Bacterial Diversity Indices Research Articles

Response of rhizosphere microbial community of Chinese chives under different fertilization treatments.

Soil microorganisms play an irreplaceable role in agricultural production, however, an understanding of response of soil microorganisms to slow-release and common fertilizer applications is limited. In this study, different amounts of slow- release fertilizer were used to overwintering Chinese chives growing area in a plastic greenhouse to investigate the effects of on rhizosphere soil physicochemical properties and soil microbial communities (bacteria and fungi) of Chinese chives. The result displayed that application of slow-release fertilizer significantly improved soil nutrients, soil enzyme activity, and soil microbial community structure and diversity compared to conventional fertilizer application. Compared with T1 treatment, the content of total nitrogen (TN) and available phosphorus (AP), and the SU-E activity in the soil of T2 (NPK: 62.8 kg · 667 m-2) increased by 42.58%, 16.67%, and 9.70%, respectively, showing the best effects. In addition, soil bacterial diversity index and soil microbial community structure were improved as indicated by increased relative abundance of each species, such as Byssovorax, Sandaracinus, and Cellvibrio. Oppositely, the both soil fungal diversity and the number of species decreased after fertilizationthe relative abundance of Ascomycota increased in each fertilization treatment detected by ITS sequencing. Further, the relative abundance of pathogenic fungi such as Pezizomycetes, Cantharellales, and Pleosporales decreased in the T2 treatment. Principal Coordinates Analysis (PCoA) showed that both the amount of fertilizer applied and the type of fertilizer applied affected the soil microbial community structure. RDA evidenced that soil bacteria, Proteobacteria and Gemmatimonadetes, were closely correlated with soil AN, SOM, and AK. Acidobacteria were closely correlated with soil pH, TN, and AP. Ascomycota was closely correlated with soil pH and TN. In conclusion, the application of slow-release fertilizers and reduced fertilizer applicationcould improve soil physical and chemical properties as well as soil microbial community structure and diversity, contributing to sustainable soil development. The recommended fertilization rate for overwintering Chinese chives is NPK: 62.8 kg · 667 m-2.

Disentangling the role of soil bacterial diversity in phosphorus transformation in the maize rhizosphere

Here, we hypothesized that there is a positive correlation between the soil bacterial diversity and the availability of phosphorus (P) from less soluble (organic calcium phytate and Araxá rock phosphate) or soluble (triple superphosphate) source under maize cultivation in a mesocosm experiment. This hypothesis was evaluated over a gradient of soil bacterial diversity (estimated by the Shannon index) generated by the dilution-to-extinction methodology (from 10−1 to 10−9). The experiment was conducted in a greenhouse for 30 days, followed by analyses of plant characteristics (dry weight, root and shoot measurements, and leaf and root P contents) and bacterial community diversity and activity (community structure, composition, and abundance, plus enzymatic activity) in bulk and rhizospheric soils. The bacterial diversity index negatively correlated with the labile P fraction in the soil and the P content in maize. However, enrichment of P-mineralizing microorganisms (based on the abundance of the phoD gene) was detected at higher microbial dilutions (10−9). The enrichment of some bacterial groups specialized in P conversion (e.g., Chitinophagaceae) in biomass could limit P availability in the soil and the rhizosphere resulting in possible competition with plants to acquire P and convert it into biomass instead of promoting plant growth. Therefore, the reduction in bacterial diversity could result in an imbalance in microbial interactions promoted by the enrichment of specific groups compromising plant development. The results indicate that a better understanding of the microbial community associated with P cycling is critical for better use of P in sustainable agriculture.

Axillary fossaa microbial dysbiosis and its relationship with axillary osmidrosis patients

