Changes In Bacterial Community Structure Research Articles

Temporal Variability in the Rhizosphere Bacterial and Fungal Community Structure in the Melon Crop Grown in a Closed Hydroponic System

Microbes can establish a pathogenetic or symbiotic relationship with plants in soil and aquatic ecosystems. Although change in bacterial and fungal community in soil and their interaction with plants have been widely studied, little is known about their community structure in hydroponic systems across plant growth stages under different nutrient treatments. This study used next-generation sequencing analysis to assess the temporal changes in melon rhizosphere bacterial and fungal community structure across six different nutrient treatments. We found significant changes in the microbial community composition (especially for bacteria) between growth stages (R = 0.25–0.63, p < 0.01) than nutrient treatments. Proteobacteria dominated the bacterial community at the phylum level across melon growth stages (59.8% ± 16.1%). The genera Chryseobacterium, Pseudomonas, and Massilia dominated the rhizosphere in the flowering and pollination stage, while Brevibacillius showed the highest relative abundance in the harvesting stage. However, the rhizosphere was dominated by uncultured fungal taxa, likely due to the application of fungicides (Ridomil MZ). Further, linear regression analysis revealed a weak influence of bacterial community structure on melon yield and quality, while fruit weight and quality moderately responded to Mg and K deficiency. Nevertheless, the relative abundance of bacterial genus Chryseobacterium in the vegetative stage showed a strong correlation with fruit weight (R2 = 0.75, p < 0.05), while genera Brevibacillus, Lysobacter, and Bosea in late growth stages strongly correlated with fruit sweetness. Overall, temporal variability in the microbial (especially bacterial) community structure exceeds the variability between nutrient treatments for the given range of nutrient gradient while having little influence on melon yield.

Continuous cropping of alfalfa (Medicago sativa L.) reduces bacterial diversity and simplifies cooccurrence networks in aeolian sandy soil

Alfalfa is a perennial herbaceous forage legume that is remarkably and negatively affected by monocropping. However, the contribution of the changes in bacterial communities to soil sickness in alfalfa have not been elucidated. Therefore, we investigated bacterial community structures in response to monocropped alfalfa along the chronosequence. Continuous cropping remarkably reduced bacterial alpha diversity and altered community structures, and soil pH, total P and available P were strongly associated with the changes of bacterial diversity and community structures. Intriguingly, 10 years of monocropped alfalfa might be a demarcation point separating soil bacterial community structures into two obvious groups that containing soil samples collected in less and more than 10 years. The relative abundances of copiotrophic bacteria of Actinobacteria and Gammaproteobacteria significantly increased with the extension of continuous cropping years, while the oligotrophic bacteria of Armatimonadetes, Chloroflexi, Firmicutes and Gemmatimonadetes showed the opposite changing patterns. Among those altered phyla, Actinobacteria, Chloroflexi, Alphaproteobacteria and Acidobacteria were the most important bacteria which contributed 50.86% of the community variations. Additionally, the relative abundances of nitrogen fixation bacteria of Bradyrhizobium and Mesorhizobium obviously increased with continuous cropping years, while the abundances of Arthrobacter, Bacillus, Burkholderiaceae and Microbacterium with potential functions of solubilizing phosphorus and potassium remarkably decreased after long-term continuous cropping. Furthermore, bacterial cooccurrence patterns were significantly influenced by continuous cropping years, with long-term monocropped alfalfa simplifying the complexity of the cooccurrence networks. These findings enhanced our understandings and provided references for forecasting how soil bacterial communities responds to monocropped alfalfa.

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake.

While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n=198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57days) and 333.8 ADD (~37days), respectively.

