Bacterial Co-occurrence Patterns Research Articles

The bacterial patterns suggesting the dynamic features of tick-associated microorganisms in hard ticks

BackgroundTicks are blood-feeding significant arthropods that can harbour various microorganisms, including pathogens that pose health risks to humans and animals. Tick-symbiont microorganisms are believed to influence tick development, but the intricate interactions between these microbes and the relationships between different tick-borne microorganisms remain largely unexplored.ResultsBased on 111 tick pool samples presenting questing and engorged statuses including 752 questing tick and 1083 engorged tick from cattle and goats, which were collected in two types of geographic landscape (semi-desert and alpine meadow). We observed significant variations in the composition of tick-borne microorganisms across different environments and blood-engorgement statuses, with a pronounced divergence in symbionts compared to environmental bacteria. Metabolic predictions revealed over 90 differential pathways for tick-borne microorganisms in distinct environments and more than 80 metabolic variations in response to varying blood engorgement statuses. Interestingly, nine pathways were identified, particularly related to chorismate synthesis and carbohydrate metabolism. Moreover, microbial network relationships within tick-borne microorganism groups were highly distinct across different environments and blood-engorgement statuses. The microbial network relationships of symbionts involve some pathogenic and environmental microorganisms. Regression modelling highlighted positive correlations between the Coxiella symbiont and related pathogens, while some environmental bacteria showed strong negative correlations with Coxiella abundance. We also identified commensal bacteria/pathogens in bacterial cooccurrence patterns. Furthermore, we tested pathogenic microorganisms of each tick sample analysis revealed that 86.36% (1601/1855) of the tick samples carried one or more pathogenic microorganisms, The total carrier rate of bacterial pathogens was 43.77% ((812/1855). Most blood samples carried at least one pathogenic microorganism. The pathogens carried by the ticks have both genus and species diversity, and Rickettsia species are the most abundant pathogens among all pathogens.ConclusionOur findings underscore that the bacterial pattern of ticks is dynamic and unstable, which is influenced by the environment factors and tick developmental characteristics.

Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant.

As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands.

Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions. To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China. We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Co-occurrence patterns in biofloc microbial communities revealed by network analysis and their impact on the host

The complex aggregation of bacteria flocs (bioflocs) plays a vital role in the inorganic nitrogen transformation process within biofloc systems. However, few reports have focused on the bacterial co-occurrence of flocs supplemented with different carbohydrate sources. In this study, a correlation-based microecological network analysis method was applied to reveal the bacterial interactions of flocs under three different aquaculture systems: a clear water system (CON group), a biofloc system using glucose (GLU) as a carbon source, and a biofloc system using starch (STA) as a carbon source. The results showed that (i) the GLU group exhibited higher nitrogen removal efficiency and a higher DOC/total inorganic nitrogen ratio (68.80 ± 9.18% and 19.19 ± 6.78, respectively) than the STA group (55.59 ± 16.26% and 15.30 ± 11.08, respectively). The bacterial co-occurrence patterns in the three systems were not random, with each carbohydrate corresponding to a unique bacterial community niche. (ii) Firmicutes was the core phylum in the biofloc technology (BFT) system, while Bacillus, Carnobacterium, and Staphylococcus were the core genera that ensured the stability of nitrogen removal in the system based on network analysis results. (iii) In the GLU group, the abundance of Firmicutes was increased and corresponded to a higher Firmicutes/Bacteroidetes (F/B) ratio in the fish gut, which promoted host in situ growth performance. Application of the ecological concepts in this study could lead to the identification of core/satellite genera in bioflocs and promote scientific hypotheses toward more in-depth metabolic and functional research on biofloc systems.

The preservation of bacterial community legacies in archived agricultural soils

Archived soils are immensely valuable and irreplaceable samples for microbial ecological research, allowing reanalysis of published data and direct comparison across studies using the latest technologies. However, comparatively few studies have explored the influences of prolonged archived soil on the preservation of soil microbial community. Here, archived fertilized soils (DS) and frozen soils (FS) stored at − 80 ℃ for as long as 7-year were sequenced for reconstructing soil bacterial communities. The archived soils treated with propidium monoazide (PMA) to remove extracellular and dead microbes DNA (relic DNA) were also considered (DSP). The results showed that the prolonged desiccation had strong impacts on bacterial diversity and community structure. Removal of relic DNA improved the accuracy of bacterial diversity by 13.3% and total taxonomic turnover by 4.27%, and reduced the differences of bacterial community structure between archived and frozen soils. Archived soils preserved over 90% sequences of bacterial phyla, while bacterial genera exhibited various life-strategies to desiccation stress. Nevertheless, prolonged desiccation did not significantly distort the fertilization legacies on bacterial diversity, community structure and resistance. Moreover, soil archives destabilized bacterial co-occurrence pattern with higher node degree and lower path distance relative to frozen soil, while the relic DNA removal from archived soils improve these properties. Together, these findings revealed that the effects of desiccation on soil bacterial communities could be improved by removal of relic DNA, and the fertilization legacies of bacterial communities were still identified using the archived soils even stored as long as 7-year. This provided the great value of worldwide archived soils that might be applied in microbial ecology research.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53–F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

