scholarly journals Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8047 ◽  
Author(s):  
Weike Li ◽  
Xiaodong Liu ◽  
Shukui Niu
Keyword(s):  
Community Structure ◽  
Soil Ph ◽  
Soil Layer ◽  
Illumina Miseq ◽  
Research Area ◽  
Shannon Index ◽  
Fire Disturbance ◽  
Pinus Tabulaeformis ◽  
Soil Layers ◽  
Cellulose Decomposition

Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.

scholarly journals Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

2021 ◽  
Vol 12 ◽  
Author(s):  
Beat Frey ◽  
Lorenz Walthert ◽  
Carla Perez-Mon ◽  
Beat Stierli ◽  
Roger Köchli ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Vertical Distribution ◽  
Soil Depth ◽  
Shannon Index ◽  
Fungal Communities ◽  
Soil Microbiome ◽  
Deep Soil ◽  
Soil Layers ◽  
The Vertical Distribution

Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.

scholarly journals Effects of Grazing Intensity on Soil Nematode Community Structure and Function in Different Soil Layers in a Meadow Steppe

2021 ◽  
Author(s):  
Fengjuan Pan ◽  
Ruirui Yan ◽  
Jinling Zhao ◽  
Linghao Li ◽  
Yanfeng Hu ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Layer ◽  
Nematode Community ◽  
Soil Nematode ◽  
Soil Nematodes ◽  
Meadow Steppe ◽  
Soil Layers ◽  
Soil Nematode Community ◽  
Nematode Diversity ◽  
Grazing Intensities

Abstract Aims Grazing is a key driver of plant communities and soil functions in grassland ecosystems. Soil nematodes play a vital role in soil ecological functions. however, few studies have explored how grazing shapes soil nematode community in different soil layers.Methods we investigated the composition, abundance, diversity, metabolic footprint, and food web metrics of soil nematodes over a gradient of grazing in the 0-10 cm and 10-20 cm soil layers in a meadow steppe. The relationships between nematode community structure and biotic and abiotic factors were analyzed by principal component analysis (PCA) and structural equation model (SEM) analysis. Results Light grazing tended to increase the abundance of soil nematodes. Intensive grazing decreased the biomass carbon and metabolic footprints of plant parasites, fungivores, and total soil nematodes in 0-10 cm soils. There was no difference in the biomass carbon and metabolic footprints of soil nematodes among different grazing intensities in the 10-20 cm soil layer. Soil moisture, aboveground biomass, belowground biomass and Shannon diversity of grass contributed more to changes in soil nematode composition in both soil layers. In the 0-10 cm soil layer, grazing directly and indirectly affected soil nematode diversity via soil moisture and aboveground biomass, while grazing directly affected soil nematode diversity in 10-20 cm soil layer. Conclusions Our results indicate that soil depth can weaken the effect of grazing intensities on soil nematode fauna. Grazing affected the soil nematode community structure via different paths in different soil layers.

scholarly journals Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Toke Bang-Andreasen ◽  
Mette Peltre ◽  
Lea Ellegaard-Jensen ◽  
Lars Hestbjerg Hansen ◽  
Morten Ingerslev ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Ph ◽  
Abiotic Factors ◽  
Soil Column ◽  
Wood Ash ◽  
Exchangeable Cations ◽  
Small Scale ◽  
Prokaryotic Community ◽  
Soil Layers ◽  
Vertical Gradients

AbstractWood ash is alkaline and contains base-cations. Application of wood ash to forests therefore counteracts soil acidification and recycle nutrients removed during harvest. Wood ash application to soil leads to strong vertical gradients in physicochemical parameters. Consequently, we designed an experimental system where small-scale vertical changes in soil properties and prokaryotic community structure could be followed after wood ash application. A mixed fly and bottom ash was applied in dosages of 3 and 9 t ha−1 to the surface of soil mesocosms, simulating a typical coniferous podzol. Soil pH, exchangeable cations and 16S prokaryotic community was subsequently assessed at small depth intervals to 5 cm depth at regular intervals for one year. Wood ash significantly changed the prokaryotic community in the top of the soil column. Also, the largest increases in pH and concentrations of exchangeable cations was found here. The relative abundance of prokaryotic groups directionally changed, suggesting that wood ash favors copiotrophic prokaryotes at the expense of oligotrophic and acidophilic taxa. The effect of wood ash were negligible both in terms of pH- and biological changes in lower soil layers. Consequently, by micro-vertical profiling we showed that wood ash causes a steep gradient of abiotic factors driving biotic changes but only in the top-most soil layers.

scholarly journals Modelling community structure and temporal spreading on complex networks

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Vesa Kuikka
Keyword(s):  
Community Structure ◽  
Complex Networks ◽  
Community Detection ◽  
Network Structure ◽  
Network Connectivity ◽  
Network Models ◽  
Building Blocks ◽  
Detection Algorithm ◽  
Research Area ◽  
Detection Methods

AbstractWe present methods for analysing hierarchical and overlapping community structure and spreading phenomena on complex networks. Different models can be developed for describing static connectivity or dynamical processes on a network topology. In this study, classical network connectivity and influence spreading models are used as examples for network models. Analysis of results is based on a probability matrix describing interactions between all pairs of nodes in the network. One popular research area has been detecting communities and their structure in complex networks. The community detection method of this study is based on optimising a quality function calculated from the probability matrix. The same method is proposed for detecting underlying groups of nodes that are building blocks of different sub-communities in the network structure. We present different quantitative measures for comparing and ranking solutions of the community detection algorithm. These measures describe properties of sub-communities: strength of a community, probability of formation and robustness of composition. The main contribution of this study is proposing a common methodology for analysing network structure and dynamics on complex networks. We illustrate the community detection methods with two small network topologies. In the case of network spreading models, time development of spreading in the network can be studied. Two different temporal spreading distributions demonstrate the methods with three real-world social networks of different sizes. The Poisson distribution describes a random response time and the e-mail forwarding distribution describes a process of receiving and forwarding messages.

