Changes In Bacterial Community Structure Research Articles

Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.

Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.

Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome

In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.

Changes in soil bacterial community diversity and its network stability under different grazing intensities in plateau rangelands

Grassland degradation is a significant ecological challenge, it changes the grassland environment, including the structure of soil microbial communities. Grazing is a critical factor in this process, yet the impact of different grazing intensities on soil bacterial communities, particularly in unique environments like the Qinghai-Tibet Plateau, remains poorly understood. This study utilized a full-length 16 S rRNA gene sequencing technology combined with environmental factors to assess the impacts of the Holba sheep grazing on soil bacterial community diversity in Zhongba County, Shigatse City, Qinghai-Tibet Plateau. The specific aim was to explore the changes in soil bacterial community diversity and stability under contrasting grazing intensities: prohibited grazing, light grazing, moderate grazing, and heavy grazing. The results showed that grazing activities significantly altered the diversity of bacterial communities, particularly under light and heavy grazing. The spatial dissimilarity in soil bacterial communities was mainly driven by species turnover (i.e., species replacement), which was more pronounced under heavy grazing. The number of keystone species increased with the grazing intensity of the bacterial co-occurrence network. Under heavy grazing, bacterial communities showed the highest number of keystone species and the community stability. Environmental factors such as exchangeable magnesium (EM), soil available kalium (SAK), and soil pH were the most important environmental variables impacting changes in bacterial community structure by influencing community α-diversity and stability. This study enhances our understanding of the response mechanisms of soil microbial communities to grazing intensities and other environmental stresses in grassland ecosystems. In addition, this study also provides important references and guidance for microbial diversity research in extreme environments. These findings are crucial for promoting the sustainable management and conservation of grassland ecosystems in climatically harsh areas such as the Qinghai-Tibet Plateau.

Species interactions and bacterial inoculation enhance plant growth and shape rhizosphere bacterial community structure in faba bean – wheat intercropping under water and P limitations

Grain legumes / cereals intercropping systems with microbial inoculants, hold promise for improving crop productivity under stressful conditions. However, the tripartite interaction involving intercropping system, associated microbiota and stress combining water deficit and low phosphorus (P) availability remains understudied. This study evaluated the impact of three bacterial consortia (C4, C6, and Cref containing Rhizobium and PSB strains) including single Rhizobium (Rhizobium laguerreae) on the agro-physiological performance of wheat (Triticum durum) and faba bean (Vicia faba) grown as intercrops or sole-crops under P and water deficient conditions. Inoculation, especially with C6, significantly improved shoot and root biomasses of both wheat (up to 66 and 81 %) and faba bean (up to 54 and 266 %) intercrops compared to single Rhizobium inoculation and control treatments. Intercropping generally outperformed sole-cropping in above-ground physiology, root morphological traits, shoot and root P content, with a notable effect in response to C6 exhibiting low microbial biomass P. Changes in bacterial community structure were primarily driven by cropping pattern and water regime rather than bacterial inoculation. Intercropping maintained bacterial diversity but shifted community structure, favoring Proteobacteria. Overall, inoculating intercropped wheat and faba bean with Rhizobium-containing consortia induced beneficial below-ground interspecies interactions under water and P-limiting conditions.

Soil organic carbon, pH, and ammonium nitrogen controlled changes in bacterial community structure and functional groups after forest conversion

IntroductionLand-use changes significantly impact soil properties in forests, which is an area of concern. Therefore, the effects of changing forest types on soil microbial communities and their functions in northern subtropical forest regions need to be further researched.MethodsWe used 16S rDNA sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to assess the variation of soil bacterial communities and potential functions related to carbon (C) and nitrogen (N) cycling in two soil layers (0–10 and 10–30 cm) after the conversion of the secondary masson pine (Pinus massoniana, PM) forest to plantations of slash pine (Pinus elliottii, PE) and Chinese fir (Cunninghamia lanceolata, CL) located in Jingde County, Anhui Province, China.ResultsThe study found that converting coniferous secondary forests to coniferous plantations resulted in a notable increase in soil pH and a decrease in nitrate nitrogen and organic carbon contents. Additionally, soil microbial diversity increased significantly, and microbial community structure changed, particularly in the topsoil. These changes might affect the C- and N-cycling mediated by soil bacteria. The analysis revealed a significant decrease in the abundance of functional groups associated with C-cycling and a significant increase in the abundance of functional groups associated with N-cycling, particularly those associated with denitrification. Soil organic carbon, pH, and ammonium nitrogen were the most critical variables affecting changes in the soil microbial community.DiscussionThese findings provide valuable information for ecological restoration and future sustainable forest management.

