Shifts In Bacterial Communities Research Articles

Community adaptation to temperature explains abrupt soil bacterial community shift along a geothermal gradient on Iceland

Understanding how and why soil microbial communities respond to temperature changes is important for understanding the drivers of microbial distribution and abundance. Studying soil microbe responses to warming is often made difficult by concurrent warming effects on soil and vegetation and by a limited number of warming levels preventing the detection of non-linear effects. A unique area in Iceland, where soil temperatures have recently increased due to geothermic activity, created a stable warming gradient in both grassland (dominated by Agrostis capillaris) and forest (Picea sitchensis) vegetation. By sampling soils which had been subjected to four years of temperature elevation (ambient (MAT 5.2 °C) to +40 °C), we investigated the shape of the response of soil bacterial communities to warming, and their associated community temperature adaptation. We used 16S rRNA amplicon sequencing to profile bacterial communities, and bacterial growth-based assays (3H-Leu incorporation) to characterize community adaptation using a temperature sensitivity index (SI, log (growth at 40 °C/4 °C)). Despite highly dissimilar bacterial community composition between the grassland and forest, they adapted similarly to warming. SI was 0.6 (equivalent to a minimum temperature for growth of between −6 and −7 °C) in both control plots. Both diversity and community composition, as well as SI, showed similar threshold dynamics along the soil temperature gradient. There were no significant changes up to soil warming of 6–9 °C above ambient, beyond which all indices shifted in parallel, with SI increasing from 0.6 to 1.5. The consistency of these responses provide evidence for an important role for temperature as a direct driver of bacterial community shifts along soil temperature gradients.

Effect of fresh and aged biochar on electrogenic hydrocarbon degradation in soil microbial electrochemical remediation

The remediation of petroleum hydrocarbon-contaminated soil is a global problem. A bioelectrochemical system (BES) is an environmentally friendly technique. In BESs, microbes on the anode play central roles in electricity generation and pollutant degradation. Here, we utilized fresh and aged biochar (marked by FB and AB) as amendments to assess the spatial-temporal hydrocarbon removal, bacterial community shift and functional gene changes in the anode and cathode vicinity. After 78 days, an accumulated charge of 750 C for FB was gained, which was 12% and 98% higher than that of AB and the no-biochar control (CK), respectively. Moreover, the removal of total petroleum hydrocarbons was enhanced in the order of CK (17–26%) < AB (22–28%) < FB (24–29%) in the cathodic area, while in the anodic region, the removal was enhanced in the order CK (22–31%) < FB (24–30%) < AB (28–30%) on days 43–78. Additionally, the top six phyla were Proteobacteria, Desulfobacterota, Firmicutes, Chloroflexi, Actinobacteriota and Bacteroidota, accounting for > 92% of the total bacterial community, with a declining tendency over time. The cathode vicinity favoured Proteobacteria growth, whereas the anode region favoured Desulfobacterota and Firmicutes. Functional genes emphasized petroleum hydrocarbons as the carbon source and relationships with nitrogen, sulfur and iron compounds in soil. This study validated the aptitudes and application effects of fresh and aged biochar in BESs.

Differential modulation of the bacterial endophytic microbiota of Festuca arundinaceae (tall fescue) cultivars by the plant-growth promoting strain Streptomyces albidoflavus UYFA156

AimsThe bacterial endophyte Streptomyces albidoflavus UYFA156 was isolated from seeds of tall fescue, Festuca arundinaceae cultivar SFRO Don Tomás, promoting growth specifically in its host cultivar. Under the hypothesis that along with the growth promotion effect by UYFA156, a shift of the endophytic bacterial community occurs, we aimed to explore the effect of inoculation of this strain on the endophytic bacterial microbiota in F. arundinaceae cultivars SFRO Don Tomás and in cultivar Tacuabé, in which no growth promotion has been observed.MethodsInitially, growth inhibition of fourteen bacterial endophytes from both cultivars was tested in vitro, and then endophytic microbiota of plants and seeds were explored through high throughput sequencing of 16S rRNA.ResultsDiversity and composition in the seeds, along plant development, and in response to inoculation were examined in both cultivars, finding significant differences between them. In 7 days old uninoculated plants, endophytic bacterial diversity was lower in cultivar SFRO Don Tomás than in cv. Tacuabé. However, upon inoculation, Simpson's diversity index in the cultivar in which growth promotion was observed increased significantly, approximately two-fold in inoculated plants with respect to uninoculated plants. However, no differences were observed in cultivar Tacuabé. In addition, microbiota composition was significantly altered in plants of the cultivar SFRO Don Tomás, whereas in Tacuabé plants, changes by inoculation did not reach statistical significance.ConclusionOur results show that growth promotion by UYFA156 is accompanied by an early effect in endophytic diversity and composition and encourage further explorations in the relationship between the observed community modulation and plant growth promotion.