BackgroundSkin is one of the largest human bacterial reservoirs, especially the human axilla. The microbiota of the human axilla plays an important role in the creation of axillary smell. AimsTo explore the structure and composition of the axillary fossa microbiota between bromhidrosis patients and normal people, skin samples were collected from the armpits of 40 individuals, including 20 patients (10 males (aM), 10 females (aF), osmidrosis), and 20 healthy individuals (10 males (NM), 10 females (NF), control). MethodsHigh-throughput sequencing of the 16S rRNA gene was carried out on a Hiseq2500 platform with the V3+V4 regions. ResultsAccording to the bacterial Shannon diversity index and Simpson, we found that aF was significantly higher than the control but aM had no obvious distinction. Actinobacteria, Firmicutes, Proteobacteria and Deinococcus-Thermus were the dominant phyla in the four groups. Actinobacteria was distinctly higher in aM, while Firmicutes was significantly lower in aM. Furthermore, the aF displayed inverse results with aM. Corynebacterium-1 and Staphylococcus were the dominant genera in the four groups. Interestingly, Staphylococcus was the most abundant in aF, and Corynebacterium-1 was the dominant genus in aM and Corynebacterium-kroppenstedtii was significantly different in aM. Moreover, functional capacity analysis showed that genes associated with amino acid metabolism and lipid metabolism were higher in aM than in other groups, while pyruvate metabolism (carbohydrate metabolism) was obviously high in aF. ConclusionThere were clearly distinct of axillary microbiota undergoes changes between bromhidrosis patients and controls. Staphylococcus and Corynebacterium-1 in aF and aM, respectively, were detected with distinctly elevated proportions, which might be strongly related to human axilla odor.

Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes.

The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such asobesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencingwas performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations betweennormal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.

How the flow and sediment pulse influencing the distribution and functional gene composition of bacterial communities? Case study of the lower Yellow River, China

Discharge containing large amount of sediment will cause a series of ecological effects on downstream river systems. To solve the siltation problem of Yellow River and Xiaolangdi reservoirs, water and sediment regulation has been carried out since 2000. To clarify the impact of the regulation on bacterial communities in the lower Yellow River, the composition of bacterial communities and functional groups in the riverbed and suspended sediment was analyzed by high-throughput sequencing and functional annotation of prokaryotic taxa method. The results showed that the overall diversity index of the Yellow River bacterial community was 3.014–7.045, and at a medium level compared to other large rivers in China. During the water and sediment regulation, the bacterial diversity index slightly decreased compared to the previous stage, while significantly increased at the post-stage of regulation, consideringrelatively small changes in chemical factors among three stages, it was thought that the The variation of bacterial community diversity was more influenced by the fluctuations of discharge, turbulent kinetic energy and sediment concentration. The relationship between suspended and riverbed samples to environmental factors also showed differences at three stages of regulation. During the regulation, increasing discharge and high velocity caused the ammoxidation related groups, such as nitrate and nitrite ammoxidation groups, to displace nitrification, nitrate reduction, and nitrate respiration groups, hence inhibit the water purification capabilities, while at the post-stage, the functional group of most sites recovered to similar level to the pre-stage. In summary, we reveal a characteristic pattern on how the microorganism in the high sediment river respond to the severe disturbance.

Predictive value of the presence of Prevotella and the ratio of Porphyromonas gingivalis to Prevotella in saliva for esophageal squamous cell carcinoma.

BackgroundImbalance of oral salivary microbiota has been linked to the pathogenesis of a variety of systemic diseases, and oral bacterial species have been shown to be useful biomarkers for systemic diseases.This study aimed to characterize the alterations of oral microbiota in patients with esophageal squamous cell carcinoma (ESCC) and to evaluate the diagnostic performance of oral microbial biomarkers for ESCC.MethodsThe relative abundance of flora in saliva samples was analyzed by 16S rDNA sequencing, and differences in the species present in samples from ESCC patients and healthy controls (HCs) were identified by analyzing species diversity and performing LEfSe analysis. Receiver operating characteristic (ROC) curve analysis was applied to evaluate the diagnostic performance of the characteristic bacteria individually and in combination.ResultsDifferences in bacterial diversity indexes were observed for the saliva of ESCC patients versus HCs (P<0.05), but principal coordinate analysis did not detect a significant difference in the composition of oral microbiota between ESCC patients and HCs (P>0.05). LEfSe analysis showed that Leptotrichia, Porphyromonas (Pg), Streptococcus, Rothia, Lactobacillus and Peptostreptococcus were more abundant in ESCC patient saliva than in HC saliva, whereas Haemophilus, Alloprevotella (All), Prevotella_7, Prevotella (Pre), Prevotella_6, Pasteurellaceae and Pasteurellales were significantly less abundant in ESCC patient saliva (P<0.05). From ROC curve analysis, Pg could detect ESCC with an area under the ROC curve (AUC) of 0.599, sensitivity of 62.2%, and specificity of 70%, whereas the ratio of Pg/Pre had an AUC of 0.791, sensitivity of 93.3%, and specificity of 62.3%. Moreover, the combination of the Pg/Pre and Pg/All ratios showed further improved diagnostic performance for ESCC (AUC=0.826) and even good sensitivity and specificity for the diagnosis of early ESCC (68.2% and 86%, respectively; AUC=0.786).ConclusionThis study shows that Pg in saliva can be used as a characteristic marker of ESCC, and the ratios of Pg/Pre and Pg/All offered significantly improved diagnostic performance, especially for early ESCC.