Impact of high-altitude acclimatization and de-acclimatization on the intestinal microbiota of rats in a natural high-altitude environment.

Intestinal microorganisms play an important role in the health of both humans and animals, with their composition being influenced by changes in the host's environment. We evaluated the longitudinal changes in the fecal microbial community of rats at different altitudes across various time points. Rats were airlifted to high altitude (3,650 m) and acclimatized for 42 days (HAC), before being by airlifted back to low altitude (500 m) and de-acclimatized for 28 days (HADA); meanwhile, the control group included rats living at low altitude (500 m; LA). We investigated changes in the gut microbiota at 12 time points during high-altitude acclimatization and de-acclimatization, employing 16S rRNA gene sequencing technology alongside physiological indices, such as weight and daily autonomous activity time. A significant increase in the Chao1 index was observed on day 14 in the HAC and HADA groups compared to that in the LA group, indicating clear differences in species richness. Moreover, the principal coordinate analysis revealed that the bacterial community structures of HAC and HADA differed from those in LA. Long-term high-altitude acclimatization and de- acclimatization resulted in the reduced abundance of the probiotic Lactobacillus. Altitude and age significantly influenced intestinal microbiota composition, with changes in ambient oxygen content and atmospheric partial pressure being considered key causal factors of altitude-dependent alterations in microbiota composition. High-altitude may be linked to an increase in anaerobic bacterial abundance and a decrease in non-anaerobic bacterial abundance. In this study, the hypobaric hypoxic conditions at high-altitude increased the abundance of anaerobes, while reducing the abundance of probiotics; these changes in bacterial community structure may, ultimately, affect host health. Overall, gaining a comprehensive understanding of the intestinal microbiota alterations during high-altitude acclimatization and de-acclimatization is essential for the development of effective prevention and treatment strategies to better protect the health of individuals traveling between high- and low-altitude areas.

Changes in soil bacterial community structure in a short-term trial with different silicate rock powders

BackgroundThe use of rock powders in soil has emerged as a nature-based technology to improve soil properties relevant to crop development and for atmospheric carbon dioxide removal (CDR) via enhanced rock weathering (ERW). Although modeling this process is crucial, the soil microbiome has been identified as the main reason why several experimental and field results do not fit the geochemical and kinetic theoretical models. Here, the hypothesis that the bacterial community structure is modulated by the application of different silicate rock powders was tested. One phonolite, three basalt variations and one granite, as well as KCl treatments, were applied to a Ferralsol cultivated with Brachiaria in short-term pedogeochemical experiments and assessed after 1 (1M), 4 (4M) and 8 (8M) months.ResultsThe main changes in soil bacterial structure were observed at 8M and found to be modulated according to rock type, with petrochemistry and mineralogy acting as the main drivers. The content of microbial biomass carbon tended to decrease over time in the Control and KCl treatments, especially at 4M, while the rock treatments showed constant behavior. The sampling time and treatment affected the richness and diversity indices. The Si, Ca and Fe from mafic minerals were the main chemical elements related to the soil bacterial changes at 8M.ConclusionsThe type (acidity) of silicate rock powder modulated the soil bacterial community (SBC) in a pot experiment with tropical soil. The specificity of the SBC for each rock type increased with time until the end of the experiment at 8 months (8M). The carbon content in the microbial biomass was lower in the rock powder treatments in the first month (1 M) than in the control and KCl treatments and was equal to or higher than that in the 8 M treatment. This result illustrates the challenge of modeling rock powder dissolution in soil since the soil medium is not inert but changes concurrently with the dissolution of the rock.Graphical

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Study on the effect and regularity of plating parts cleaning wastewater by enhanced aerobic process with high-density bacterial flora

In this research, we established an enhanced aerobic biological method utilizing a high-density bacterial flora for the treatment of low-biochemical plating parts washing wastewater. The elucidation of pollutant removal mechanisms was achieved through a comprehensive analysis of changes in sludge characteristics and bacterial community structure. The results demonstrated that throughout the operational period, the organic load remained stable within the range of 0.01–0.02 kgCOD/kgMLSS·d, the BOD5/COD ratio increased from 0.004 mg/L to 0.33 mg/L, and the average removal rates for key pollutants, including COD, NH4+-N, and TN, reached 98.13%, 99.86%, and 98.09%. MLSS concentration remained at 7627 mg/L, indicating a high-density flora. Notably, Proteobacteria, Bacteroidota, and Acidobacteriota, which have the ability to degrade large organic molecules, had been found in the system. This study affirms the efficacy of the intensive aerobic biological method for treating low-biochemical plating washing wastewater while ensuring system stability.