Effects of on- and off-year management practices on the soil organic C fractions and microbial community in a Moso bamboo (Phyllostachys edulis) forest in subtropical China.

On- and off-year management practices are usually adopted in Moso bamboo (Phyllostachys edulis) forests to achieve higher productivity. However, little is known about the effects of these management practices on soil C sequestration and microbial community structure. In the present study, soil nutrient content, organic C fractions, and bacterial and fungal communities were comparatively investigated in on- and off-year bamboo stands. The results showed that soil organic C (SOC), alkali-hydrolyzable N (AN), and available P (AP) in the on-year were significantly lower (p ≤ 0.05) than those in the off-year. Among the different soil organic C fractions, easily oxidizable organic C (EOC), microbial biomass C (MBC), Ca-bound SOC (Ca-SOC), and Fe/Al-bound SOC (Fe/Al-SOC) also had significantly higher contents in the off-year than in the on-year, with MBC and EOC decreasing by 56.3% and 24.5%, respectively, indicating that both active and passive soil organic C pools increased in the off-year. However, the alpha diversities of both soil bacteria and fungi were significantly lower in the off-year soils than in the on-year soils. The bacterial taxa Actinobacteria, Planctomycetes, WPS-2, Acidothermus, Candidatus_Solibacter, Burkholderia-Caballeronia-Paraburkholderia, and Candidatus_Xiphinematobacter were increased in off-year soils relative to on-year soils. Meanwhile, fungal taxa Ascomycota, Mortierella, Hypocrea, Cryptococcus, Clitopilus, and Ceratocystis were significantly increased in on-year soils. Soil pH, SOC, AP, MBC, EOC, and Ca-SOC were significantly correlated with bacterial and fungal communities, with soil pH being the most important driving factor for the shift in bacterial and fungal communities. Our findings showed that the studied bamboo forest possessed an inherent restorative ability in the off-year, which can reverse the soil nutrient and C depletion in the on-years and ensure soil fertility in the long term.

The Dynamic Shift of Bacterial Communities in Hybrid Anaerobic Baffled Reactor (ABR)—Aerobic Granules Process for Berberine Pharmaceutical Wastewater Treatment

Because of its anticancer, anti-inflammatory, and antibiotic properties, berberine has been used extensively in medication. The extensive production of berberine results in the generation of wastewater containing concentrated residual berberine. However, to date, limited related studies on the biological treatment of berberine wastewaters have been carried out. A lab-scale anaerobic baffled reactor (ABR)–aerobic granular sludge (AGS) process was developed for berberine removal from synthetic wastewater. The system showed effective removal of the berberine. In order to better understand the roles of the bacterial community, the ABR–aerobic granular sludge system was operated in the state with the highest BBR removal rate in this study. The bacterial community dynamics were studied using the 16S rDNA clone library. The results showed that the hybrid ABR-AGS process achieved 92.2% and 94.8% overall removals of berberine and COD, respectively. Bacterium was dominant species in ABR, while the CFB group bacteria and Betaproteobacteria were dominant species in AGS process. The uncultured bacterium clone B135, Bacillus endophyticus strain a125, uncultured bacterium mle1-42, uncultured bacterium clone OP10D15, and uncultured bacterium clone B21.29F54 in ABR, and uncultured bacterium clone F54, uncultured bacterium clone ZBAF1-105, uncultured bacterium clone SS-9, and uncultured bacterium clone B13 in AGS process were identified as functional species in the biodegradation of berberine and/or its metabolites. Both anaerobic and aerobic bacterial communities could adapt appropriately to different berberine selection pressures because the functional species’ identical functions ensured comparable pollutant removal performances. The information provided in this study may help with future research in gaining a better understanding of berberine biodegradation.

Effects of modified biochars on the shifts of short-chain fatty acid profile, iron reduction, and bacterial community in paddy soil.