The Influence of Distinct Seasons on the Succession and Diversity of Bacteria on the Anticorrosive Coatings Surfaces in a Marine Environment

Epoxy resin has been frequently used as a coating paint for anticorrosion protection because of its excellent chemical properties. However, the long-term succession of bacteria colonizing coatings surfaces in the different seasons of the year remains uncharacterized. In this work, amplicon-based 16s rDNA sequencing was used to characterize the tempol change of bacterial communities growing on the epoxy resin surfaces. The results showed that bacterial diversity indices on spring and autumn immersion samples were higher than that of the samples immersed on summer and winter samples. Proteobacteria was found to be the dominant bacteria of all different seasons and accounted for 57.9% of the total sequence. Gammaproteobacteria and Alphaproteobacteria were the dominant classes in all of the samples, whereas the most abundance bacteria at the genus level had the significant differences with a change of season. Firmicutes also displayed a distinct temporal change pattern in that it was the second abundance in the summer and autumn samples, but had a marked decrease in the other season samples. These results demonstrated that bacterial community composition underwent obvious changes over the distinct seasons of a year. This study will be helpful for the seasonal change of bacterial diversity and development of corrosion-resistant paints.

A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches.

Soil microbes act as “players” in regulating biogeochemical cycles, whereas environmental heterogeneity drives microbial community assembly patterns and is influenced by stochastic and deterministic ecological processes. Currently, the limited understanding of soil microbial community assembly patterns and interactions under temperate forest stand differences pose a challenge in studying the soil microbial involvement during the succession from coniferous to broad-leaved forests. This study investigated the changes in soil bacterial and fungal community diversity and community structure at the regional scale and identified the pathways influencing soil microbial assembly patterns and their interactions. The results showed that broad-leaved forest cover in temperate forests significantly increased soil pH, and effectively increased soil water content, total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents. Both soil bacterial and fungal alpha diversity indices were correlated with soil physicochemical properties, especially in broad-leaved forest. The bacterial and fungal community composition of coniferous forest was dominated by deterministic process (bacteria: 69.4%; fungi: 88.9%), while the bacterial community composition of broad-leaved forest was dominated by stochastic process (77.8%) and the fungal community composition was dominated by deterministic process (52.8%). Proteobacteria, Acidobacteriota, Actinobacteriota, and Verrucomicrobiota were the dominant phyla of soil bacterial communities in temperate forests. Whereas Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota were the dominant phyla of soil fungal communities in temperate forests. Most members of dominant phylum were regulated by soil physical and chemical properties. In addition, the succession from temperate coniferous forest to broad-leaved forest was conducive to maintaining the complex network of soil bacteria and fungi, and the top 20 degree of the major taxa in the network reflected the positive response of microbial interactions to the changes of soil nutrients during forest succession. This study not only shows the mechanism by which species differences in temperate forests of northern China affect soil microbial community assembly processes, but also further emphasizes the importance of the soil microbiome as a key ecosystem factor through co-occurrence network analysis.

Role of Lactiplantibacillus paraplantarum during anaerobic storage of ear-removed corn on biogas production

To optimize the volatile fatty acid production for anaerobic fermentation, the ear-removed corn was ensiled without (control) or with Lactiplantibacillus plantarum (LP), Lacticaseibacillus paracasei (LC) and L. paraplantarum (LpP). Inoculation of LpP increased acetic acid content by 40%, and decreased butyric acid content by 38% in relative to control. Moreover, inoculation of LpP decreased the bacterial alpha diversity indices, while inherent species of Lentilactobacillus buchneri and L. hilgardii dominated the anaerobic fermentation. In particular, inoculation of LpP restricted the growth of yeasts and production of propionic acid at the early stage of storage, but continuously stimulated anaerobic fermentation, resulting in a higher maximal cumulative gas emissions of methane (by about 20 %) than that of LP and LC. Therefore, inoculation of LpP during anaerobic storage was favorable to produce intermediate metabolites (acetic acid) for subsequent biogas production of ear-removed corn.