Effect of Forest Fires on the Alpha and Beta Diversity of Soil Bacteria in Taiga Forests: Proliferation of Rare Species as Successional Pioneers

Forest fires are among the most influential drivers of changes in forest soil bacterial diversity. Nevertheless, little is known regarding the effects of forest fires on maintaining the complex interactions that preserve forest ecosystem stability. Therefore, this study characterized alterations in soil bacterial community composition and diversity within taiga forests subjected to varying disturbance intensities. Particularly, this study examined the bacterial community within a Larix gmelinii fire-burnt site in Daxinganling, analyzing the changes in bacterial community structure and function across light, moderate, and heavy fire-burnt sites, as well as a control sample site, utilizing Illumina MiSeq technology. Through an assessment of bacterial community diversity and soil physicochemical properties (moisture content (MC), pH, microbial biomass carbon (MBC), organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AP)), we explored the influence of the soil microenvironment on the soil bacterial community structure at the burnt site under different disturbance intensities. Our findings demonstrated that (1) there was no significant change in the Chao index of soil bacteria in the burnt site under different disturbance intensities, whereas the Shannon index decreased significantly (p < 0.05) and the Simpson index increased significantly (p < 0.05) in the burnt site under light and moderate disturbance. (2) The relative abundance of dominant phyla, such as Proteobacteria, Proteobacteria, and Actinobacteriota, did not change significantly in the fire-burnt site under different disturbance intensities, whereas rare species, such as Acidipila, Occallatibacter, and Acidibacter, experienced a significant increase in relative abundance at the genus level. (3) The results of principal coordinates analysis (PCoA) and canonical correlation analysis (CCA) revealed significant differences in the Beta diversity of soil bacteria in the fire-burnt site under varying interference intensities. The Beta diversity of soil bacteria exhibited significant differences (p = 0.001), with MC, pH, TN, AN, and AK identified as significant influencing factors. (4) FAPROTAX functional prediction analyses were conducted to assess the changes in soil bacteria involved in Cellulolysis, Chemoheterotrophy, and Aerobic_Chemoheterotrophy in the fire-burnt site, with the relative abundance of bacteria involved in Chemoheterotrophy being significantly increased (p < 0.05) under different disturbance intensities. Collectively, our findings demonstrated that different disturbance intensities caused by fires significantly affected the Alpha diversity, Beta diversity, and functional abundance of soil bacterial communities in taiga forests, with MC, pH, TN, AN, and AK being identified as key influencing factors. Additionally, the presence of numerous rare species suggests their role as pioneer communities in the succession of soil bacterial communities.

Biochar's role in improving pakchoi quality and microbial community structure in rhizosphere soil.

Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes. The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq. The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application. Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.

Effects of intercropping teak with Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu on rhizosphere soil nutrients and bacterial community diversity, structure, and network.

Teak is a precious hardwood species in tropical and subtropical regions with a long growth cycle and slow economic returns. Intercropping medicinal plants is an effective method for obtaining early returns during the growth period of teak. However, currently, we lack sufficient knowledge about the impact of intercropping on the soil microenvironment, especially on rhizosphere soil bacterial communities. We selected two medicinal plants Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu, for an intercropping experiment with teak, and the non-intercropping teak forest area was used for comparison. By collecting soil rhizosphere samples and conducting 16S rDNA sequencing and property analysis, we aimed to investigate the influence of teak intercropping on soil microbial communities. The results showed that intercropping significantly improved soil nutrients contents, such as soil organic matter, soil total potassium and soil available nitrogen, and significantly altered bacterial community structure. Co-occurrence network analysis revealed that intercropping tightened the connections of the soil bacterial network and increased its complexity (by increasing the number of nodes and the proportion of positive edges). Teak intercropping with Amomum longiligulare T.L. Wu resulted in tighter network connections than teak intercropping with A. katsumadai Hayata. Changes in the soil bacterial community structure may related to environmental factors such as total potassium content and pH. These results demonstrated that the introduction of medicinal plants exerts a significant impact on the soil bacterial community of teak, fostering the enrichment of specific bacterial taxa (such as Firmicutes and Methylomirabilota), and makes the rhizosphere bacterial network denser and more complex. This study provides valuable insights for the management of teak plantations.

