Bacterial Community Composition Research Articles

Reducing Total Plate Count of Bacteria through Dark Sealed Storage for Plant Factory Nutrient Solution Sterilization

Plant factories are efficient systems for vegetable production under a clean and controlled environment. To improve the sterilization efficiency of nutrient solutions (NS) in plant factories, this study examined the changes in the number and composition of colonies from in-use and post-use stored NS. The sterilization effect under ultraviolet (UV) light-emitting diode light was also investigated. The results indicated that the total plate count of bacteria (TPC) of newly prepared NS was 3.99 lg CFU/mL (9870 CFU/mL); within 7 days of cultivation, this number sharply increased ∼7.8 times to 4.88 lg CFU/mL (76,000 CFU/mL), then remained stable. After dark sealed storage (DSS) of post-use NS, TPC dramatically decreased by 82.8% and reached its lowest point at 4.29 lg CFU/mL (19,566 CFU/mL) on day 3, equivalent to a log survival ratio of −0.76, then rapidly rebounded by 235.6% to 4.82 lg CFU/mL (65,666 CFU/mL) on day 4. During storage, bacterial community composition was also remarkably changed, and the relative abundance of heterotrophic bacteria such as Variovorax paradoxus and Pararhizobium giardinii and photosynthetic bacteria such as Pseudo-Nitzschia multiseries were greatly decreased. The log survival ratio for in-use and post-use stored NS under UV sterilization were −1.29 and −1.30, respectively, and was not significantly different. Coupled with the dramatic decrease in TPC during DSS, the overall log survival ratio of post-use NS UV sterilization was −2.06 and was the most effectively form of sterilization in our study. In short, TPC of in-use NS remained high for a long period, and DSS may serve as a low-cost NS sterilization method in plant factories.

Field study on the dynamics of microbial communities following biostimulation at organochlorine-contaminated sites

Chlorinated ethenes (CEs) have become widespread contaminants in soils, sediments, and groundwater due to extensive historical use, improper handling, and disposal. At many sites, biostimulation is an effective remediation strategy for treating CEs, involving the addition of electron donors to support bacteria capable of degrading these compounds. This study aimed to understand how microbial communities adapt to environmental changes induced by biostimulation interventions. We investigated changes in microbial communities on biomass carriers transferred from a non-biostimulated, CE-contaminated environment to a previously biostimulated environment at two sites. In the non-biostimulated wells, a predominance of bacteria with nitrate-reducing or iron-reducing metabolisms was evident. Some of which are known to aerobically degrade CEs or other organic pollutants. Following the transfer of the carriers, these bacteria were outcompeted by anaerobic microorganisms with respiratory and fermentative metabolisms. The newly formed microbial community on the transferred biomass carriers exhibited greater diversity and higher abundance of organohalide-respiring bacteria. This rapid adaptability indicates the potential for these bacteria to flourish in favorable conditions, particularly at Site 2, where five days after carrier transfer, Dehalococcoides abundance increased 14,200-fold, and the biomarker vcrA increased 28,500-fold. PCoA revealed that that greater differences in hydrogeochemical conditions between biostimulated and non-biostimulated wells resulted in accelerated changes in bacterial community composition and diversity. In conclusion, our study demonstrates a rapid proliferation of CE-degrading bacteria after the transfer of biomass carriers into biostimulated wells at two different sites. The transfer stimulated shifts toward organohalide-respiring and other anaerobic bacteria in biostimulated environment and increased microbial diversity.

Soil multifunctionality and nutrient cycling-related genes in Cunninghamia lanceolata plantations: metagenomic perspective insights into ecological restoration

The widespread cultivation of Cunninghamia lanceolata in China has led to soil degradation and decline in microbial diversity, which have a significant impact on supporting forest ecological services. However, little is known about the long-term consequences from forest management practices on the bacterial functional genes associated with soil nutrient cycling. Here, metagenomic sequencing was used to investigate the soil bacterial functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling in a 16-year pair experiment of pure (C. lanceolata) and mixed plantations (C. lanceolata + Betula luminifera). The results showed that the mixed plantations had much higher soil nutrient content as well as enzyme activity, thereby improving soil multifunctionality (SMF). Forest management practices resulted in differences in the structural and functional composition of soil bacterial communities, such as Chloroflexi, Firmicutes and acid metabolism were enriched in pure plantations, while Acidobacteria, Planctomycetes and amino acid metabolism were enriched in mixed plantations. Compared with monocultures, mixed plantations had higher abundance of genes participated in C degradation, C fixation, methanogenesis, N cycling and P solubilization. The CNP cycling genes also varied with taxon-specific responses to forest management. Forty-seven nearly entire bacterial metagenome-assembled genomes (MAGs) were obtained, in which MAGs enriched in mixed plantations had more functional genes involved in CNP cycling. Notably, acidophilic Acidobacteria played important roles in reduction of Fe(III) and the subsequent release of organic P. In all, our results demonstrated that the use of mixed plantations enhances a number of soil functions via its influence on the abundances of keystone taxa and functional genes, providing a foundation for developing forest management strategies in subtropical regions. In future researches, attention should be paid to the effects of mixed plantations on soil microbial diversity and nutrient cycling across various seasons.