Aboveground vegetation and soil physicochemical properties jointly drive the shift of soil microbial community during subalpine secondary succession in southwest China

Based on long-term ecological research, microorganisms are sensitive to environmental changes in the process of ecosystem succession. However, few works have focused on the response of different groups of soil microorganisms to subalpine secondary succession and the driving forces behind the stepwise community development. To explore the changes in the microbial community structure and the driving mechanisms, we selected three replicated secondary succession gradients consisting of grass, shrub, different secondary forests (picea, pine and birch) and primary forest in a subalpine area in southwestern China. A high-throughput sequencing method was used to compare differences in the soil fungal and bacterial community structures. In combination with aboveground plant diversity and soil properties, the different mechanisms controlling the soil microbial community were revealed by the Mantel test. A two-way correlation network was also used to explore the connections among stages. The results show that the change in bacterial and fungal community structure was obvious, and these changes of bacteria were significantly correlated with soil acid phosphatase, LAP, soil moisture and aboveground vegetation communities during succession development in subalpine forests. Moreover, the fungal community was related to soil organic carbon, nitrogen, vegetation diversity, abundance and community structure. We also found that different dominant fungi play crucial roles in the succession sequence, and the relationship between soil microbes and vegetation is gradually simplified and stabilized. Our work suggests that both the relatively stable bacterial communities and the significantly changing fungal communities are notably associated with abiotic and biotic factors in secondary succession. As the ecosystem evolves, the dominant fungi obviously respond to succession and can successively establish close relationships with plants. Consequently, our results have important implications for understanding the driving mechanisms that control the soil microbial community during subalpine forest secondary succession.

Role of microbial communities in conferring resistance and resilience of soil carbon and nitrogen cycling following contrasting stresses

Soils frequently experience environmental stresses that may have transient or persistent impact on important ecosystem services, such as carbon (C) and nitrogen (N) cycling. Microbial communities underpin resistance (the ability to withstand a stress) and resilience (the ability to recover from a stress) of these functions. Whilst functional stability and resilience have been studied extensively, the link to genetic stability is missing. In this study, the resistance and resilience of C mineralization, ammonia oxidation and denitrification, their associated gene abundances (16S rRNA, bacterial amoA, nirK, nirS, nosZ-I and nosZ-II) and bacterial community structures (T-RFLP 16S rRNA) were compared in two managed soils for 28 days after stressing the soils with either a persistent (1 mg Cu soil g−1) or a transient (heat at 40 °C for 16 h) stress. The average resistance of C mineralization to Cu was 60%, which was significantly greater than the resistance of ammonia oxidation (25%) and denitrification (31%) to Cu. Similarly, the average resilience of C mineralization to Cu was 52%, which was significantly greater than the resilience of ammonia oxidation (12%) and denitrification (18%) to Cu. However, this pattern was not significant after heat stress, indicating the critical role of different stressors. Changes in total bacterial community structure rather than abundance of 16S rRNA reflected the responses of C mineralization to Cu and heat. Both Cu and heat significantly decreased functional gene abundance (amoA, nirK, nirS, nosZ-I and nosZ-II), however, a significant recovery of denitrifying gene abundance was observed after 28 days following heat. There were lack of constant relationships between functional and genetic stability, highlighting that soil physiochemical properties, the nature of the stressor, and microbial life history traits combine to confer functional resistance and resilience. Genetic responses on their own are therefore inadequate in predicating changes to soil functions following stresses.

Changes of soil bacterial community structure at the secondary successional stages in the Pinus yunnanensis forest.

Soil bacterial diversity is a key factor for the maintanence of forest ecosystem function. Soil bacterial community would change along forest succession. We analyzed the variations of soil bacterial diversity and community composition at different successional stages in the Pinus yunnanensis forest, which would help understand the mechanism underlying forest restoration. We investigated soil bacterial diversity, community composition, and effect factors at different successional stages (including coniferous forest, mixed coniferous and broadleaf forest, and evergreen broadleaf forest) using Illumina Hiseq platform. The results showed that OTUs, Chao1 index, Ace index, and Shannon index of soil bacterial community decreased with the process of secondary succession. The highest soil bacterial total OTUs, richness, and complexity appeared at early successional stage. Soil bacterial community composition varied across different stages, with the mixed coniferous and broadleaf forest showing largest variation. Proteobacteria and Acidobacteria were common dominant phyla at secondary successional stages. Actinobacteria, Chloroflexi, and Patescibacteria were dominant phyla at the early successional stage, the abundance of which decreased with successional process in the P. yunnanensis forest. Proteobacteria and WPS-2 increased with the succession. Soil pH and tree species richness were key factors in driving soil bacterial community structure. The soil bacterial diversity decreased with forest succession, while the variations of soil bacterial community composition became larger.