Effects of temperature and microbial disruption on juvenile kelp Ecklonia radiata and its associated bacterial community

Ocean warming can affect the development and physiological responses of kelps, and under future climate change scenarios, increasing seawater temperatures pose a major threat to these habitat-forming species. However, little is known about the effects of warming on epiphytic bacterial communities and how an altered microbiome may interact with temperature stress, affecting the condition and survival of kelp, particularly of the potentially more vulnerable early life stages. Here, we tested the effects of thermal stress on the growth and physiological responses of juvenile kelp Ecklonia radiata in which their epiphytic bacterial community was experimentally disrupted using antimicrobials, simulating dysbiosis. We hypothesized that, under thermal stress (23°C, simulating a extreme scenario of ocean warming in Tasmania), kelp with a disrupted bacterial community would be more strongly affected than kelp with an undisrupted microbiome or kelp under ambient temperature (14°C) but with a disrupted microbiota. Thermal stress reduced growth, increased tissue bleaching and negatively affected net photosynthesis of kelp. In addition, a substantial change in the epiphytic bacterial community structure was also found under thermal stress conditions, with an increase in the abundance of potentially pathogenic bacterial groups. However, microbial disruption did not act synergistically with thermal stress to affect kelp juveniles. These results suggest that effects of elevated temperature on juvenile kelps is not microbially-mediated and that juveniles may be less susceptible to disruptions of their microbiome.

Change of soil bacterial communities in chemically stabilized chromium contaminated soils in an accelerated aging experiment

Chemical stabilization is a common strategy to clean Cr(VI) contaminated soils. Although many studies have reported both short-term and long-term performance of chemical stabilization, there is no work addressing the impacts of long-term Cr stability on soil bacterial communities after stabilization. In this study, an accelerated aging system that synchronized simulation acid rain leaching and freeze-thaw cycles was established for the first time. We investigated the change of Cr content, environmental variables and bacterial community structure after chemical stabilization by 50-year acid rain leaching and freeze-thaw cycle simulation. Chemical stabilization effectively decreased the content of soil Cr(VI), total Cr in leachate and Cr(VI) in leachate. Different aging conditions altered soil Cr(VI), total Cr in leachate and Cr(VI) in leachate to different extents, hinting at distinct mechanisms of long-term Cr instability between acid rain leaching and freeze-thaw cycle. Cr(VI) and chemical stabilization were identified as the most influential factors affecting soil bacterial community structure, and acid rain leaching and freeze-thaw cycle exhibited considerable but distinct impacts. Our findings provided deeper insights into the long-term restoration of bacterial community in chemically stabilized Cr(VI) contaminated soil and the long-term risk assessment of contaminated soil remediation.

Effects of coffee pericarp and litter mulsching on soil microbiomes diversity and functions in a tropical coffee plantation, South China.

In recent decades, ecological cyclic cultivation models have attracted increasing attention, primarily because the decomposition of crop residues and litter enhances soil organic matter content, thereby altering the soil microenvironment and regulating the diversity and functions of soil microbial communities. However, the effects of different coffee waste mulching on the diversity of soil microbial communities and their functions are still unclear. Therefore, this study set up four kinds of covering treatments: uncovered coffee waste (C), covered coffee litter (L), covered coffee pericarp (P), and both covered coffee litter and pericarp (PL). The results showed that compared to the control, coffee pericarp mulching significantly increased the soil available potassium (SAK) content by 18.45% and alkali hydrolyzed N (SAN) content by 17.29%. Furthermore, coffee pericarp mulching significantly increased bacterial richness and diversity by 7.75 and 2.79%, respectively, while litter mulching had little effect on bacterial abundance and diversity was smaller. The pericarp mulching significantly increased the abundance of Proteus by 22.35% and the abundance of Chlamydomonas by 80.04%, but significantly decreased the abundance of Cyanobacteria by 68.38%, while the coffee litter mulching significantly increased the abundance of Chlamydomonas by 48.28%, but significantly decreased the abundance of Cyanobacteria by 73.98%. The increase in soil SAK promoted bacterial Anoxygenic_photoautotrophy, Nitrogen_respiration, Nitrate_respiration, Nitrite_respiration, and Denitrification functions. The above results indicate that the increase in available soil potassium and alkali hydrolyzed N content under coffee pericarp cover is the main reason for promoting the diversity and richness of bacterial community and promoting the changes in bacterial community structure and function. The use of coffee pericarps in coffee plantations for ecological recycling helps to improve the diversity of the soil microbial community and maintain the relative stability of the microbial community structure and function, promoting soil health conservation and the sustainable development of related industries.