Effects of Cr6+ stress on chromium chemical speciation distribution and bacterial community structure in the Coix lacryma-jobi L. constructed wetlands

ABSTRACT In this study, micro Coix lacryma-jobi L. vertical flow constructed wetlands with 0, 10 and 30 mg/L Cr6+ (in the form of K2Cr7O2) in the water sources were constructed to study the purification efficiency of chromium-contaminated wastewater, bacterial community diversity, chromium chemical speciation distribution and other indicators. The results showed that the constructed wetlands had high purification efficiency for chromium-contaminated wastewater. The removal rate of Cr6+ reached 99.61% and 95.45% in 10 and 30 mg/L Cr6+ treatment. The bacterial diversity index was unaffected by Cr6+ treatment; however, the bacterial richness index declined dramatically as Cr6+ treatment concentration increased. The bacterial community structure was influenced by the substrates pH, moisture content, organic matter and total chromium content. The abundance of Burkholderiaceae (uncultured) and Saccharimonadales (uncultured) were positively correlated with non-residual chromium content. The results contributed to understand the effect of chromium on bacterial community structure by considering the chromium chemical speciation.

The diversity analysis and gene function prediction of intestinal bacteria in three equine species.

The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) was significantly different (P < 0.05) between the same species in the two wildlife parks, but neither the intestinal bacterial diversity index (Shannon) nor the community composition were significantly different (P > 0.05). The bacterial abundance index (Chao1) was significantly higher in MA than SP (P < 0.05) and highly significantly higher than PZ (P < 0.01); the bacterial diversity index (Shannon) was higher in MA than PZ, but there was no significant difference, but both MA and PZ were significantly higher than SP (P < 0.05). Moreover, the intestinal bacterial community composition was significantly different among the three equine species (P = 0.001). The dominant bacterial phyla for SP, MA, and PZ were Firmicutes and Bacteroidota; among them, the bacterial family with the highest relative abundance was Lachnospiraceae and the bacterial genus was Rikenellaceae_RC9_gut_group. Analysis of the metabolic gene functions of intestinal bacteria revealed that the highest relative abundance at Pathway level 2 was for global and overview maps; at Pathway level 3, the highest relative abundance was for biosynthesis of secondary metabolites. In sum, the intestinal bacterial community composition and diversity of the above three equine species differed significantly, but their metabolic gene functions were similar. Moreover, the results of this manuscript fill the gap in the study of intestinal bacterial diversity in SP, MA, and PZ. It also provides a reference for the study of the dominant bacteria in the intestinal microorganisms of these three equine species and the discovery of novel functional genes.

Effects of dietary palygorskite supplementation on the growth performance, oxidative status, immune function, intestinal barrier and cecal microbial community of broilers

The present study aimed to investigate the effects of palygorskite (PAL) as an alternative to antibiotic on the growth performance, oxidative status, immune function, intestinal barrier and cecal microbial community of broilers. A total of 360 1-day-old male Ross-308 broilers were randomly allotted to three treatments with eight replicates. Broilers in the three groups were designated as follows: basal diet (CON group), basal diet+50 mg/kg chlorotetracycline (ANT group), and basal diet+ 10 g/kg PAL (PAL group). Supplementing PAL reduced feed to gain ratio in broilers during 22 to 42 days of age (P < 0.05), with its value being similar to that of the ANT group (P > 0.05). Broilers fed a PAL-supplemented diet exerted decreased contents of interferon-γ (IFN-γ) and interleukin-1β in serum, and the same reduction was found in jejunal IFN-γ level, when compared to the CON group (P < 0.05). Moreover, compared with the CON group, broilers after PAL treatment had a lower malondialdehyde content in jejunal mucosa (P < 0.05). Supplementing PAL elevated jejunal villus height (VH) and ratio of VH to crypt depth compared with the ANT group (P < 0.05). Cecal microbiota communities among the three groups were significant different, as demonstrated by distinct clusters from partial least squares discriminant analysis, although dietary treatments had no significant effects on the bacterial richness and diversity indices (P > 0.05). At genus level, the addition of PAL increased the relative abundance of norank_f__Barnesiellaceae and decreased that of unclassified_f__Oscillospiraceae in cecal digesta compared with those in the CON group (P < 0.05); the proportion of genus norank_f__Barnesiellaceae was increased by PAL treatment when compared with the ANT group (P < 0.05). Moreover, spearman's correlations showed that the modulation of cecal microflora composition by PAL supplementation was closely correlated with the promotion of growth performance (feed to gain ratio) and intestinal health-related (contents of malondialdehyde and IFN-γ, and VH value in jejunum) variables of broilers (P < 0.05). Taken together, dietary PAL could improve the growth performance, antioxidant capacity, and immune status, as well as intestinal barrier function in broilers, which might be partially associated with the alteration of cecal microbiota. Moreover, dietary PAL may be a promising alternative to antibiotic growth promoter for broilers.

