scholarly journals Chemical Properties and Bacterial Community Reaction to Acidified Cattle Slurry Fertilization in Soil from Maize Cultivation

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 601
Author(s):  
Paweł Stanisław Wierzchowski ◽  
Jakub Dobrzyński ◽  
Kamila Mazur ◽  
Marek Kierończyk ◽  
Witold Jan Wardal ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Organic Fertilizer ◽  
Chemical Properties ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Gaseous Ammonia ◽  
Short Term ◽  
Class Level ◽  
Maize Cultivation

Acidified slurry is a novel organic fertilizer that limits gaseous ammonia emissions and reduces nitrogen losses. Our research aimed to determine the effects of short-term fertilization with acidified slurry on the chemical properties and bacterial community of soil used for maize cultivation. In the months after spreading, raw slurry fertilization had a significant impact on the increase in values of N-NO3. In contrast, soil fertilized with acidified slurry had lower N-NO3 values when compared to raw slurry fertilization treatments. Bacterial sequencing using Illumina MiSeq showed no differences in the genetic diversity of bacterial communities. In all tested soil samples, dominants at the phylum level were Actinobacteria, Proteobacteria, and Acidobacteria, while dominants at the class level were Actinobacteria, Alphaproteobacteria, Thermoleophilia, Gammaproteobacteria, and Acidimicrobiia. The values of biodiversity indices (Shannon index, Simpson index) in tested samples were similar. Our results suggest that short-term fertilization with acidified slurry does not adversely affect the biodiversity and structure of the bacterial communities and has a slight impact on soil chemical properties.

scholarly journals 408 Effect of monensin intake during a stocker phase and subsequent finishing phase on rumen bacterial diversity of beef steers

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 163-164
Author(s):  
Caleb P Weiss ◽  
Paul A Beck ◽  
John T Richeson ◽  
Dexter J Tomczak ◽  
Jianmin Chai ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pennisetum Glaucum ◽  
Rumen Fluid ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Beef Steers ◽  
Diet Change ◽  
Gluten Feed

Abstract Three monensin levels during a stocker phase (0, 800, 1600 g/ton fed in a free choice mineral) and two levels during finishing [0 (U) or 37.5 mg/kg diet DM (M)] were used to determine the effects of monensin supplementation during a stocker and subsequent finishing phase on rumen bacterial communities of beef steers. Thirty calves were fed pearl millet (Pennisetum glaucum) hay with soybean hull and corn gluten feed supplement (0.5% BW daily, AF basis) or grazed fall wheat pasture (Triticum aestivum) during a stocker phase and then transported 1,067 km to Canyon, TX, for finishing. Rumen fluid was collected on d 0, 28, and the end of the stocker phase (d 85). Samples were also obtained at feedlot d 0, 14, 28, 56, and immediately prior to a diet change to include a beta-adrenergic agonist and before shipping for harvest. Rumen microbiota were characterized by next generation sequencing the 16S v4 hypervariable region with the Illumina MiSeq platform. During the stocker phase, Prevotella and Bacteroidetes were the most dominant genus regardless of diet or treatment. Monensin decreased (P ≤ 0.01) alpha diversity (Shannon Index) for cattle consuming hay on d 28 of the stocker phase. In the feedlot, Prevotella, Lachnospiraceae, and Bacteroidetes were the most abundant genus. Steers that were previously on the 0 and 1600 treatments during the stocker phase and were fed monensin at the feedlot had decreased alpha diversity (P = 0.04) on feedlot d 14 compared to those that did not. Monensin at the feedlot tended to increase alpha diversity on d 28 for cattle previously on the 1600 treatment (P = 0.06), and on d 56 for cattle previously on the 0 treatment (P = 0.06). This experiment provides a better understanding of the effect of monensin on rumen bacterial communities throughout production.

scholarly journals The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

Gut ◽  
2016 ◽  
Vol 67 (2) ◽  
pp. 216-225 ◽  
Author(s):  
Christian Schulz ◽  
Kerstin Schütte ◽  
Nadine Koch ◽  
Ramiro Vilchez-Vargas ◽  
Melissa L Wos-Oxley ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Gi Tract ◽  
Upper Gi ◽  
Miseq Platform ◽  
H Pylori ◽  
Bacterial Assemblages ◽  
First Time ◽  
Upper Gi Tract