Biochar is well known as an effective means for soil amendment, and modification on biochar with different methods could improve the benefits for environmental remediation. In this study, two modified biochars were generated with nitric acid (NBC) and hydrogen peroxide (OBC) pretreatment, and a control biochar was produced after washing with deionized water (WBC). The dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in rice paddy soil amended with different biochars or without adding biochar (CK) were studied during 70 days of anaerobic incubation. Compared to CK treatment, the accumulation of SCFAs was largely inhibited by the amendment of biochars. Besides, OBC and WBC increased the accumulation of Fe(II) at the initial stage of incubation. Via 16S rRNA gene sequencing, modified biochars caused significant response of bacterial community in comparison to WBC at Day 0-1, and three biochars favored bacterial α-diversity in the paddy soil at the end of the incubation. Interestingly, positive and negative correlations between NBC and several bacteria taxa (e.g. Geobacter, Fonticella and Clostridium) were observed. The study revealed that modified biochars had significant effects on the shifts of SCFAs, Fe(III) reduction and bacterial diversity, which provides fundamental information for future application of modified biochars in rice cropping ecosystem.

Arbuscular Mycorrhiza Support Plant Sulfur Supply through Organosulfur Mobilizing Bacteria in the Hypho- and Rhizosphere.

This study aimed to elucidate the role of bacteria colonising mycorrhizal hyphae in organically bound sulfur mobilisation, the dominant soil sulfur source that is not directly plant available. The effect of an intact mycorrhizal symbiosis with access to stable isotope organo-34S enriched soils encased in 35 µm mesh cores was tested in microcosms with Agrostis stolonifera and Plantago lanceolata. Hyphae and associated soil were sampled from static mesh cores with mycorrhizal ingrowth and rotating mesh cores that exclude mycorrhizal ingrowth as well as corresponding rhizosphere soil, while plant shoots were analysed for 34S uptake. Static cores increased uptake of 34S at early stages of plant growth when sulfur demand appeared to be high and harboured significantly larger populations of sulfonate mobilising bacteria. Bacterial and fungal communities were significantly different in the hyphospheres of static cores when compared to rotating cores, not associated with plant hosts. Shifts in bacterial and fungal communities occurred not only in rotated cores but also in the rhizosphere. Arylsulfatase activity was significantly higher in the rhizosphere when cores stayed static, while atsA and asfA gene diversity was distinct in the microcosms with static and rotating cores. This study demonstrated that AM symbioses can promote organo-S mobilization and plant uptake through interactions with hyphospheric bacteria, enabling AM fungal ingrowth into static cores creating a positive feedback-loop, detectable in the microbial rhizosphere communities.

Significant Shifts in Microbial Communities Associated with Scleractinian Corals in Response to Algae Overgrowth.

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral-algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.

A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem

Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.

Bacterial Community Shifts in Casing Soil Before and After the Cultivation of Oudemansiella raphanipes

Casing soil is a key step in the production of Oudemansiella raphanipes. Bacterial community in casing soil plays key roles in the growth and development of edible fungi. However, a knowledge gap remains regarding the bacterial community shifts in casing soil before and after the cultivation of O. raphanipes (CSBACO). Casing soil samples before and after the cultivation of O. raphanipes (CSBC and CSAC) were collected and examined by high-throughput 16S rRNA gene sequencing technology. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were dominant phyla in casing soil of O. raphanipes, which accounted for 77.32% of the total abundance. After the cultivation of O. raphanipes, the alpha diversity of bacterial community and the relative abundance of some beneficial genera such as Marmoricola, Nocardioides, Sphingomonas, and Streptomyces decreased, while that of bacteria belonging to the candidate class MB-A2-108 tolerant to adverse environment significantly increased. Meanwhile, physicochemical properties of casing soil changed significantly in CSBACO. Soil ammonium nitrogen and organic matter greatly decreased in CSAC and they mainly influenced bacterial community before the cultivation of O. raphanipes. In contrast, available potassium and pH significantly increased in CSAC and mainly affected bacterial community after the cultivation of O. raphanipes. Furthermore, the relative abundance of bacteria with the function of amino acid and lipid metabolism decreased, while that of bacteria functions related to parasites and pathogens increased, which further revealed the significance of bacterial community in casing soil. Diversity, composition, and the potential function of bacterial community shifted dramatically in CSBACO. The results deepen the understanding of the bacterial community and its microecological mechanism in casing soil of O. raphanipes.

Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier.

We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.

Shifts in bacterial communities in the rumen, vagina, and uterus of beef heifers receiving different levels of concentrate.

This experiment investigated the effects of diet composition on rumen, vaginal, and uterine microbiota of beef heifers. Fifteen rumen-cannulated, pubertal Angus-influenced heifers were used in a replicated 3 × 3 Latin square design (28-d periods and 21-d washout intervals). Dietary treatments included diets based on (as-fed) 100% grass hay (HF), 60% grass hay + 40% corn-based concentrate (INT), or 25% grass hay + 75% corn-based concentrate (HG). Treatments were offered individually to heifers once daily at 2% body weight. Rumen, vaginal, and uterine samples were collected on days 0 and 28 of each period. Data were analyzed using orthogonal contrasts (linear and quadratic), using results from day 0 as independent covariates and heifer as the experimental unit. Ruminal pH on day 28 decreased linearly (P < 0.01) as concentrate inclusion increased. Uterine and vaginal pH on day 28 were not affected by treatments (P ≥ 0.35). Within the rumen samples, Bacteriodetes was the most abundant phylum and its relative abundance linearly decreased (P ≤ 0.01) with the inclusion of concentrate. Prevotella was the most abundant genus within the rumen but was not affected by treatments (P ≥ 0.44). Genera with relative abundance ≥1% (average across treatments) in the rumen that were impacted by treatments (P ≤ 0.01) included Bacteroides, Pedobacter, Dysgonomonas, Caloramator, and Ruminococcus. Firmicutes was the most abundant phylum in the vagina and uterus, but it was unaffected by treatments (P ≥ 0.16). Prevotella was the most abundant genus in the vagina, and its relative abundance increased (P < 0.01) with the inclusion of concentrate. Other genera with relative abundance ≥1% that were significantly affected (P ≤ 0.05) by treatments were Clostridium, Pedobacter, Roseburia, Oscillospira, Faecalibacterium, Caloramator, Paludibacter, Rhodothermus, and Porphyromonas. In uterine samples, Prevotella was the most abundant genus but was unaffected by treatments (P ≥ 0.29). Genera with relative abundance ≥1% in the uterus that were significantly affected (P < 0.01) by treatments were Caloramator, Paludibacter, and Thalassospira. Collectively, inclusion of concentrate in the diet altered the bacterial composition within the rumen as well as shifting bacterial populations within the vagina and uterus. Research is warranted to further understand the impacts of these diet-induced microbiota changes on reproductive function and performance of beef heifers.

Bacterial community shifts in a di-(2-ethylhexyl) phthalate-degrading enriched consortium and the isolation and characterization of degraders predicted through network analyses

Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used and toxic phthalate plasticizer that is widely reported in marine environments. Degradation of DEHP by bacteria from several environments have been studied, but little is known about marine sediment bacteria that can degrade DEHP and other phthalate plasticizers. Therefore, in this study, we enriched a bacterial consortium C10 that can degrade four phthalate plasticizers of varying alkyl chain lengths (DEHP, dibutyl phthalate, diethyl phthalate, and dimethyl phthalate) from marine sediment. The major bacterial genera in C10 during degradation of the phthalate plasticizers were Glutamicibacter, Ochrobactrum, Pseudomonas, Bacillus, Stenotrophomonas, and Methylophaga. Growth of C10 on DEHP intermediates (mono-ethylhexyl phthalate, 2-ethylhexanol, phthalic acid, and protocatechuic acid) was studied and these intermediates enhanced the Brevibacterium, Ochrobactrum, Achromobacter, Bacillus, Sporosarcina, and Microbacterium populations. Using a network-based approach, we predicted that Bacillus, Stenotrophomonas, and Microbacterium interacted cooperatively and were the main degraders of phthalate plasticizers. Through selective isolation techniques, we obtained twenty isolates belonging to Bacillus, Microbacterium, Sporosarcina, Micrococcus, Ochrobactrum, Stenotrophomonas, Alcaligenes, and Cytobacillus. The best DEHP-degraders were Stenotrophomonas acidaminiphila OR13, Microbacterium esteraromaticum OR16, Sporosarcina sp. OR19, and Cytobacillus firmus OR20 (83.68%, 59.1%, 43.4%, and 40.6% degradation of 100 mg/L DEHP in 8 d), which agrees with the prediction of key degraders. This is the first report of DEHP degradation by all four bacteria and, thus, our findings reveal as yet unknown PAE-degradation capabilities of marine sediment bacteria. This study provides insights into how bacterial communities adapt to degrade or resist the toxicities of different PAEs and demonstrates a simple approach for the prediction and isolation of potential pollutant degraders from complex and dynamic bacterial communities.

