scholarly journals Characteristics and Driving Factors of Rhizosphere Bacterial Communities of Chinese Fir Provenances

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1362
Author(s):  
Yao Yan ◽  
Bingjun Li ◽  
Zhijun Huang ◽  
Hui Zhang ◽  
Xiaojian Wu ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Geographic Location ◽  
Soil Nutrient ◽  
Nutrient Content ◽  
Chinese Fir ◽  
Driving Factors ◽  
Stoichiometric Ratio ◽  
Sequencing Analysis ◽  
Α Diversity

Rhizosphere bacteria affect the diversity of soil functions, playing important roles in the growth and expansion of Chinese fir. Understanding the driving factors of rhizosphere bacterial distribution is imperative when comparing bacterial diversity and composition under different Chinese fir provenances. We investigated the growth of Chinese fir belts and the effects of climate, geographic location, and soil nutrients. Using 16S rDNA next-generation sequencing analysis, the bacterial communities of 16 Chinese fir provenances were compared. The bacterial compositionsof Dechang, Junlian, Shangrao, Zhenxiong, Yangxin, Xinyang, Luotian, and Tianmushan provenances weredistinct from others. Generally, higher-latitude provenances showed more biomarkers (LDA = 2). Rhizosphere bacterial α-diversity was the highest in Hunan Youxian and lowest in Henan Xinyang (p < 0.05). From south to north, bacterial α-diversity initially increased and then decreased. From east to west in the middle belt, bacterial α-diversity followed a “W” trend, with the eastern middle belt having the highest values, especially near Hunan, Fujian, and Zhejiang provinces. Amongst environmental factors, soil nutrient content (Mg, P and K) and stoichiometric ratio (Ca/Mg, K/Ca and N/P), along with precipitationrate primarily controlled rhizosphere bacterial diversity. Soil pH had a significant impact on the relative abundance of rhizosphere soil bacteria. Our findings offer insight into the evolution of Chinese fir and provide a scientific basis for soil microbial community improvement of Chinese fir provenances.

scholarly journals Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1338
Author(s):  
Susanna Gorrasi ◽  
Andrea Franzetti ◽  
Roberto Ambrosini ◽  
Francesca Pittino ◽  
Marcella Pasqualetti ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Generalized Linear Models ◽  
Bacterial Communities ◽  
Linear Models ◽  
Salinity Gradient ◽  
Sampling Site ◽  
Α Diversity ◽  
Spatio Temporal ◽  
Abundance Variation ◽  
Microbiological Aspects

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

scholarly journals Bacterial diversity and predicted enzymatic function in a multipurpose surface water system – from wastewater effluent discharges to drinking water production

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Ananda Tiwari ◽  
Anna-Maria Hokajärvi ◽  
Jorge Santo Domingo ◽  
Michael Elk ◽  
Balamuralikrishna Jayaprakash ◽  
...  
Keyword(s):  
Drinking Water ◽  
Surface Water ◽  
Bacterial Community ◽  
Human Health ◽  
Bacterial Diversity ◽  
Water Samples ◽  
Bacterial Communities ◽  
Treatment Process ◽  
Pollution Sources ◽  
Production Well

Abstract Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics —from the source of contamination, through the watershed to the DW production process—may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemäenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <  0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 ± 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 ± 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66–80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (≥13%) than in other groups (≤3%). Acidobacteria was more abundant in the DW treatment process (≥13%) than in others (≤2%). In total, the share of PHRB reads was higher in sewage and surface water than in the DW treatment samples. The seasonal effect in bacterial communities was observed only on surface water samples, with the lowest diversity during summer. Conclusions The low bacterial diversity and absence of PHRB read in the DW samples indicate AGR can produce biologically stable and microbiologically safe drinking water. Furthermore, the significantly different bacterial communities at the pollution sources compared to surface water and DW samples highlight the importance of effective wastewater treatment for protecting the environment and human health.

scholarly journals Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sandeep Kumar ◽  
M. Ajmal Khan ◽  
Emma Beijer ◽  
Jinxin Liu ◽  
Katherine K. Lowe ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Body Weight ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Serum Protein ◽  
Bacterial Communities ◽  
Short Chain Fatty Acids ◽  
Short Chain ◽  
Milk Replacer ◽  
Protein Levels

Abstract Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance. Results Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life. Conclusions Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning.