On-site chlorination responsible for effective disinfection of wastewater from hospital.

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

English

The microbial activity and soil enzyme activity are closely related to soil ecological functions. In this study, a flue-cured tobacco (Nicotiana tabacum) variety, K326, was planted and subjected to tillage methods of 20 cm of rotary tillage (control, RT20), 30 cm of deep tillage (DT30), 30 cm (ST30) and 40 cm (ST40) of subsoiling tillage. The expression profiling was conducted using Illumina MiSeq high-throughput sequencing, and the changes of bacterial community structure and enzyme activity in the rhizosphere soil under different tillage treatments were assessed. In the results, the DT30, ST30 and ST40 measures significantly reduced activity of catalase, increased the activities of urease, acid phosphatase and cellulose, and increased the diversity and richness of bacterial communities in the rhizosphere soil. Compared to RT20 (control), the Shannon index of DT30 treatment increased by 3.58%, the Simpson index decreased by 47.46% and the ACE and Chao1 indexes of ST40 treatment increased by 2.77 and 3.38%, respectively. At the phylum and genus levels, the dominant bacterial communities and relative abundance of the bacterial communities under different tillage treatments were significantly different. Compared with RT20, the DT30, ST30 and ST40 treatments increased the relative abundance of Gemmatimonadetes phylum by 30.93, 20.97 and 11.44% and the relative abundance of Nitrospirae phylum increased by 54.55, 22.73 and 11.36%, respectively. In addition, the relative abundances of beneficial microorganisms such as Nocardioides, Gemmatimonas, and Sphingomonas genus in DT30 and ST30, ST40 treatments were more than control (RT20) treatments. In conclusion, the different ecological niche may create by great disturbance to soil in DT and ST treatments, the selection and adaptation of different microorganisms to the ecological niche may result in great changes in microbial species composition and community structure. © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers©

Low-ammonia wastewater treatment by integration of partial nitritation and anaerobic ammonium oxidation (anammox) at 20 ℃

This study investigated a combined partial nitritation and anammox process for treating low-strength ammonia synthetic wastewater (~50 mg-NH4+-N/L) at 20 °C. The nitrifying bioreactor consisted of immobilized nitrifying bacteria in poly(vinyl alcohol) gel beads, which was operated under limited dissolved oxygen (DO) concentrations of 0.3–0.5 mg-O2/L to suppress nitrite-oxidizing bacteria (NOB) activity. The temperature in the nitrifying bioreactor decreased from 35 °C to 20 °C, and the hydraulic retention time (HRT) was shortened from 6 h to 3 h. The limited DO concentration enabled partial oxidation of ammonia to nitrite (55.8%), but an undesired nitrite oxidation rate of 31.5% was observed at 20 °C. The changes in bacterial community structure in response to the different operating conditions were observed by high-throughput 16S rRNA gene sequencing analysis. The lowered temperature resulted in a significant shift in the bacterial community structure, while the effect of HRT was negligible. Nitrosomonas ureae and Nitrospira moscoviensis played critical roles in nitrification at low DO concentrations. Interestingly, a high nitrogen-removal efficiency of 71.4% was achieved in the integrated nitrifying bioreactor and anammox at 20 °C despite incomplete NOB suppression in the nitrifying bioreactor. Denitratisoma oestradiolicum and Petrimonas sp., which are capable of nitrate reduction, were dominant in the anammox reactor, which might allow the provision of additional nitrite for the anammox reaction. The number of Candidatus Jettenia asiatica decreased in response to the lowered temperature, while the population of Candidatus Brocadia sinica increased.

Effects of Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) and Mycobacterium sp. on the degradation of PAHs and bacterial community in soil.