Changes in bacterial community structure and root metabolites in Themeda japonica habitat under slight and strong karst rocky desertification

Microorganisms can quickly respond to vegetation succession, and plants also regulate the structure of microbial community through root exudates or by affecting soil nutrients. Themeda japonica is a dominant plant species in karst rocky desertification (KRD) regions, but it is currently unclear the role of soil bacterial communities, interact with T. japonica during the KRD process. The purpose of this study is to explore the variation of soil metal element content, soil enzyme activity, soil bacterial communities and soil environment factor/root metabolites of T. japonica, and the relationship between soil bacterial communities and root metabolites in different degrees of KRD. Our results showed that the significant changes was found in soil metal element content and soil enzyme activity from slight KRD to strong KRD. Metabolic analysis demonstrated that the strong KRD environment increased the organic acid content of T. japonica roots, decreased the amino acids and sugars content. The specific metabolic pathways of Citrate cycle (TCA cycle), carbon fixation in photosynthetic organisms, glyoxylate and dicarboxylate metabolism and pyruvate metabolism were altered to help T. japonica adapt to the harsh environment. In addition, there was significant difference in beta diversity among bulk soil, rhizosphere and root endophytic bacterial community. With the aggravation of KRD, the abundance of Proteobacteria was decreased, while the abundance of Actinobacteria was increased. KRD also enhanced positive interactions between bacterial communities, and made the inter species associations of endophytic bacteria more sensitive. Mantel analysis showed that potassium (K), magnesium (Mg), cadmium (Cd) lead (Pb) and invertase (Inv), alkaline phosphatase (Alp), catalase (Cat), and aconitic acid, alanine, fructose, glucose, L-malic acid, palmitic acid, saccharic acid and serine significantly influence bacterial communities in bulk soil and rhizosphere. These results implied that root metabolites and soil characteristics might jointly affect the bacterial community in KRD area during the process of T. japonica in adapting to different rocky desertification.

Changes in bacterial community structure and carbon metabolism in sandy soil under the long-term application of chitin-rich organic material and attapulgite

Continuous expansion of sandy soil deeply threatens crop security and has become one of the main challenges facing modern society. Chitin-rich organic material and attapulgite have been considered efficient materials to improve degraded soil based on their rich nutrient contents and unique structures. However, their potential effects on microbial community and functions in sandy soil are poorly understood. Therefore, we conducted a 4-year field experiment featuring amendment with chitin-rich organic material and attapulgite and investigated the effect of amendments on microbial community diversity, structure and function using amplicons (16S and ITS) and metagenomic sequencing. The four treatments were as follows: (1) CK: no soil amendment; (2) SA: CK + attapulgite amendment; (3) SC: CK + chitin-rich organic material; and (4) SCA: CK + chitin-rich organic material + attapulgite amendment. The results indicated that the concentrations of soil organic carbon (SOC), total nitrogen, available phosphate (AP), available potassium, and enzyme activities increased while pH decreased in the treatments with chitin-rich organic material application (SC and SCA). Microorganisms have different responses to different soil amendments. Bacteria are the main components of microorganisms and their community structure was altered under chitin-rich organic material treatments (SC and SCA). Furthermore, 14 OTUs belonging to five phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, and Patescibacteria) related to the decomposition of organic matter were enriched in SC, while 22 OTUs belonging to six phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, Patescibacteria, and Cyanobacteria) were enriched significantly in SCA, suggesting that the combination of the two amendments had the potential to further alter the bacterial community compared with a single amendment. The metagenomic analysis revealed a decrease in the relative abundance of genes involved in carbon metabolism in SCA, with soil pH, AP, enzyme activity, SOC, and bacterial community structure identified as primary influencing factors. In conclusion, we conducted a comprehensive analysis of the effects of chitin-rich organic material and attapulgite on microorganisms in sandy soil and found a robust link between soil properties, bacterial community structure, and microbial carbon metabolism function.