Soil properties and microbial evolution during cropping system conversion: Insights from a 105-year study in southern China

Understanding the mechanisms by which soil environments and microbial communities evolve in response to long-term changes in cropping systems is essential for the development of effective ecological conservation and restoration strategies. In this study, variations of soil characteristics and the succession of microbial community assemblages and functions were investigated in southern Chinese deciduous forests and adjacent converted tea plantations at different ages (20, 40, 60, and 105 years). The results revealed significant alterations in soil properties and the emergence of distinct diversity patterns and assembly mechanisms for bacterial and fungal communities over the century-long succession period. Bacterial α-diversity exhibited a declining trend throughout succession, while fungal α-diversity experienced a rebound in the later stages. Null model analysis indicated that stochastic processes primarily drove the assembly of the bacterial community in both forests and tea plantations, whereas fungal community assembly gradually shifted from stochastic dominance to deterministic dominance. The strength of interactions between bacterial taxa in tea plantations decreased over time, but the topological properties of fungal networks were restored in tea plantations aged 60 and 105 years. The functional groups of bacteria associated with carbon cycling and saprotrophic fungi significantly increased after tea cultivation, which was closely linked to the proliferation of r-strategists stimulated by sufficient nutrients in tea plantations. It is noteworthy that in addition to typical environmental variables such as nutrients and pH, soil polyphenols in tea plantations also have a profound effect on the composition and assembly processes of bacterial and fungal communities. These findings advance the current understanding of how long-term cropping system changes affect soil microbial community assembly and functionality, and highlight the distinct strategies by which bacteria and fungi respond to cropping system change.

Effects of grassland degradation on soil ecological stoichiometry and soil microbial community on the South of the Greater Khingan Mountains

Grassland which covers 40% of terrestrial land is an important ecosystem having a multitude of functions, which has suffered various degrees of degradation with the interaction between global climate change and unreasonable human utilization (e.g., grazing and reclamation). Improved understanding of soil and microbial community diversity during meadow steppe degradation is crucial for predicting degradation mechanisms and restoration strategies. Here, we used Illumina sequencing technology to investigate the patterns of soil microbial community structure and the driving factors of its change across different degradation degrees of meadow steppe [i.e., non-degraded grasslands (NDG), lightly degraded grasslands (LDG), moderately degraded grasslands (MDG), and severely degraded grasslands (SDG)] south of the Greater Khingan Mountains. Our results showed a significant variation in soil properties, enzyme activity, and soil metal elements across the degraded meadows. Soil available phosphorus (AP), urease (UE), and cellulase (CL) in soils increased with the intensity of grassland degradation. Grassland degradation significantly decreased soil bacterial and fungal richness. In addition, grassland degradation significantly increased the relative abundance of Firmicutes (from 1.65% to 5.38%) and Myxococcota (from 2.13% to 3.13%). Degradation considerably increased the relative abundance of Ascomycota (from 66.54% to 75.05%), but decreased Basidiomycota (from 18.33% to 9.92%). The relative abundance of nitrogen fixation and cellulolysis decreased significantly due to grassland degradation. For fungal functional guilds, the relative abundance of pathotrophs increased while saprotrophs decreased significantly with increasing severity of degradation. Total nitrogen (TP), AP, available potassium (AK), manganese (Mn), lead (Pb), UE, sucrase (SC), and alcalase protease (ALPT) were the main drivers of soil bacterial community composition, while TP, AP, AK, Pb, UE, and SC were the main drivers of soil fungal community composition in the degraded grassland. Our findings demonstrated that severe grassland degradation has an enormous effect on soil microbial communities and soil physicochemical dynamics. These findings improve our theoretical understanding of the interactions between soil microbial populations and soil environmental variables in degraded grassland.

Host genotype and infection status interact to shape microbiomes in Daphnia magna.

Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

Phyllospheric bacterial communities in spinach are influenced by soil nitrogen availability

Nitrogen is an essential macronutrient for the growth and development of plants. As with most crops, nitrogen-based fertilizers are used to improve productivity and quality of spinach. Although the significance of the soil microbiome in the inorganic nitrogen cycle is recognized, soil nitrogen's impact on phyllosphere bacterial communities remains unclear. This study investigates changes in the bacterial community composition and diversity residing on spinach leaves cultivated in soils with varying nitrogen levels. Sixty-eight spinach samples were processed using culture-dependent and independent methods to evaluate phyllosphere-associated bacterial communities. In culture-dependent methods, populations of Mesophiles (MS), Psychrotrophs (PY), coliforms (CL), and lactic acid bacteria (LAB) were quantified by plate counts using appropriate culture media. In culture-independent methods, bacteria were determined by amplicon sequencing based on the V3-V4 region of the bacterial 16S rRNA gene. Counts of MS, PY, CL, and LAB on low-nitrogen soil-grown spinach were 7.4, 7.1, 6.9, and 5.5 log CFU/g, respectively, while high-nitrogen soil-grown spinach showed counts of 7.5, 7.0, 7.0, and 5.7 log CFU/g. These counts did not differ significantly between the nitrogen levels used for spinach cultivation (p > 0.05). Amplicon sequencing, however, revealed differences in relative abundance between different taxa levels and soil nitrogen levels. The relative abundance of Erwinaceae and Planococcaceae was higher in high-nitrogen soil-grown spinach. The relative abundance of Pseudomonadaceae, Enterobacteriaceae, and Rhizobiaceae was higher in low-nitrogen soil-grown spinach. Soil nitrogen content significantly affected spinach phyllosphere microbiome beta-diversity. Our results suggest that bacterial communities of spinach phyllosphere are influenced by soil nitrogen content.

Shifts in bacterial community composition during symbiotic seed germination of a terrestrial orchid and effects on protocorm development.

It is well known that orchid seeds depend on mycorrhizal fungi to supply the necessary nutrients that support germination in natural environments. Apart from fungi, bacteria may also be involved in the germination process of orchid seeds, but so far, their role has not been intensively studied. This research provides evidence that bacterial community composition changes during seed germination of the terrestrial orchid Gymnadenia conopsea. Interestingly, in vitro experiments showed that Pseudomonas spp., which were the most dominant bacteria in the later germination stages, improved protocorm growth. These results suggest that bacteria contribute to the germination of orchid seeds, which may open new perspectives to apply bacteria as a biofertilizer in the introduction and restoration of G. conopsea populations.

Microbial Basis for Suppression of Soil-Borne Disease in Crop Rotation

The effect of crop rotation on soil-borne diseases is a representative case of plant–soil feedback in the sense that plant disease resistance is influenced by soils with different cultivation histories. This study examined the microbial mechanisms inducing the differences in the clubroot (caused by Plasmodiophora brassicae pathogen) damage of Chinese cabbage (Brassica rapa subsp. pekinensis) after the cultivation of different preceding crops. It addresses two key questions in crop rotation: changes in the soil bacterial community induced by the cultivation of different plants and the microbial mechanisms responsible for the disease-suppressive capacity of Chinese cabbage. Twenty preceding crops from different plant families showed significant differences in the disease damage, pathogen density, and bacterial community composition of the host plant. Structural equation modelling revealed that the relative abundance of four key bacterial orders in Chinese cabbage roots can explain 85% and 70% of the total variation in pathogen density and disease damage, respectively. Notably, the relative dominance of Bacillales and Rhizobiales, which have a trade-off relationship, exhibited predominant effects on pathogen density and disease damage. The disease-suppressive soil legacy effects of preceding crops are reflected in compositional changes in key bacterial orders, which are intensified by the bacterial community network.

Litter Removal Counteracts the Effects of Warming on Soil Bacterial Communities in the Qinghai–Tibet Plateau

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence strategies remain unclear. In this study, we used a fiberglass open-top chamber to simulate global change, and moderate grazing in winter was simulated by removing above-ground litter from all plants in the Qinghai–Tibet Plateau, China, to investigate the effects of warming, litter removal, and interactions on soil microbial communities. The treatments included (1) warming treatment (W); (2) litter removal treatment (L); (3) the combined treatment (WL); and (4) control (CK). The results show that compared with the control treatment, warming, litter removal, and the combined treatments increased bacterial Shannon diversity but reduced fungal Shannon diversity, and warming treatment significantly changed the bacterial community composition. Warming, litter removal, and the combined treatments reduced the colinear network connectivity among microorganisms but increased the modularity of the network, and the average path distance and average clustering coefficient were higher than those in the control group. Stochastic processes played a more important role in shaping the microbial community composition, and soil–available phosphorus and soil ammonium contributed more to the βNTI of the bacterial community, while total phosphorus and NAG enzyme in the soil contributed more to the βNTI of the fungal community. Notably, litter removal counteracts the effects of warming on bacterial communities. These results suggest that litter removal may enhance bacterial community stability under warming conditions, providing insights for managing alpine meadow ecosystems in the context of climate change.