Forest gaps alter the soil bacterial community of weeping cypress plantations by modulating the understory plant diversity.

Weeping cypress is an endemic tree species that is widely planted in China, and the simple stand structure and fragile ecosystem of its plantation are common issues. Exploring the effect of different gap sizes on the soil bacterial community structure of weeping cypress plantations can provide a theoretical basis for the near-natural management of forest plantations. We, therefore, constructed three kinds of forest gaps with different sizes in weeping cypress plantations, namely, small (50–100 m2), medium (100–200 m2), and large gaps (400–667 m2), for identifying the key factors that affect soil bacterial communities following the construction of forest gaps. The results suggested that the herb layer was more sensitive than the shrub layer, while the Simpson, Shannon, and richness indices of the herb layer in plots with gaps were significantly higher than those of designated sampling plots without any gaps (CK). The presence of large gaps significantly increased the understory plant diversity and the Shannon and Simpson indices of the soil bacterial alpha diversity. There were obvious changes in the community composition of soil bacteria following the construction of forest gaps. The dominant bacterial phyla, orders, and functions were similar across the plots with different gap sizes. Of the indicator bacterial species, the abundance of the nitrogen-fixing bacteria, Lysobacter_ yangpyeongensis, and Ensifer_meliloti, was significantly different across plots with different gap sizes and accounted for a large proportion of the bacterial population of plots with medium and large gaps. The understory plant diversity was mostly related to the soil bacterial community than to other soil factors. The results of structural equation modeling indicated that the understory plant diversity was the most important environmental factor in driving the composition and diversity of bacterial communities. The construction of forest gaps significantly improved the understory plant diversity, physicochemical properties of the soil, and bacterial diversity in weeping cypress plantations, and the results of the comprehensive evaluation were in the order: large gaps > small gaps > medium gaps > CK. Our results suggested that large gaps are beneficial for the diversity of above-ground plant communities and underground soil bacterial communities.

Positive effects of maize incorporation into the traditional tobacco cropping systems on soil nutrients, microbial biomass, enzyme activities, and bacterial compositions

ABSTRACT To reduce tobacco production suggested by the Chinese government, a 12-year field experiment was established by planting other crops in a traditional tobacco growing system every 2 years. Thus, tobacco-wheat, tobacco-canola, tobacco-wheat-maize, and tobacco-canola-maize rotations were implemented to compare the changes in soil properties. Compared to the initial soil, available N, P, and K increased or changed little after 12-year cropping except for decreased available N in the tobacco-wheat rotation soil. Compared with two-crop rotations, soil organic matter, available N, microbial biomass, enzyme activities (urease, phosphatase, and dehydrogenase), and bacterial community indexes (16S rDNA sequences, operational taxonomic units (OTUs), and richness and diversity indexes) increased in the three-crop rotations. The return of voluminous maize stubble should be the important reason for the change of these soil properties. All cropping soils were dominated by five bacteria (Proteobacteria, Acidobacteria, Firmicutes, Actinobacteria, and Bacteroidetes) accounting for 53.5–62.3% of the 16S rDNA sequences. Among the top 20 predominant bacteria, 10 were commonly found in all soils and only 2–5 were unique. Therefore, maize incorporation into the traditional two-crop systems increased stubble return and improved soil properties. However, bacterial community composition was more influenced by the soil itself than cropping systems.