Phytomicrobial remediation technology of PAH-contaminated soils has drawn great attention due to its low-cost, eco-friendly, and effective characteristics, but the mechanism underlying the removal of PAHs by rhizosphere in wastewater-irrigated soil is so far not clear. To evaluate the dissipation of PAHs and the shifts of bacterial community structure under plant-microorganism symbiotic system in an agricultural soil, a rhizo-box experiment with Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) or/and inoculated Mycobacterium sp. was conducted for 60 days. The changes of bacterial community structure and the contents of PAHs were analyzed by denaturing gradient gel electrophoresis (DGGE) and high-performance liquid chromatography (HPLC), respectively. The results showed that the removal rate of PAHs in phytomicrobial combined treatment was 53.7% after 60 days. The PAH-degraders were dominated by Microbacterium sp., Sphingomonas sp., Mycobacterium sp., and Flavobacterium sp. The plant of Fire Phoenix induced the appearance of Pseudomonas sp. and TM7 phylum sp. oral clone. The highest of bacterial diversity index was observed in unrhizosphere soils (MR-), rather than that in rhizosphere soils (MR+). In combination, phytomicrobial combined treatment of Fire Phoenix and Mycobacterium strain enhanced the removal rate of PAHs and changed the structure of bacterial community and bacterial diversity. Bacterial community has great effect on PAH degradation in PAH-contaminated soil from the wastewater-irrigated site. Our study can provide support information for PAH degradation enhancement by the synergetic effect of Fire Phoenix and Mycobacterium sp.

Changes in Bacterial Community Structure and Enriched Functional Bacteria Associated With Turfgrass Monoculture.

There is increasing attention being paid to utilizing microbial communities to improve plant health while reducing management inputs. Thus, the objectives of this research were to assess changes in the rhizosphere bacterial community structure associated with long-term turfgrass monoculture and to demonstrate the feasibility of using functional bacteria as beneficial biocontrol agents. Large patch disease, caused by the fungal pathogen Rhizoctonia solani AG2-2, is a significant threat to turfgrass cultivation. Rhizosphere samples were collected from 2-, 13- and 25-year turfgrass (Zoysia japonica) monocultures. The 13-year monoculture field had a higher pathogen population density than both the 2- and 25-year monoculture fields. Analyses of the rhizosphere bacterial communities revealed that Streptomyces was dominant in the 2-year field and Burkholderia was enriched in the 25-year field. Based on the culturable rhizosphere bacteria, Streptomyces neyagawaensis J6 and Burkholderia vietnamiensis J10 were obtained from the 2- and 25-year fields, respectively. Application of S. neyagawaensis J6 and B. vietnamiensis J10 led to excellent inhibition of large patch disease as well as enhanced tolerance against drought and temperature stresses. The results showed that the selected bacteria could be developed as biocontrol and abiotic stress tolerance agents for turfgrass cultivation.

Effects of subsurface drip irrigation on alfalfa (Medicago sativa L.) growth and soil microbial community structures in arid and semi-arid areas of northern China

Water shortage is a common environmental stressor encountered by agricultural production in arid and semiarid areas of the world. Under this situation, the impacts of different irrigation methods on the forage yield, select soil physiochemical properties, and soil microbial community structures were identified after alfalfa was planted for three years in Ningxia, northern China. The experiment consisted of five irrigation methods/treatments with three replicates for each treatment, including flood irrigation (FL), sprinkler irrigation (SP), and three subsurface drip irrigation systems, with drip tapes buried at a depth of 10 cm (SSL), 20 cm (SSM) and 30 cm (SSD). The results showed that all water-conserving irrigation methods increased the soil water content compared with FL, but only SSM and SSD presented higher potential in increasing alfalfa yield by improving soil water content, pH value and available P. Moreover, compared with FL, SSM and SSD also presented greater effects in altering microbial community structures, such as the α-diversity, β-diversity, and bacterial composition at the order level, but did not significantly affect microbial taxon composition at the phylum level. Among all determined parameters, alfalfa yield was detected as the strongest factor, which simultaneously associated with the bacterial and fungal community composition, α-diversity, and β-diversity. Moreover, the abundance changes of predicted microbial functional genes revealed that improved alfalfa growth also resulted in more nutrient exhaustion and organic matter depletion in those soils under SSM and SSD treatments. In addition, the changes in bacterial community structure were more sensitive than those in the fungal community structure to soil physicochemical properties and alfalfa growth. In conclusion, the SSM and SSD treatments have great potential to improve alfalfa growth and alter soil microbial community structures in the arid and semiarid areas of northern China.