Long-term cultivation alter soil bacterial community in a forest-grassland transition zone.

Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.

Shifts in uterine bacterial communities associated with endogenous progesterone and 17β-estradiol concentrations in beef cattle

The relation between circulating concentrations of progesterone and 17β-estradiol prior to insemination play a key role in optimizing fertility in cattle. This study aimed to determine the impact of endogenous progesterone (P4) and estradiol (E2) concentrations on uterine bacterial community abundance and diversity in beef cattle. Angus-influenced heifers were subjected to an industry standard estrous synchronization protocol. Uterine flushes were collected on d -2 (endogenous P4) and d 0 (endogenous E2) and used for targeting the V4 hypervariable region of 16S rRNA bacterial gene. Plasma was collected on d -2 and 0 for quantification of P4 and E2 concentrations by radioimmunoassay, respectively. Heifers were allotted to one of the following groups: High P4 + High E2 (H-H; n = 11), High P4 + Low E2 (H-L; n = 9), Low P4 + High E2 (L-H; n = 9), Low P4 + Low E2 (L-L; n = 11). Results indicated that Shannon's diversity index tended to be greater for H-L heifers compared to L-H heifers on d 0 (P = 0.10). For H-L heifers from d -2 to d 0, the relative abundance of Actinobacteria decreased and Tenericutes increased (P < 0.01). Within phylum Actinobacteria, the relative abundance of Corynebacterium decreased from d -2 to d 0 in treatment groups H-H, H-L, and L-L (P < 0.05); however, did not differ by d for L-H heifers. Within phylum Tenericutes, the relative abundance of Ureaplasma increased from d -2 to d 0 for H-L heifers (P = 0.01). Additionally for H-L heifers, the relative abundance of Bacteroidetes tended to increase from day -2 to on d 0 (P = 0.07). For H-L heifers, uterine pH increased from day -2 to d 0 (P = 0.05). These results suggest that differing endogenous concentrations of P4 and E2 may be associated with shifts in uterine microbiota and pH, and this could ultimately impact fertility outcomes in beef cattle.

Management‐induced shifts in rhizosphere bacterial communities contribute to the control of pathogen causing citrus greening disease

AbstractIntroductionCitrus greening (aka Huanglongbing, HLB) caused primarily by the bacterial pathogen Candidatus Liberibacter asiaticus (CLas) has devastating effects on the global citrus industry. Agricultural management‐induced changes in microbial communities are hypothesised to contribute toward HLB resistance by reducing pathogen titre and increasing root and soil health. However, we have a limited understanding of the impacts of management practices on the soil microbiome, making the extent of HLB management uncertain.Material and MethodsHere we investigated the effect of agricultural management practices on reducing CLas titer via changes in rhizosphere‐associated bacterial communities. Rhizosphere and root samples were collected from two sites in Florida where different management practices (e.g., metalized reflective mulch ground covers, compost application and microbial inoculations) are currently being implemented to prevent HLB. Management‐induced changes in the rhizosphere bacterial community were assessed using amplicon sequencing. qPCR assays were used to quantify the titer of the pathogen CLas in roots. In addition, we measured soil properties and the activities of microbial enzymes involved in soil nutrient cycling.ResultsOur results indicated that certain management practices lead to shifts in the community structure of rhizosphere bacterial communities that negatively interact with the HLB pathogen. Management practices improved soil quality and reduced CLas titer. Additionally, we found that Actinobacteria were frequently enriched in the successful treatment sites, suggesting that Actinobacteria taxa could be indicators for HLB suppression properties in the soil.ConclusionOur results suggest that microbiome manipulation, either through changes in the management practices or microbial amendment, can increase the suppressive potential of soils, resulting in the reduction in CLas titer and potentially leading to HLB suppression in citrus groves.