ObjectivePatients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.DesignSaliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1–V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.ResultsOverall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.ConclusionsThe detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.

scholarly journals Silicon application and related changes in soil bacterial community dynamics reduced ginseng black spot incidence in Panax ginseng in a short-term study

2019 ◽  
Author(s):  
Meijia Li ◽  
Qiuxia Wang ◽  
Zhengbo Liu ◽  
Xiaoxi Pan ◽  
Yayu Zhang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Panax Ginseng ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Bacterial Flora ◽  
Black Spot ◽  
Rrna Gene ◽  
Short Term ◽  
Physical And Chemical

Abstract Background This study analyzed the effect of silicon (Si) application on the occurrence of ginseng black spot caused by Alternaria panax . We explored the differences in soil physical and chemical factors and microbial community structure following Si application as well as the key factors that affected the occurrence of ginseng black spot in soil. Potted Panax ginseng plants were used to assess the effect of Si treatment on ginseng black spot. Soil physical and chemical properties were comprehensively analyzed. Bacterial communities were analyzed using Illumina HiSeq sequencing targeting the 16S rRNA gene. Results After inoculation with A. panax , the morbidity (and morbidity index) of ginseng with and without Si was 52% (46) and 83% (77), respectively. Soil physical and chemical analysis showed that under the ginseng black spot inoculation, bacterial communities were mainly affected by pH and available potassium, followed by ammonium nitrogen and available Si. NMDS and PLS-DA analyses and the heat maps of relative abundance revealed that Si application elevated the resistance of ginseng black spot as regulated by the abundance and diversity of bacterial flora in rhizosphere soils. Heatmap analysis at the genus level revealed that A. panax + Si inoculations significantly increased the soil community abundance of Sandaracinus , Polycyclovorans , Hirschia , Haliangium , Nitrospira , Saccharothrix , Aeromicrobium , Luteimonas , and Rubellimicrobium and led to a bacterial community structure with relative abundances that were significantly similar to that of untreated soil. Conclusions Short-term Si application also significantly regulated the structural impact on soil microorganisms caused by ginseng black spot. Our findings indicated that Si applications may possibly be used in the prevention and treatment of ginseng black spot.

scholarly journals The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6147 ◽  
Author(s):  
Shu-Hong Wu ◽  
Bing-Hong Huang ◽  
Jian Gao ◽  
Siqi Wang ◽  
Pei-Chun Liao
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Chemical Properties ◽  
Soil Chemical Properties ◽  
Soil Microbiome ◽  
Apparent Lack ◽  
Soil P ◽  
Soil Bacterial Communities ◽  
Abundant Otus ◽  
Soil Bacterial

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

scholarly journals Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9612
Author(s):  
Tong Jia ◽  
Tingyan Guo ◽  
Baofeng Chai
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Imperata Cylindrica ◽  
Copper Tailings ◽  
Α Diversity ◽  
Degraded Ecosystems ◽  
And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

scholarly journals Effect of formaldehyde exposure on bacterial communities in simulating indoor environments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jianguo Guo ◽  
Yi Xiong ◽  
Taisheng Kang ◽  
Hua Zhu ◽  
Qiwen Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Human Health ◽  
Bacterial Communities ◽  
Shannon Index ◽  
Chemical Degradation ◽  
Indoor Environments ◽  
Operational Taxonomic Units ◽  
Formaldehyde Exposure ◽  
Recommended Level