The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Hang Qian ◽  
Chunli Hou ◽  
Hao Liao ◽  
Li Wang ◽  
Shun Han ◽  
...  
Keyword(s):  
Soil Properties ◽  
Paddy Soil ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Negative Relationship ◽  
Sequencing Analysis ◽  
Nitrogen Use ◽  
Microbial Network ◽  
Α Diversity ◽  
Positive Effect

ABSTRACT To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.

scholarly journals No Evidence of an Impact on the Rhizosphere Diazotroph Community by the Expression of Bacillus thuringiensis Cry1Ab Toxin by Bt White Spruce

2007 ◽  
Vol 73 (20) ◽  
pp. 6577-6583 ◽  
Author(s):  
Josyanne Lamarche ◽  
Richard C. Hamelin
Keyword(s):  
Bacillus Thuringiensis ◽  
Bacterial Communities ◽  
White Spruce ◽  
Sequencing Analysis ◽  
Nitrogen Fixing ◽  
Cloning And Sequencing ◽  
Insecticidal Toxin ◽  
Soil Bacterial Communities ◽  
Cry1ab Toxin ◽  
Natural Stands

ABSTRACT Nitrogen fixation is one of the most important roles played by soil bacterial communities, as fixation supplies nitrogen to many ecosystems which are often N limited. As impacts on this functional group of bacteria might harm the ecosystem's health and reduce productivity, monitoring that particular group is important. Recently, a field trial with Bt white spruce, which constitutively expresses the Cry1Ab insecticidal toxin of Bacillus thuringiensis, was established. The Bt white spruce was shown to be resistant to spruce budworm. We investigated the possible impact of these genetically modified trees on soil nitrogen-fixing bacterial communities. The trial consisted of untransformed controls, GUS white spruce (transformed with the β-glucuronidase gene), and Bt/GUS white spruce (which constitutively expresses both the Cry1Ab toxin and β-glucuronidase) in a random design. Four years after planting, soil samples from the control and the two treatments from plantation as well as from two natural stands of white spruce were collected. Diazotroph diversity was assessed by extracting soil genomic DNA and amplifying a region of the nitrogenase reductase (nifH) gene, followed by cloning and sequencing. Analysis revealed that nitrogen-fixing communities did not differ significantly among the untransformed control, GUS white spruce, and Bt/GUS white spruce. Nevertheless, differences in diazotroph diversity were observed between white spruce trees from the plantation site and those from two natural stands, one of which grew only a few meters away from the plantation. We therefore conclude, in the absence of evidence that the presence of the B. thuringiensis cry1Ab gene had an effect on diazotroph communities, that either site and/or field preparation prior to planting seems to be more important in determining diazotroph community structure than the presence of Bt white spruce.

scholarly journals Estimation of Soil Nutrient Content Using Hyperspectral Data

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1129
Author(s):  
Yiping Peng ◽  
Lu Wang ◽  
Li Zhao ◽  
Zhenhua Liu ◽  
Chenjie Lin ◽  
...  
Keyword(s):  
Least Squares ◽  
Soil Nutrients ◽  
Cross Validation ◽  
Regional Scale ◽  
Soil Nutrient ◽  
Nutrient Content ◽  
New Method ◽  
Accurate Estimation ◽  
Support Vector ◽  
Soil Nutrient Content

Soil nutrients play a vital role in plant growth and thus the rapid acquisition of soil nutrient content is of great significance for agricultural sustainable development. Hyperspectral remote-sensing techniques allow for the quick monitoring of soil nutrients. However, at present, obtaining accurate estimates proves to be difficult due to the weak spectral features of soil nutrients and the low accuracy of soil nutrient estimation models. This study proposed a new method to improve soil nutrient estimation. Firstly, for obtaining characteristic variables, we employed partial least squares regression (PLSR) fit degree to select an optimal screening algorithm from three algorithms (Pearson correlation coefficient, PCC; least absolute shrinkage and selection operator, LASSO; and gradient boosting decision tree, GBDT). Secondly, linear (multi-linear regression, MLR; ridge regression, RR) and nonlinear (support vector machine, SVM; and back propagation neural network with genetic algorithm optimization, GABP) algorithms with 10-fold cross-validation were implemented to determine the most accurate model for estimating soil total nitrogen (TN), total phosphorus (TP), and total potassium (TK) contents. Finally, the new method was used to map the soil TK content at a regional scale using the soil component spectral variables retrieved by the fully constrained least squares (FCLS) method based on an image from the HuanJing-1A Hyperspectral Imager (HJ-1A HSI) of the Conghua District of Guangzhou, China. The results identified the GBDT-GABP was observed as the most accurate estimation method of soil TN ( of 0.69, the root mean square error of cross-validation (RMSECV) of 0.35 g kg−1 and ratio of performance to interquartile range (RPIQ) of 2.03) and TP ( of 0.73, RMSECV of 0.30 g kg−1 and RPIQ = 2.10), and the LASSO-GABP proved to be optimal for soil TK estimations ( of 0.82, RMSECV of 3.39 g kg−1 and RPIQ = 3.57). Additionally, the highly accurate LASSO-GABP-estimated soil TK (R2 = 0.79) reveals the feasibility of the LASSO-GABP method to retrieve soil TK content at the regional scale.

