61 flavor compounds. Finally, bacterial metabolic function prediction indicated that sulfide and aromatic ester may be biosynthesized by sulfur metabolism, cysteine and methionine metabolism, pyruvate metabolism, and butanoate metabolism. Overall, these findings provide important guidance for improving the manufacturing and quality of Laotan Suancai.

How binomial (traditional rainfed olive grove-Crocus sativus) crops impact the soil bacterial community and enhance microbial capacities

Intercropping can favour the yield of the main crop. However, because of the potential competition among woody crops, this system is rarely used by farmers. To increase knowledge about the intercropping system, we have explored three different combinations of alley cropping in rainfed olive groves compared to conventional management (CP): (i) Crocus sativus (D-S); (ii) Vicia sativa/Avena sativa in annual rotation (D-O); and (iii) Lavandula x intermedia (D-L). Different soil chemical properties were analyzed to evaluate the effects of alley cropping, while 16S rRNA amplification and enzymatic activities were determined to study the changes that occurred in soil microbial communities and activity. In addition, the influence of intercropping on the potential functionality of the soil microbial community was measured.Data revealed that the intercropping systems highly affected the microbial community and soil properties. The D-S cropping system increased soil total organic carbon and total nitrogen that were correlated with the bacterial community, indicating that both parameters were the main drivers shaping the structure of the bacterial community. The D-S soil cropping system had significantly higher relative abundances of the phyla Bacteroidetes, Proteobacteria, and Patescibacteria compared to the other systems and the genera Adhaeribacter, Arthrobacter, Rubellimicrobium, and Ramlibacter, related to C and N functions. D-S soil was also related to the highest relative abundances of Pseudoarthrobacter and Haliangium, associated with the plant growth–promoting effect, antifungal activity, and a potential P solubilizer. A potentially increase of C fixation and N fixation in soils was also observed in the D-S cropping system. These positive changes were related to the cessation of tillage and the development of a spontaneous cover crop, which increased soil protection. Thus, management practices that contribute to increasing soil cover should be encouraged to improve soil functionality.

The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties.

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.