Decoding the influence of bacterial community structure and algicidal bacteria in a Karenia longicanalis bloom event

IntroductionHarmful algal blooms (HABs) have been increasing in frequency and expanding their ranges on coastlines worldwide in recent decades. Algicidal bacteria play a pivotal role in eliminating HABs, yet the characteristics of bacterial communities and their algicidal activity during a Karenia longicanalis bloom remain poorly understood.MethodsIn this study, we investigated bacterial communities using 16S rRNA sequencing during a K. longicanalis bloom to identify bacteria with high algicidal activity that could be isolated. Five sampling sites in Tongxin Bay, located in Lianjiang County, China, including TX1 to TX5, were selected based on the concentration of K. longicanalis cells.ResultsOur 16S rRNA sequencing results revealed that the TX4 site was enriched with genera known to contain algicidal bacteria, such as Pseudoalteromonas and Alteromonas, which are members of the Gammaproteobacteria class, while Sulfitobacter, a member of the Alphaproteobacteria class, was enriched in the TX5 site. Among the 100 cultivable bacteria isolated from the 5 sampling sites, 6 exhibited an algicidal rate of over 80%, with FDHY-MQ5, isolated from the TX4 site, exhibiting an algicidal rate of approximately 100% against Karenia mikimotoi after 48 hours of challenge with 2% (v/v) bacterial volume (OD600=4.5) concentration. Our 16S rRNA sequencing result showed FDHY-MQ5 was a member of the Pseudoalteromonas genus, and this bacterium also demonstrated high algicidal activity against Heterosigma akashiwo and Alexandrium tamarense.DiscussionOur findings shed light on the changes in bacterial community structure and the algicidal behavior of bacteria towards algae during a K. longicanalis bloom, providing a research basis for a better understanding of HAB management.

Drip irrigation shapes the soil bacterial communities and enhances jujube yield by regulating the soil moisture content and nutrient levels

In the agricultural zones of the arid Xinjiang region of China, reducing irrigation is mandatory. However, irrigation affects the composition and diversity of the soil bacterial community which is vital to crop yield. To the best of our knowledge, very little research has been conducted on the relationships among the soil bacterial community, irrigation method, and yield as well as their underlying in jujube agroecosystems. Here, we investigated the soil physicochemistry and bacterial communities in jujube fields subjected to drip irrigation (DI) and traditional flood irrigation (FI), and their associations with yield at the flowering and fruit set (FFS) and end-of-growth (EG) stages. Under DI, the jujube yield was 8712.00 ± 24.54 kg/hm2, which was 7.64% higher than that obtained under FI (8094.33 ± 43.67 kg/hm2). DI increased the relative soil bacteria community diversity by decreasing the moisture content and increasing the nutrient levels in the soil. DI also transformed the soil bacterial community so that Bacteroidota predominated at the FFS stage and the probiotics Chloroflexi and Firmicutes predominated at the EG stage. A co-occurrence network analysis showed that DI created stable complex Soil bacteria communities in jujube fields, Though Dependentiae and Deferriberota had low relative abundance, they were nonetheless key nodes in the soil bacterial community network. A neutral community model (NCM) revealed that stochastic processes drove the soil bacterial community assembly whereas DI promoted deterministic processes by regulating the soil moisture content and nutrient levels. Partial least squares path modeling (PLS-PM) disclosed that DI affected the soil bacterial community structure by decreasing the moisture content (−0.342 **) and increasing the nutrient levels (0.557 **) in the soil. The PLS-PM also demonstrated that the observed change in the soil bacterial community structure was the main reason for the increase in jujube yield (1.098 **). The present work provides insights into the mechanisms underlying the correlations between the soil bacterial community and crop yield in response to changes in the irrigation method.

Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera.

Understanding the changes in bacterial community structure in different microenvironments of Camellia oleifera is essential to better explore the benign interaction between beneficial microorganisms and plants. Using Camellia oleifera trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla (Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia) of Camellia oleifera show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria (Hymenobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Mesorhizobium, Bradyrhizobium, Bacillus, Ochrobactrum, Pantoea, Pseudomonas, etc.) with nitrogen-fixed potentials are enriched in Camellia oleifera tissue. In addition, the hub bacterial groups of Camellia oleifera are Nitrospira, Haemophilus, Staphylococcus, Ruminiclostridium, and Ochrobactrum. They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of Camellia oleifera. These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.IMPORTANCEMicroorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.