scholarly journals Seasonal variation in AMF colonisation, soil and plant nutrient content in gypsum specialist and generalist species growing in P-poor soils

2021 ◽  
Author(s):  
Andreu Cera ◽  
Estephania Duplat ◽  
Gabriel Montserrat-Martí ◽  
Antonio Gómez-Bolea ◽  
Susana Rodríguez-Echeverría ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Nutrient Availability ◽  
Soil Nutrient ◽  
Nutrient Status ◽  
Nutrient Content ◽  
P Availability ◽  
Plant Nutrient ◽  
Rhizospheric Soil ◽  
Soil Nutrient Availability ◽  
Generalist Species

Abstract Aims Gypsum soils are P-limited atypical soils that harbour a rich endemic flora. These singular soils are usually found in drylands, where plant activity and soil nutrient availability are seasonal. No previous studies have analysed the seasonality of P nutrition and its interaction with the arbuscular mycorrhiza fungi (AMF) colonisation in gypsum plants. Our aim was to evaluate the seasonal changes in plant nutrient status, AMF colonisation and rhizospheric soil nutrient availability in gypsum specialist and generalist species. Methods We evaluated seasonal variation in the proportion of root length colonised by AMF structures (hyphae, vesicules and arbuscules), plant nutrient status (leaf C, N and P and fine root C and N) and rhizospheric soil content (P, organic matter, nitrate and ammonium) of three gypsum specialists and two generalists throughout a year. Results All species showed arbuscules within roots, including species of Caryophyllaceae and Brassicaceae. Root colonisation by arbuscules (AC) was higher in spring than in other seasons, when plants showed high leaf P-requirements. Higher AC was decoupled from inorganic N and P availability in rhizospheric soil, and foliar nutrient content. Generalists showed higher AC than specialists, but only in spring. Conclusions Seasonality was found in AMF colonisation, rhizospheric soil content and plant nutrient status. The mutualism between plants and AMF was highest in spring, when P-requirements are higher for plants, especially in generalists. However, AMF decoupled from plant demands in autumn, when nutrient availability increases in rhizospheric soil.

scholarly journals Effect of Fertilizers on Nutrient Content and Uptake of Aromatic Local Transplant Aman Rice Varieties in Acid Soil

2020 ◽  
pp. 35-48
Author(s):  
Kamrun Nahar Mousomi ◽  
Mohammad Noor Hossain Miah ◽  
Md. Abul Kashem ◽  
Imtiaz Miah
Keyword(s):  
Nutrient Uptake ◽  
Acid Soil ◽  
Block Design ◽  
Soil Nutrient ◽  
Nutrient Status ◽  
Nutrient Content ◽  
Control Treatment ◽  
Aromatic Rice ◽  
Rice Varieties ◽  
Nutrient Analyses

A pot experiment was conducted at the experimental net house of the Department of Soil Science, Sylhet Agricultural University, Sylhet, Bangladesh to observe the effect of fertilizers on yield and nutrient uptake of local aromatic rice varieties during the Aman season of 2015. The experiment was laid out in a Randomized Complete Block Design with three replications. Five local aromatic rice varieties (Kalizira: V1, Muktasail: V2, Nagrasail: V3, Maloti: V4 and Chinigura: V5) and four packages of fertilizers (F1:  Recommended package i.e. 45-10-20-10-0.5 kg ha-1 of N-P-K-S-Zn, F2: 2/3rd of recommended package, F3: 1/3rd of recommended package, and F4: Control) were used. Urea, TSP, MoP, gypsum and ZnSO4 were used as N, P, K, S and Zn source, respectively. According to the treatment, all fertilizers were applied as basal during final pot preparation while urea was applied in two equal splits (one half as basal and another half at 40 DAT). Nutrient content and uptake of the aromatic rice varieties were significantly affected by the application of different fertilizer packages (with few exceptions). Mostly Kalizira (1.10-0.44-2.31-0.67-13.75 g pot-1 of N-P-K-S-Zn) and/or Nagrasail (1.15-0.46-2.70-0.62-11.74 g pot-1 of N-P-K-S-Zn) varieties showed the highest nutrient uptake in grain and straw with recommended package of fertilizers. While in maximum cases Chinigura (0.41-0.16-0.76-0.197-3.17 g pot-1 of N-P-K-S-Zn) was observed to have the lowest with control treatment. In case of post harvest soil nutrient analyses, Kalizira and/or Chinigura variety associated with recommended package of fertilizers showed the highest nutrient status.

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