527 Characteristics of the gut microbiome in solid organ transplant recipients

Solid organ transplantation is the ultimate life-saving intervention in patients with end stage organ damage. However, despite revolutionary advances in transplant medicine, complications such as allograft rejection, malignancy, and disseminated infection continue be a major challenge. A growing body of evidence suggests a potential influence of microbial dysbiosis on transplant outcomes. We therefore aimed to investigate the gut microbiome of solid organ transplant recipients for comparison with healthy controls to identify possible dysbiosis. Microbial genomic data, both bacterial and fungal, was generated from fecal samples of 20 solid organ transplant recipients and 20 matched healthy controls. Analyses included testing for differences in microbial diversity measures and relatively abundant species between cohorts. The bacterial median Shannon diversity index, a measure for alpha diversity of the gut microbiome, was significantly higher in solid organ transplant samples with a median of 3.125 versus 2.449 for healthy controls (p<0.05). Additionally, principal coordinate analyses, based on Bray-Curtis distance, displayed significant differences in the bacterial and fungal microbiota composition between stool of transplant patients and healthy controls (PCo1 vs. PCo2, p<0.05). Furthermore, several alterations in abundance existed at different taxonomic levels, including a a 15-fold increased abundance of Clostridium perfringens (p<0.0001), a 3-fold increased abundance of Staph epidermidis (p<0.0001), and 2-fold increased abundance of Staph aureus (p<0.001) at the species level in transplant patients. Ultimately, we demonstrated that solid organ transplant recipients have gut microbiome dysbiosis, characterized by an increase in microbial diversity and several alterations in taxa abundance. This is in discordance with current trends in microbiome research that associate lower diversity with worse health outcomes; however, it supports the emerging role of the microbiome as a therapeutic target.

Identification of Bacterial Flora and Metabolic Function of Sediments in Different Channels of Duliujian River Basin, Tianjin

Bacterial communities are highly sensitive to environmental changes, but their metabolic functions may be convergent under similar ecological conditions. In order to test this environmental attribute of the bacterial community and verify the feasibility in using the bacterial metabolic data to divide functional units at the river basin scale, the surface sediments in three continuous spatial units of the main stream (MS), left tributary (LT), and right tributary (RT) of the Duliujian River basin were selected as the research objects. Therefore, 16S rDNA high-throughput sequencing and the PICRUSt platform were used to analyze the bacterial diversity and metabolic function of sediments in different units. The results showed that there were no significant differences for the Shannon and Simpson indices between the different river channels (P>0.05); however, the bacterial diversity indices of Chao1, ACE, Observed_species, and PD_whole_tree of LT and RT were significantly higher than those of the MS (P<0.05). Moreover, the dominant bacterial phyla were not significantly different among the different river channels. In the present study, a total of 41 metabolic pathways were predicted based on the KEGG database, among which 34 metabolic pathways such as membrane transport, amino acid metabolism, and carbohydrate metabolism were significantly different. The functional metabolic abundance was higher in MS than that in RT and LT (P<0.05); however, there was no significant difference between those of RT and LT (P>0.05). Except for exchangeable phosphorus and nitrate nitrogen, there were no significant differences in other physicochemical properties among the different river channels (P>0.05). Furthermore, pH and iron/aluminum-phosphorus were found to significantly affect the bacterial structure, and SOM and TN were found to significantly affect the bacterial metabolic function. Overall, the sediments of MS and tributaries (LT and RT) of the river were clearly divided into level-1 and level-2 groups, indicating that the metabolic abundance of the bacterial community can be used as the key indicator in the division of functional units at the river basin scale. This study provided a theoretical basis and technical support for ecological functional division and management in coastal river basins.

The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau.

Ruminal microbiota and metabolites play crucial roles in animal health and productivity. Exploring the dynamic changes and interactions between microbial community composition and metabolites is important for understanding ruminal nutrition and metabolism. Tibetan sheep (Ovis aries) are an important livestock resource on the Qinghai-Tibetan Plateau (QTP), and the effects of various dietary protein levels on ruminal microbiota and metabolites are still unknown. The aim of this study was to investigate the response of ruminal microbiota and metabolites to different levels of dietary protein in Tibetan sheep. Three diets with different protein levels (low protein 10.1%, medium protein 12.1%, and high protein 14.1%) were fed to Tibetan sheep. 16S rRNA gene sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) were used to study the profile changes in each group of ruminal microbes and metabolites, as well as the potential interaction between them. The rumen microbiota in all groups was dominated by the phyla Bacteroidetes and Firmicutes regardless of the dietary protein level. At the genus level, Prevotella_1, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-001 were dominant. Under the same forage-to-concentrate ratio condition, the difference in the dietary protein levels had no significant impact on the bacterial alpha diversity index and relative abundance of the major phyla and genera in Tibetan sheep. Rumen metabolomics analysis revealed that dietary protein levels altered the concentrations of ruminal amino acids, carbohydrates and organic acids, and significantly affected tryptophan metabolism (p < 0.05). Correlation analysis of the microbiota and metabolites revealed positive and negative regulatory mechanisms. Overall, this study provides detailed information on rumen microorganisms and ruminal metabolites under different levels of dietary protein, which could be helpful in subsequent research for regulating animal nutrition and metabolism through nutritional interventions.