Bacterial co-occurrence patterns are more complex but less stable than archaea in enhanced oil recovery applied oil reservoirs

A complex microbial community exists in oil reservoirs after the application of chemical enhanced oil recovery (EOR) technologies, where the dynamic interactions of microorganisms are thought to be critical to petroleum composition, recovery, and production technologies but are poorly understood. Here, we used the 16S rRNA gene to construct co-occurrence networks for bacterial and archaeal communities associated with water-, polymer-, and alkaline surfactant polymer (ASP)-flooded oil reservoirs. Nonmetric multidimensional scaling analysis showed that bacterial and archaeal community structures differed significantly (p < 0.01) among the oil reservoirs with different EOR compositions. The microbial co-occurrence pattern in water-flooded reservoirs was more complex, with more nodes, edges, and average degrees (i.e., average links per node in the network) than in the polymer- and ASP-flooded reservoirs. However, the archaeal co-occurrence pattern maintained a more robust structure than that of bacteria under the application of polymer and ASP flooding technologies, suggesting that the application of different enhanced oil recovery techniques has diverse effects on the bacterial and archaeal co-occurrence patterns in reservoirs. The pH and [HCO3−] were significantly correlated with the variations in bacterial and archaeal network structures. Our findings provide new insights into the response of microbes to diverse EOR processes by regulating their interactions in deep oil reservoirs. Revealing the effects of water, polymer, and ASP flooding on the co-occurrence patterns of bacteria and archaea in oil reservoirs, which may facilitate the implementation of microbial enhanced oil recovery technology in the future.

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.

New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria.

Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.

Microplastics affect soybean rhizosphere microbial composition and function during vegetative and reproductive stages

Microplastics (MPs) are emerging contaminants in agricultural soil, whereas their effects on the rhizosphere microbial ecosystems and biogeochemical nitrogen cycles during plant growth remain unknown. Here, a 70-day greenhouse experiment was carried out with black and fluvo-aquic soil to evaluate the influence of polyamide (PA), polyethylene (PE), polyester (PES), and polyvinyl chloride (PVC) MPs on the bacterial communities and functions in the soybean rhizosphere. The PA treatment consistently affected the rhizobacterial alpha diversity in the fluvo-aquic soil at soybean vegetative and reproductive growth stages, whereas the PE, PES, and PVC treatments had a short-term effect on the bacterial alpha diversity. At two growth stages, 6 and 23 biomarkers were consistently abundant in the PA treatment in the black soil and fluvo-aquic soil, respectively, and order Rhizobiales was found to be a biomarker for PA MPs contamination in both soils. Additionally, PA treatment decreased bacterial network complexity and tightness, whereas the effects of the PE, PES, and PVC on bacterial co-occurrence patterns varied depending on the soil types. Furthermore, PES and PVC treatments inhibited ammonification processes in the soybean rhizosphere, and PE could temporarily inhibit ammonia oxidation and denitrification processes according to the variations of N-cycling gene abundances. These effects on soil N-cycling also varied with soil types and soybean growth stages. This study provides profound information for understanding of MPs residues on the assembly of the soybean rhizosphere communities and function during plant development.

Decreased precipitation reduced the complexity and stability of bacterial co-occurrence patterns in a semiarid grassland.

Grasslands harbor complex bacterial communities, whose dynamic interactions are considered critical for organic matter and nutrient cycling. However, less is known about how changes in precipitation impact bacterial interactions. We conducted precipitation manipulation experiments in the Eastern Eurasian Steppe in China and constructed co-occurrence networks for bacterial communities. The network topological features of the bacterial communities exhibited considerable differences among increased precipitation, control, and decreased precipitation gradients. The bacterial co-occurrence pattern in the increased precipitation gradient was the most complex and stable, with a large network size, followed by those of the control and decreased precipitation gradients. Soil moisture (SM) was the primary factor influencing the complexity, size, and stability of bacterial networks across different precipitation gradients, followed by total nitrogen (TN), belowground biomass, aboveground biomass, and total carbon (TC). Our results indicate that drought conditions reduce the complexity and stability of the bacterial community, and future changes in precipitation will greatly reshape bacterial interactions in semiarid grasslands. Overall, these findings could enhance our understanding of how microbes respond to changing precipitation patterns by regulating their interactions in water-limited ecosystems and will improve our ability to predict the impacts of precipitation regime change on ecosystem nutrient cycling and feedback between ecosystem processes and global climate change.