Tobacco straw biochar improved the growth of Chinese cherry (Prunus pseudocerasus) via altering plant physiology and shifting the rhizosphere bacterial community

Tobacco straws are byproducts during cigarette manufacturing, which have drawn attention for how to dispose them not at the cost of environment. Processing them into biochar might turn waste into wealth given their potentials for soil amelioration and crop growth promotion. However, the effects of biochar application are variable which severely limits their application. The aim of this study was to reveal the effect of tobacco straw biochar (TBC) on growth of Chinese cherry and the underlying mechanism. In present work, the response of Chinese cherry ‘Manaohong’ (Prunus pseudocerasus Lindl.), an economically valuable cultivar in Guizhou Province, to TBC was investigated using a six-month pot experiment. The TBC facilitated photosynthesis and uptake of nitrogen, phosphorus, potassium and manganese, and further promoted the plant growth. In addition, accumulation of endogenous phytohormones was affected. Higher level of indoleacetic acid, gibberellin A3, zeatin and lower level of abscisic acid were observed in TBC. In combination with high-throughput sequencing, the activation of indoleacetic acid and inactivation of abscisic acid signal transductions were detected at gene level, which further backed up the assumption that phytohormone signaling was affected by TBC addition. Moreover, according to our proposed pathway, majority genes for flavonoid biosynthesis were upregulated indicating that flavonoids were highly synthesized in roots in response to TBC, which reshaped the rhizosphere bacterial community by allowing growth-promoting bacteria to burgeon and suggested labile organic carbon fraction was the powerful factor for rhizosphere bacterial community shift. The results of our study partially explain the underlying mechanism of biochar-mediated growth promotion and provide crucial information for application of biochar on plants with high economic value.

Microbial mechanism of zinc fertilizer input on rice grain yield and zinc content of polished rice.

Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha–1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34–19.52%) and enriched the Zn content of polished rice (1.40–20.05%). Specifically, redundancy analysis (RDA) and Mantel’s test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil–microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Tomato microbiome under long-term organic and conventional farming.

The compartment niche is the main reason behind the shifts in endophytic bacterial communities. Long-term organic greenhouse exerted limited influence on the variations of endophytic bacterial communities. Organic greenhouse and root had more complex co-occurrence networks than conventional greenhouse and stem, respectively. Cultivable method results found that Protecbacteria, Bacteriodes, and Actinobacteria are the dominant phyla in the endophytes.

Hormetic effect of 17α-ethynylestradiol on activated sludge microbial community response.

Synthetic estrogen analogues are among the most potent estrogenic contaminants in effluents from wastewater treatment plants. Although its effects have been well elucidated in the feminization of male fish and interference with the endocrine systems in humans, it has not been fully explored in the activated sludge (AS) microbiome, particularly EE2 (17α-ethynylestradiol). Therefore, in this study, the bacterial community shift in a 6-day laboratory-scale reactor in environmental (0, 5, 10, and 100 ng/L) and predictive elevated concentrations (5, 10, and 100 mg/L) of EE2 was investigated using culture-based and metagenomics approaches. Results showed significant changes (t-test, all p < 0.05) between initial and final physicochemical parameters (pH, DO, and EC). Although environmental concentrations showed a slight decrease in microbial counts (5.6 × 106 to 4.6 × 106 CFU/ml) after a 24-h incubation for the culturable approach, the predictive elevated concentrations (5 to 100 mg/L) revealed a drastic microbial counts reduction (5.6 × 106 to 8 × 102 CFU/ml). The metagenomic data analysis uncovered that bacterial communities in the control sample were dominated by Proteobacteria, followed by Bacteroidetes and Firmicutes. The taxonomic classification after exposure of microbial communities in various concentrations revealed significant differences in community composition between environmental concentration (Shannon indices between 2.58 to 3.68) and predictive elevated concentrations (Shannon indices between 2.24 and 2.84; t-test, all p < 0.05). The EE2 enriched seven OTUs were Novosphingobium, Cloacibacterium, Stenotrophomonas, Enterobacteriaceae_unclassified, Stenotrophomonas, Enterobacteriaceae_unclassified and Rhodobacteraceae_unclassified. These results were supported by a dehydrogenase activity (DHA) test, which demonstrated less (about 40%) DHA in predictive elevated concentrations than in environmental concentrations. Notwithstanding, these findings suggest that EE2 may possess potent hormetic effect as evidenced by promotion of microbiome richness and dehydrogenase activity of AS in lower EE2 doses.