AbstractIndoor formaldehyde (CH2O) exceeding the recommended level is a severe threat to human health. Few studies have investigated its effect on indoor surface bacterial communities, affecting habitants' health. This study used 20-L glass containers to mimic the indoor environment with bacterial inputs from human oral respiration. The behavior of bacterial communities responding to CH2O varied among the different CH2O levels. The bacterial community structure significantly changed over time in the 0.054 mg·m−3 CH2O group, which varied from the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. The Chao1 and Shannon index significantly increased in the 0.054 mg·m−3 CH2O group at 6 week, while they remained unchanged in the 0.25 mg·m−3 CH2O group. At 12 week, the Chao1 significantly increased in the 0.25 mg·m−3 CH2O group, while it remained unchanged in the 0.054 mg·m−3 CH2O group. Only a few Operational Taxonomic Units (OTUs) significantly correlated with the CH2O concentration. CH2O-induced OTUs mainly belong to the Proteobacteria and Firmicutes. Furthermore, bacterial communities formed at 6 or 12 weeks differed significantly among different CH2O levels. Functional analysis of bacterial communities showed that inferred genes related to chemical degradation and diseases were the highest in the 0.25 mg·m−3 CH2O group at 12 weeks. The development of nematodes fed with bacteria collected at 12 weeks was applied to evaluate the bacterial community's hazards. This showed significantly impaired growth in the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. These findings confirmed that CH2O concentration and exposure time could affect the indoor bacterial community and formed bacterial communities with a possibly more significant hazard to human health after long-term exposure to high CH2O levels.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

scholarly journals Bacteria diversity and microbial biomass in forest, pasture and fallow soils in the southwestern Amazon basin

2009 ◽  
Vol 33 (4) ◽  
pp. 907-916 ◽  
Author(s):  
Karina Cenciani ◽  
Marcio Rodrigues Lambais ◽  
Carlos Clemente Cerri ◽  
Lucas Carvalho Basílio de Azevedo ◽  
Brigitte Josefine Feigl
Keyword(s):  
Microbial Biomass ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Amazon Basin ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Chemical Properties ◽  
Total Carbon ◽  
Wet Season ◽  
Al Content ◽  
C And N

It is well-known that Amazon tropical forest soils contain high microbial biodiversity. However, anthropogenic actions of slash and burn, mainly for pasture establishment, induce profound changes in the well-balanced biogeochemical cycles. After a few years the grass yield usually declines, the pasture is abandoned and is transformed into a secondary vegetation called "capoeira" or fallow. The aim of this study was to examine how the clearing of Amazon rainforest for pasture affects: (1) the diversity of the Bacteria domain evaluated by Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE), (2) microbial biomass and some soil chemical properties (pH, moisture, P, K, Ca, Mg, Al, H + Al, and BS), and (3) the influence of environmental variables on the genetic structure of bacterial community. In the pasture soil, total carbon (C) was between 30 to 42 % higher than in the fallow, and almost 47 % higher than in the forest soil over a year. The same pattern was observed for N. Microbial biomass in the pasture was about 38 and 26 % higher than at fallow and forest sites, respectively, in the rainy season. DGGE profiling revealed a lower number of bands per area in the dry season, but differences in the structure of bacterial communities among sites were better defined than in the wet season. The bacterial DNA fingerprints in the forest were stronger related to Al content and the Cmic:Ctot and Nmic:Ntot ratios. For pasture and fallow sites, the structure of the Bacteria domain was more associated with pH, sum of bases, moisture, total C and N and the microbial biomass. In general microbial biomass in the soils was influenced by total C and N, which were associated with the Bacteria domain, since the bacterial community is a component and active fraction of the microbial biomass. Results show that the genetic composition of bacterial communities in Amazonian soils changed along the sequence forest-pasture-fallow.

scholarly journals Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

Solid Earth ◽  
2017 ◽  
Vol 8 (5) ◽  
pp. 1119-1129 ◽  
Author(s):  
Chengyou Cao ◽  
Ying Zhang ◽  
Wei Qian ◽  
Caiping Liang ◽  
Congmin Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Land Use Changes ◽  
Chemical Properties ◽  
Soil Bacterial Communities ◽  
Land Use Types ◽  
Soil Bacterial ◽  
Physical And Chemical ◽  
And Chemical Properties

Abstract. The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

scholarly journals Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

SOIL ◽  
2016 ◽  
Vol 2 (3) ◽  
pp. 459-474 ◽  
Author(s):  
Michael P. Ricketts ◽  
Rachel S. Poretsky ◽  
Jeffrey M. Welker ◽  
Miquel A. Gonzalez-Meler
Keyword(s):  
Climate Change ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Chemical Properties ◽  
Winter Precipitation ◽  
Snow Accumulation ◽  
Soil Microbial ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Abstract. Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow  ∼ 100 % and intermediate snow  ∼ 50 % increased snowpack relative to the control, and low snow ∼ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

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