Diurnal Variation of Epiphytic Microbiota: an Unignorable Factor Affecting the Anaerobic Fermentation Characteristics of Sorghum-Sudangrass Hybrid Silage.

Forage epiphytic microbiota exhibits pronounced changes in composition and function throughout the day. However, the effects of these changes on silage fermentation are rarely explored. Here, we transplanted the epiphytic microbiota of sorghum-sudangrass hybrid (SSG) harvested at 7:00h (AM), 12:00h (M), and 17:00h (PM) to sterilized SSG to evaluate the effects of diurnal variation of epiphytic microbiota on fermentation characteristics. During fermentation, remarkable differences in bacterial community successions were observed between silages inoculated with AM and M microbiota. Compared to AM microbiota, M microbiota inoculation increased the proportions of Pantoea dispersa, Leuconostoc lactis, Enterobacter, and Klebsiella variicola, whereas it decreased the proportions of Weissella cibaria and Lactobacillus plantarum during fermentation. This led to the most rapid pH declines and organic acid production in AM silage and the slowest in M silage. Both M and PM microbiota affected the bacterial cooccurrence patterns, indicated by decreased complexity and stability in the community structures of M and PM silages compared to that of AM silage. The predicted functions indicated that some key carbohydrate metabolism pathways related to lactic acid synthesis were downregulated, while some competing pathways (ascorbate and aldarate metabolism and C5-branched dibasic acid metabolism) were upregulated in M silage compared to AM silage after 3days of fermentation. Correlation analysis revealed positive correlations between competing pathways and enterobacterial species. The current study highlights the importance of diurnal variation of epiphytic microbiota in affecting the silage bacterial community, potentially providing an effective strategy to improve silage quality by optimizing harvest time. IMPORTANCE Ensiling is a way to preserve wet biomass for animal and bioenergy production worldwide. The fermentation quality of silage is largely dependent on the epiphytic microbiota of the material. Plant epiphytic microbiota exhibit diurnal changes in composition and function. However, the effects of these changes on silage fermentation are rarely explored. The results presented here demonstrated that diurnal variation of epiphytic microbiota could affect the fermentation characteristics and bacterial community during SSG fermentation. Marked bacterial community differences were observed between AM and M silages during the initial 3days of fermentation. The dominance rate of Lactobacillus plantarum was highest in AM silage, whereas enterobacterial species were more abundant in M silage. The predicted function revealed downregulated lactic acid synthesis pathways and upregulated competing pathways in M silage compared to those in AM silage. This study provides clues for technological-parameter optimization of the fermentation process by the selection of harvest time.

Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species

The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.

Soil bacterial communities and co-occurrence changes associated with multi-nutrient cycling under rice-wheat rotation reclamation in coastal wetland

Coastal reclamation is a global threat to coastal wetland ecosystems, but the impacts of coastal reclamation on belowground biodiversity and their consequences for ecosystem nutrient cycling remain poorly understood. In this study, we examined soil bacterial communities, bacterial co-occurrence pattern and soil multi-nutrient cycling index after natural vegetated coastal wetlands were converted for 6-year and 30-year rice-wheat rotation fields. The soil multi-nutrient cycling index was higher in 6-year and 30-year rice-wheat rotation fields than natural vegetated coastal wetlands. For bacterial community, rice-wheat rotation reclamation increased soil bacterial alpha diversity but decreased beta diversity and co-occurrence network complexity than those in the vegetated coastal wetland. Rice-wheat rotation reclamation also changed soil bacterial community assemblages by increasing the relative abundance of Actinobacteriota and Desulfobacterota while decreasing the relative abundance of Alphaproteobacteria and Gammproteobacteria. Changes in the relative importance of dispersal limitation and homogenizing dispersal mainly controlled the variations in soil bacterial community assemblages. Soil bacterial community variations induced by rice-wheat reclamation were strongly related to soil multi-nutrient cycling, especially bacterial connection complexity. Our results provide experimental support that belowground microbial interactions are crucial for maintaining ecosystem functioning.

Correlating the above- and belowground genotype of Pinus pinaster trees and rhizosphere bacterial communities under drought conditions

Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed.