Pastureland intensification and diversification in Brazil mediate soil bacterial community structure changes and soil C accumulation

Conventional pasture management has been responsible for diffuse soil degradationin tropical pastures. However, sustainable management practices can be used to improve soil health. We tested the effect of adopting intensive and diversified pasture management systems, i.e., fertilized pasture (FP), integrated crop-livestock (ICL) and integrated livestock-forest (ILF), in comparison to conventional pasture management (CS) in Brazil. The treatments were located under contrasting climate conditions (tropical humid, tropical mesic and subtropical) and soil types (Oxisol and Ultisol). The conversion time from CS to FP, ICL and ILF ranged from 6, 3–15 and 3 years, respectively. We focus on management effects on soil chemical and biochemical properties and their interactions with the soil bacterial community structure and soil C accumulation. The results showed that pasture intensification and diversification in sites previously managed under CS, increased by 82% the soil chemical properties related to soil fertility and shifted the soil bacterial community structure. The soil biochemical properties such as microbial biomass C, geochemical P and the enzymes β-glucosidase and acid phosphatase were the most sensitive in the conversion of CS to FP, ICL and ILF. The structural equation modeling suggested that for FP, ICL and ILF there was a positive impact of soil bacterial community structure and mainly soil chemical properties on soil C accumulation. Results in the present study provided useful knowledge for the best understanding of soil-management-microbe interactions, and provide more insights into the controlling factors of soil C accumulation during management system changes in pastures sites in Brazil.

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation - A Two-Year Monitoring Field Trial.

To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

Effect of hydrological regime on the sediment bacterial diversity and community structure in Sultanpur Lake, Gurugram, Haryana

The present study focuses on the changes in sediment bacterial community structure and diversity of Sultanpur Lake due to changes in its hydrological regime. The assessment of the bacterial community structure was done by using the Next Generation Sequencing of 16S rRNA amplicon, a bacterial phylogenetic marker. Sultanpur Lake is located in Sultanpur National Park Gurugram, in the state of Haryana, India. This place harbors great plant and animal biodiversity and serves as an important feeding, roosting and breeding ground for both resident and migratory avian fauna. Increasing pollution level and scarcity of water during summer months impose a great threat to the lake. Sediment bacteria are considered as reliable recorders of nutrient cycling and active mediums of biogeochemical processes and thus were assessed in this study. Wet and dry sediment samples were taken and analyzed for their bacterial community structure and diversity. The amplicon sequencing generated 881,118 reads which corresponded to 93 known species in case of dry sediments and 8,71,102 reads corresponding to 44 species in case of wet sediments. In dry sediments the top ten phyla were Firmicutes (26%), Bacteroidetes (14%), Proteobacteria (15%), Cyanobacteria (12%), Parcubacteria (7%), Euryarcheota (6%), Actinobacteria (5%), Armatimonadetes (5%), Chloroflexi (2%) and Planctomycetes (2%). In case of wet sediments, the top ten phyla were Firmicutes (35%), Bacteroidetes (22%), Proteobacteria (22%), Actinobacteria (7%), Chloroflexi (5%) Parcubacteria (3%), Verrucomimicrobia (3%) and, Deinococcus-Thermus (3%). There was change in the community structure at species level too with Clostridium species as the most dominant species in case of wet sediments and Lactobacillus species as the predominant one in dry sediments. This study provides an insight into the changes in the bacterial communities due to changes in hydrology and how this change will affect the health of this wetland as irregular water supply is a major stressor of this wetland.