Dynamic succession of the quantity and composition of epiphytic microorganisms at different growth stages on rice surface

The quality of silage is uneven, which is due to the difference of epiphytic microorganisms of raw materials. To improve the quality of fermentation, the quantity and composition of epiphytic microorganisms are usually analyzed to better prepare silage. In this research, plate coating method and 16S high-throughput sequencing were used to analyze the differences in the quantity and composition of rice epiphytic microorganisms during different growth stages. The Lactic acid bacteria (LAB) and aerobic bacteria were the highest at the flowering stage, the yeast was the highest at the milk ripening stage, and the mould was the highest at the full ripening stage. And the growth stage also had a great influence on the composition of epiphytic bacterial community, at the phylum level, it was mainly composed of Proteobacteria. And at the genus level, Pantoea, Acinetobacter, Pseudomonas and Chryseobacterium were dominanted at the flowering stage; Pantoea, Stenotrophomonas and Sphingobacterium were dominanted at the milk ripening stage; Acinetobacter, Pantoea, Chryseobacterium and Lactococcus were dominanted at the dough stage; Acinetobacter and Klebsiella were dominated at the full ripening stage. Overall, the growth stage significantly affected the quantity and composition of rice epiphytic microorganisms. Therefore, rice silage can be modulated reasonably according to the number and composition of epiphytic microorganisms in different growth stages.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene.

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

Linking phylogenetic niche conservatism in bacterial communities in sorghum root compartments revealed by the Hongyingzi cultivar.

The root system harbours complex bacterial communities, which are critical for plant growth and health. Significant differences exist between bacterial communities in the root compartments; however, limited reports have explored their phylogenetic composition and niche conservatism in the root system of sorghum. We used the sorghum Hongyingzi cultivar as test plant, and applied 16S rRNA high-throughput sequencing and various statistical approaches. Phylogenetic composition of bacterial communities in root compartments were primarily driven by closely related species with similar environmental adaptations. We also found evidence of phylogenetic niche conservatism in bacterial communities for edaphic factors in the various root compartments, with pH and available N playing essential roles in shaping community composition. Environmental threshold analysis revealed threshold ranges of dominant taxa for pH and available N, indicating wider adaptive thresholds for more abundant taxa. Reconstruction of ancestral states suggested evolutionary changes in adaptability of certain bacterial taxa to edaphic factors, suggesting a shift towards slightly acidic, high N environments and reflecting the prolonged mutual interaction between bacteria and plants in cultivated soils. These findings enhance our understanding of environmental responses and evolutionary dynamics of root-associated microbiota in young sorghum plants and provide novel insights into ecological adaptations, shedding light on their responses to environmental factors. Our study contributes to a better understanding of the ecological dynamics of root-associated microbiota and offers analytical pathways for exploring the nutritional regulation of root microbiota.

Variation in the intestinal bacterial community composition under different water temperature culture conditions in largemouth bass (Micropterus salmoides).

This study aimed to investigate the impact of temperature on the intestinal microbiota of largemouth bass using 16S rRNA gene amplicon sequencing, focusing on the under-explored role of abiotic factors in shaping the gut microbial community. Five water temperature groups (20.0±0.2°C, 25.0±0.2°C, 28.0±0.2°C, 31.0±0.2°C, and 35.0±0.2°C) were established, each with three replicates. Significant variations in intestinal bacterial community composition were observed across these conditions. Elevated temperatures (31.0±0.2°C and 35.0±0.2°C) led to an increase in opportunistic pathogens such as OTU180 Vibrio and OTU2015 Vogesella (P<0.05). Species correlation network analysis showed a shift towards more positive relationships among intestinal microbes at higher temperatures (P<0.05). Ecological process analysis highlighted a greater role of ecological drift in microbial community structure at 31.0±0.2°C and 35.0±0.2°C (P<0.05). The study suggests that higher temperatures may predispose largemouth bass to opportunistic pathogens by altering their intestinal microbiota. Effective water temperature management is crucial for largemouth bass aquaculture to mitigate pathogen risks and maintain a balanced intestinal microbiota. This research provides critical insights into the temperature-microbiota relationship and offers practical recommendations for aquaculture practices.