Short-Term Grazing Exclusion Alters Soil Bacterial Co-occurrence Patterns Rather Than Community Diversity or Composition in Temperate Grasslands.

Grazing exclusion is one of the most common practices for degraded grassland restoration worldwide. Soil microorganisms are critical components in soil and play important roles in maintaining grassland ecosystem functions. However, the changes of soil bacterial community characteristics during grazing exclusion for different types of grassland remain unclear. In this study, the soil bacterial community diversity and composition as well as the co-occurrence patterns were investigated and compared between grazing exclusion (4 years) and the paired adjacent grazing sites for three types of temperate grasslands (desert steppe, typical steppe, and meadow steppe) in the Hulunbuir grassland of Inner Mongolia. Our results showed that short-term grazing exclusion decreased the complexity and connectivity of bacterial co-occurrence patterns while increasing the network modules in three types of temperate grasslands. The effects of grazing exclusion on soil bacterial α-diversity and composition were not significant in typical steppe and meadow steppe. However, short-term grazing exclusion significantly altered the community composition in desert steppe, indicating that the soil bacteria communities in desert steppe could respond faster than those in other two types of steppes. In addition, the composition of bacterial community is predominantly affected by soil chemical properties, such as soil total carbon and pH, instead of spatial distance. These results indicated that short-term grazing exclusion altered the soil bacterial co-occurrence patterns rather than community diversity or composition in three types of temperate grasslands. Moreover, our study suggested that soil bacterial co-occurrence patterns were more sensitive to grazing exclusion, and the restoration of soil bacterial community might need a long term (>4 years) in our study area.

Different bacterial co-occurrence patterns and community assembly between rhizosphere and bulk soils under N addition in the plant–soil system

Different bacterial co-occurrence patterns and community assembly between rhizosphere and bulk soils under N addition in the plant–soil system

Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil

Globally distributed earthworms affect compositions of soil compounds, microbial community structures, as well as antibiotic resistance genes (ARGs). Compared to their surroundings, earthworm gut is a simpler environment which could filter out microbes when soil passes through it. However, little is known about how earthworms affect the dissemination of ARGs in soil, and the understanding of the relationship between microbe-microbe interactions and ARGs is still lacking. Here, we designed a microcosm experiment with earthworm addition, and determined bacterial and fungal community compositions based on amplicon sequencing. We also examined mobile genetic elements (MGEs) and ARGs in earthworm gut and soils using high-throughput qPCR. The results showed significant differences of bacterial, fungal and ARG patterns between gut and soil. Earthworms indirectly impacted the patterns of ARGs in soils by affecting bacterial communities and soil properties, which play key roles in the distribution of ARGs and MGEs. The absolute abundances of MGEs in earthworm gut were significantly lower than those in soils, and earthworms reduce the absolute abundance of MGEs in soils. Earthworms changed the microbial co-occurrence patterns, and reduced bacterial connectivity, which were significantly and positively correlated with MGE abundance. These results highlight the importance of earthworm on the distribution and dissemination of ARGs in soils.

Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii.

Seagrass meadows, as typical “blue carbon” ecosystems, play critical ecological roles in the marine ecosystem and decline every year. The application of biochar in soil has been proposed as a potential soil amendment to improve soil quality and mitigate global climate change. The effects of biochar on soil bacterial activities are integrally linked to the potential of biochar in achieving these benefits. However, biochar has been rarely applied in marine ecosystems. Whether the application of biochar could work on the seagrass ecosystem remained unknown. In this study, we investigated the responses of sediment and rhizosphere bacterial communities of seagrass Thalassia hemprichii to the biochar addition derived from maize at ratios of 5% by dry weight in the soil during a one-month incubation. Results indicated that the biochar addition significantly changed the sedimental environment with increasing pH, total phosphorus, and total kalium while total nitrogen decreased. Biochar addition significantly altered both the rhizosphere and sediment bacterial community compositions. The significant changes in rhizosphere bacterial community composition occurred after 30days of incubation, while the significant variations in sediment bacterial community composition distinctly delayed than in sediment occurred on the 14th day. Biochar application improved nitrification and denitrification, which may accelerate nitrogen cycling. As a stabilizer to communities, biochar addition decreased the importance of deterministic selection in sediment and changed the bacterial co-occurrence pattern. The biochar addition may promote seagrass photosynthesis and growth by altering the bacterial community compositions and improving nutrient circulation in the seagrass ecosystem, contributing to the seagrass health improvement. This study provided a theoretical basis for applying biochar to the seagrass ecosystem and shed light on the feasible application of biochar in the marine ecosystem. Graphical

Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria

The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.