Nitrogen addition alters composition, diversity, and functioning of microbial communities in mangrove soils: An incubation experiment

Mangrove ecosystems are important for carbon storage due to their high productivity and low decomposition rates. Waterways have experienced increased nutrient loads as a result of anthropogenic activities and it is unclear how this may affect carbon and nutrient cycles in downstream mangroves that receive these nutrient-rich waters. Using a laboratory-based incubation experiment, this study aimed to assess the effects of nutrient addition on the diversity and structure of mangrove soil bacterial communities, as well as biomass and activity of the soil microbial community, under different oxygen conditions. Bacterial community diversity and composition was characterised using 16S rRNA gene sequencing and microbial activity was examined through the measurement of microbial respiration and the activities of enzymes associated with organic matter decomposition. Nitrogen addition caused clear shifts in bacterial community composition, with decreases in bacterial diversity and the abundance of sulfate-reducing bacteria. Microbial biomass also decreased with nitrogen addition under reduced oxygen incubations. Changes in bacterial community structure were accompanied by changes in the activity of some enzymes involved in carbon, nitrogen, and phosphorus cycling. Under reduced oxygen conditions, nitrogen addition resulted in a significant increase in the microbial metabolic quotient but no accompanying change in microbial respiration, which was explained by a decrease in microbial biomass. The findings of this study indicate that nitrogen loading has potential implications for microbial communities and carbon and nutrient cycling in mangrove environments that warrant further investigation under field conditions.

The key environmental influencing factors for the change of sediment bacterial community and antibiotics resistance genes in a long-term polluted lake, China.

In order to investigate the key environmental influencing factors for the change of sediment bacterial community structure (BCS) and antibiotics resistance genes (ARGs) in a long-term Quinolone antibiotics (QNs) and heavy metals (HMs) polluted lake, 16S rRNA MiSeq High-throughput Sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis methods were applied. Baiyangdian lake was subdivided into three habitats: (1) Habitat 1: greatly influenced by municipal wastewater; (2) Habitat 2: mainly impacted by aquaculture sewage and domestic wastewater; and (3) Habitat 3: with the least human activities. Through One-way ANOVA analysis, the results showed that most of QNs and HMs showed significant difference among three habitats. Both the highest richness and diversity indices of bacterial community appeared in Habitat 3. The abundance of Multidrug, Phenicol, Aminoglycoside, Teracycline, and Quinolone ARGs exhibited the highest values in Habitat 1, while the abundance of Macrolide-Lincosamide-Streptogramin (MLS), Rifamycinm, and Sulfonamide ARGs appeared the highest values in Habitat 2. The result of redundancy analysis exhibited that 68.8% and 93.8% of the change in BCS and ARGs can be explained by environmental factors, respectively. Pb (explained 37.5% (p = 0.002)) and Fleroxacin (FLE) (explained 51.3% (p = 0.026)) were the most important factors for the variation of BCS and ARGs, respectively. Therefore, the effects of antibiotics and HMs on BCS and ARGs should be simultaneously paid more attention. Furthermore, the ARGs results by PICRUSt were similar to the results by metagenomic shotgun sequencing analysis, thus the PICRUSt analysis method can be used in the future research.

Characterization of bacterial communities during persistent fog and haze events in the Qingdao coastal region

Here, we report the characteristics of bacterial communities in aerosols with different particle sizes during two persistent fog and haze events in December of 2015 and 2016 in Qingdao, China. In the early stage of pollution, the accumulation of PM2.5 led to the accumulation of microorganisms, thus increasing the bacterial richness and diversity of fine particle sizes. With the persistence and aggravation of pollution, the toxic effect was strengthened, and the bacterial richness and diversity of each particle size decreased. When the particle concentration was highest, the richness and diversity were low for each particle size. Light haze had little influence on bacterial communities. The occurrence of highly polluted humid weather and heavy haze resulted in significant changes in bacterial community diversity, composition and structure, and air pollution exerted a greater influence than particle size on bacterial community structure. During persistent fog and haze events, with the increase of pollutants, bacteria associated with each particle size may be extensively involved in aerosol chemistry, but the degree of participation varies, which requires further study.