Biotics and bacterial function: impact on gut and host health.

The human gut microbiota, the vast community of microbes inhabiting the gastrointestinal tract, plays a pivotal role in maintaining health. Bacteria are the most abundant organism, and the composition of bacterial communities is strongly influenced by diet. Gut bacteria can degrade complex dietary carbohydrates to produce bioactive compounds such as short-chain fatty acids. Such products influence health, by acting on systemic metabolism, or by virtue of anti-inflammatory or anti-carcinogenic properties. The composition of gut bacteria can be altered through overgrowth of enteropathogens (e.g., Campylobacter, Salmonella spp.), leading to dysbiosis of the gut ecosystem, with some species thriving under the altered conditions whereas others decline. Various "biotics" strategies, including prebiotics, probiotics, synbiotics, and postbiotics, contribute to re-establishing balance within the gut microbial ecosystem conferring health benefits. Prebiotics enhance growth of beneficial members of the resident microbial community and can thus prevent pathogen growth by competitive exclusion. Specific probiotics can actively inhibit the growth of pathogens, either through the production of bacteriocins or simply by reducing the gastrointestinal pH making conditions less favorable for pathogen growth. This review discusses the importance of a balanced gut ecosystem, and strategies to maintain it that contribute to human health.

Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection.

The assembly of the rhizosphere community, even the diazotroph community, is mainly shaped by soil environmental factors (including soil climate and physiochemical characteristics) and plant selection. To better understand the driving forces on the active overall and nitrogen-fixing bacterial community compositions, we characterized the communities of tobacco rhizosphere soil collected from three sampling sites with a large geographic scale (> 600km). The results indicate that the diversity and community composition of the overall bacterial and diazotroph communities are obviously differed according to the sampling sites. Still, no significant difference is found between the communities in rootzone and rhizosphere samples. Climate variables including mean annual precipitation (MAP) and mean annual temperature (MAT), soil physiochemical characteristics including available nitrogen (AN), available potassium (AK) and pH are main factors that affect the bacterial and diazotroph community structures in the three sampling sites. Furthermore, MAP and MAT, AN and available phosphorus (AP), total nitrogen (TN) and organic carbon (OC), AK and electrical conductivity (EC) showed similar effects, but pH showed independent effect on the composition of the overall bacteria and diazotroph communities. However, the alpha diversity indices of active overall and nitrogen-fixing bacteria in the rhizosphere are obviously higher than in the rootzone samples, and no significant differences are observed among different sampling sites. Proteobacteria is the predominant active phylum of all samples for overall and nitrogen-fixing bacteria. Escherichia-Shigella, Achromobacter, Streptomyces and Sphingomonas are the dominant active bacterial genera, and Bradyrhizobium, Skermanella and Extensimonas are dominant active nitrogen-fixing bacteria genera in rhizosphere. Furthermore, the high active abundance of Escherichia-Shigella but low abundance of Ralstonia in all three sampling sites indicate high root-knot nematode infection and low wilt disease endemic risk. These results indicate that soil environmental factors contribute more to the tobacco rhizosphere bacterial community assemblage, but the rhizosphere contributes more to the diversity of active overall bacteria and nitrogen-fixing bacteria in the community. Our study provides novel knowledge for the assemble of rhizosphere bacterial and active bacteria communities across a large geographical scale.

Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome

Bacteriophages (“phage”) play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.

Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles

BackgroundTicks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission.MethodsTick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at − 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables.ResultsA total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia.ConclusionsThe study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens.Graphical

Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea

BackgroundCorals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals.Results16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns.ConclusionsOverall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.

Impact of Bacillus Inoculation on Rhizosphere Bacterial Community Structure: A Review

The rhizosphere is a specialized zone where plant roots interact with the soil microbiome. Among various beneficial microbes, the genus Bacillus stands out due to its diverse functionalities and potential to boost plant growth and resilience. Bacillus is a key genus of plant growth-promoting rhizobacteria (PGPR) known for enhancing nutrient availability, producing phytohormones, and inducing plant resistance to pathogens. Inoculating Bacillus species into the rhizosphere can significantly alter the bacterial community's structure and composition. These alterations are driven by the competitive and cooperative interactions between Bacillus and the native rhizosphere microorganisms. Incorporating soil microorganisms into the host plant's beneficial bacterial community improves soil nutrient cycling and nutrient use efficiency. Using microbial inoculants is an effective strategy to address crop succession challenges, enhance microbial community structure, and improve soil fertility, thereby promoting crop growth. This review thoroughly examines the current understanding of how Bacillus inoculation impacts rhizosphere bacterial community structure.