Co-application of biochar and nitrogen fertilizer promotes rice performance, decreases cadmium availability, and shapes rhizosphere bacterial community in paddy soil

Cadmium (Cd) contamination in soil has posed a great threat to crop safety and yield as well as soil quality. Biochar blended with nitrogen fertilizer have been reported to be effective in remediating Cd-contaminated soil. However, the influence of co-application of biochar and nitrogen fertilizer on the Cd bioavailability, rice yield and soil microbiome remains unclear. In this study, eight different treatments including control (CK), 5% biochar (B), 2.6, 3.5, 4.4 g/pot nitrogen fertilizers (N1, N2 and N3), and co-application of biochar and nitrogen fertilizers (BN1, BN2, BN3) were performed in a pot experiment with paddy soil for observations in an entire rice cycle growth period. Results showed single N increased soil available Cd content and Cd uptake in edible part of rice, while the soil available Cd content significantly decreased by 14.8% and 7.4%–11.1% under the B, BN treatments, and the Cd content in edible part of rice was significantly reduced by 35.1% and 18.5%–26.5%, respectively. Besides, B, N and BN treatments significantly increased the yield of rice by 14.3%–86.6% compared with CK, and the highest yield was gained under BN3 treatment. Soil bacterial diversity indices (Shannon, Chao1, observed species and PD whole tree index) under N2, N3 were generally improved. Cluster analysis indicated that bacterial community structures under BN treatments differed from those of CK and single N treatments. BN treatments enhanced the abundances of key bacterial phylum such as Acidobacteria, positively associated with yield, and increased the abundance of Spirochaetes, negatively correlated to soil available Cd and Cd uptake of rice. Furthermore, the regression path analysis (RPA) revealed that pH, organic matter (OM), alkaline hydrolysis of nitrogen (AHN) and available Cd were the major properties influencing Cd content in edible part of rice. Redundancy analysis (RDA) revealed that pH and available Cd played key role in shaping soil bacterial community. Thus, BN is a feasible practice for the improvements of rice growth and remediation of Cd-polluted soil.

The Distribution Characteristics of Aerosol Bacteria in Different Types of Pig Houses

Simple SummaryMicrobial aerosols from pig houses can be released into the environment, posing a serious threat to biosafety and public health. At present, there are few studies on the structural characteristics of aerosol bacteria in piggeries at different growth stages. It is important to understand the characteristics of aerosol bacteria in pig houses to solve the problems of air pollution and disease control in pig houses at different growth stages. In this study, bacterial aerosol concentrations and bacterial communities were compared in pig houses at different growth stages in Hebei Province, China. It was found that bacterial concentrations, community richness, and diversity in the air increased with the age of pigs. There are many pathogenic bacteria in the microbial aerosols of piggery. Our study highlights the importance of more comprehensive research and analysis of microbial aerosols in pig houses. Precautions for air pollution should be instituted in pig houses, including wearing masks, rigorous disinfection, and hygiene procedures.With the development of modern pig raising technology, the increasing density of animals in pig houses leads to the accumulation of microbial aerosols in pig houses. It is an important prerequisite to grasp the characteristics of bacteria in aerosols in different pig houses to solve the problems of air pollution and disease prevention and control in different pig houses. This work investigated the effects of growth stages on bacterial aerosol concentrations and bacterial communities in pig houses. Three traditional types of closed pig houses were studied: farrowing (FAR) houses, weaning (WEA) houses, and fattening (FAT) houses. The Andersen six-stage sampler and high-volume air sampler were used to assess the concentrations and size distribution of airborne bacteria, and 16S rRNA gene sequencing was used to identify the bacterial communities. We found that the airborne bacterial concentration, community richness, and diversity index increased with pig age. We found that Acinetobacter, Erysipelothrix, Streptococcus, Moraxella, and Aerococcus in the microbial aerosols of pig houses have the potential risk of causing disease. These differences lead us to believe that disinfection strategies for pig houses should involve a situational focus on environmental aerosol composition on a case-by-case basis.

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

BackgroundOrganic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch.ResultsOrganic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils.ConclusionsThus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.