The application of Bacillus Megaterium alters soil microbial community composition, bioavailability of soil phosphorus and potassium, and cucumber growth in the plastic shed system of North China

The long-term continuous mono-cropping and application of large amount of chemical fertilizers have led to a dramatic degradation of soil quality in the intensive vegetable production system. It is important to develop more sustainable, environmentally friendly and high-efficiency agroecosystems for vegetable production in plastic shed systems. Field experiments were performed to explore the impacts of Bacillus megaterium application on cucumber yields, the bioavailability of soil phosphorus (P) and potassium (K), properties of soil microbial communities in a plastic shed production system with cucumber mono-cropped for more than 15 years. The field trails were set up with four treatments of conventional fertilization as control (CON), conventional fertilization with Bacillus megaterium (CON + BM), conventional fertilization reduced by 10 % P and 10 % (or 5 %) K from chemical fertilizer with Bacillus megaterium (CON + BM - PK1), conventional fertilization reduced by 20 % P and 20 % (or 10 %) K from chemical fertilizer with Bacillus megaterium (CON + BM - PK2). Results illustrated that CON + BM treatment significantly increased the cucumber yields by 11.8 %–15.2 % and P and K accumulation in cucumber fruits and roots by 27.5 %–46.1 % and 17.8 %–45.1 %, respectively. The treatments of CON + BM - PK1 and CON + BM - PK2 did not decrease the yields and quality of cucumber, and the bioavailability of soil P and K compared with CON + BM. Moreover, the strain of Bacillus megaterium can efficiently colonize the soil at the early stage of inoculation and improved the richness of soil bacterial and fungal communities significantly. High-throughput sequencing identified that the application of Bacillus megaterium did not change the compositions of the predominant bacterial phyla Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, and predominant fungal phylum Ascomycota in soil, but increased the relative abundances of the beneficial bacterial genera and fungal orders and suppressed the development of pathogenic bacterial genus significantly. Principal coordinate analysis revealed that the structures of soil bacterial and fungal communities in the CON + BM treatment were dramatically separated from CON at the early stage of inoculation. Moreover, soil pH, available K (AK), total P (TP), and total K (TK) were dramatically related to the changes of soil bacterial community structure, while soil AK and TK were dramatically linked to the variations of soil fungal community structure. The findings indicated that the application of Bacillus megaterium might contribute to the development of a more sustainable production system of vegetables in plastic shed via improving the properties of soil microbial community and the bioavailability of soil P and K.

Impacts of exogenous mineral silicon on cadmium migration and transformation in the soil-rice system and on soil health

Exogenous silicon has been shown to enhance plant growth and alleviate heavy metals toxicity, but the regulation mechanism of silicon on cadmium migration and transformation in the soil-rice system is still unclear, which is worth further study. In this study, a pot experiment was carried out to explore the influence of different doses (0, 1 and 5%) of mineral silicon on soil properties, nutrient availability, rice growth, soil enzyme activities, Cd bioavailability, and uptake and accumulation of Cd in high-accumulating (H) and low-accumulating (L) rice cultivars grown in contaminated soils. Results showed that mineral-Si treatment could increase the total biomass and grain yield, with an increased rate of 17.7–27.3% and 14.7–19.1% for H; while 26.2–33.4% and 21.3–30.3% for L. Compared with non-mineral-Si treatment, the soil EX-Cd decreased by 3.9–13.3% (H) and 2.3–10.7% (L). Additionally, the Cd content in rice grain was significantly declined by 29.5–31.3% (H) and 34.9–35.2% (L). Mineral-Si enhanced urease, sucrase, and neutral phosphatase activities in both cultivars, but suppressed catalase activity in H. A selective change in bacterial community structure was observed under mineral-Si treatment, however, the bacterial community remained stable, suggesting that the mineral-Si had no adverse effect on the microbial community. The positive response of soil enzymes activities, rice growth and the overall stabilization of microbial environment for mineral-Si addition to the Cd contaminated soils indicated that mineral-Si could mitigate the risk of Cd and well maintain the soil health, proving it to be eco-friendly and low-cost amendment for soils remediation.