scholarly journals PSVI-22 Rumen microbiome of beef cattle is modulated by backgrounding systems

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 220-220
Author(s):  
Bobwealth O Omontese ◽  
Ashok K Sharma ◽  
Jason Langlie ◽  
Joe Armstrong ◽  
Alfredo DiCostanzo ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Developmental Stages ◽  
Production Systems ◽  
Rumen Fluid ◽  
Illumina Miseq ◽  
High Energy ◽  
Shannon Index ◽  
Bacterial Gene ◽  
Beef Calves ◽  
Rumen Microbiome

Abstract Backgrounding (BKG) segment in beef production systems is characterized by utilization of different forages which affect growth performance and carcass characteristics. However, it is unclear how BKG systems impact rumen microbiome. We investigated rumen microbiome dynamics of beef calves under different BKG systems. At weaning, Angus and Angus x Simmental beef calves (n = 38) were stratified by age, weight, and sex in a completely randomized design into 1 of 3 BKG treatments for 55 d: 1) perennial pasture (PP; quackgrass, orchardgrass; smooth bromegrass, red clover, and alfalfa); 2) summer annual cover crop (CC; cereal oats, purple top turnips, hunter forage brassica, and graza forage radish); and 3) dry lot (DL; haylage, corn, and DDGS). After BKG, all calves were assigned to a high energy ration in a feedlot. Rumen sample was collected via esophageal tubing at weaning, BKG and feedlot. A total of 190 rumen fluid samples were used to sequence the hypervariable V4 region of the 16S rRNA bacterial gene on an Illumina MiSeq platform. The results showed that BKG systems largely influenced rumen bacterial communities. Specifically, microbiome composition and diversity were not different at weaning, diverged significantly during BKG (Shannon index, Bray Curtis distance metrics; P < 0.001) and homogenized during feedlot. During the BKG segment, the bacterial genera Agrobacterium, Coprococcus, and Ruminococcus were dominant in CC whereas Fibrobacteraceae and Mycoplasmataceae was most dominant in DL. Moreover, rumen microbiome patterns of CC and DL calves showed increased plasticity in early stages of development but not during feedlot with PP showing fewer changes over time. These results indicate that BKG systems significantly modulate the rumen microbiome of beef cattle and, underscore the importance of early developmental stages as potential targets for feeding interventions that can impact the animal microbiome to enhance animal performance.

Soil acidity in 1970 and 1989 in a coniferous forest in southwest Finland

1998 ◽  
Vol 78 (3) ◽  
pp. 477-479 ◽  
Author(s):  
C. J. Westman ◽  
S. Jauhiainen
Keyword(s):  
Key Words ◽  
Soil Ph ◽  
Soil Acidity ◽  
Mineral Soil ◽  
Coniferous Forest ◽  
Soil Layers ◽  
Water Suspension ◽  
Ph Values ◽  
Humus Layer ◽  
Repeated Sampling

Forest soil pH in southwest Finland was measured with identical sampling and analysing methods in 1970 and 1989. The acidity of the organic humus layer increased significantly as pH values measured on water and on salt suspensions decreased between the two sampling dates. For the mineral soil layers, no unambiguous trend was found. pH values measured on salt suspension tended to be unchanged or lower, while pH on water suspension in some soil layers were even higher in 1989 than in 1970. Key words: pH, repeated sampling

scholarly journals Depth-Dependent C-N-P Stocks and Stoichiometry in Ultisols Resulting from Conversion of Secondary Forests to Plantations and Driving Forces

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1300
Author(s):  
Xiaogang Ding ◽  
Xiaochuan Li ◽  
Ye Qi ◽  
Zhengyong Zhao ◽  
Dongxiao Sun ◽  
...  
Keyword(s):  
Soil Depth ◽  
Soil Layer ◽  
Pinus Elliottii ◽  
Slash Pine ◽  
Pine Plantations ◽  
Secondary Forests ◽  
Masson Pine ◽  
Soil Layers ◽  
Soil C ◽  
Significant Difference

Stocks and stoichiometry of carbon (C), nitrogen (N), and phosphorus (P) in ultisols are not well documented for converted forests. In this study, Ultisols were sampled in 175 plots from one type of secondary forest and four plantations of Masson pine (Pinus massoniana Lamb.), Slash pine (Pinus elliottii Engelm.), Eucalypt (Eucalyptus obliqua L’Hér.), and Litchi (Litchi chinensis Sonn., 1782) in Yunfu, Guangdong province, South China. Five layers of soil were sampled with a distance of 20 cm between two adjacent layers up to a depth of 100 cm. We did not find interactive effects between forest type and soil layer depth on soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) concentrations and storages. Storage of SOC was not different between secondary forests and Eucalypt plantations, but SOC of these two forest types were lower than that in Litchi, Masson pine, and Slash pine plantations. Soil C:P was higher in Slash pine plantations than in secondary forests. Soil CNP showed a decreasing trend with the increase of soil depth. Soil TP did not show any significant difference among soil layers. Soil bulk density had a negative contribution to soil C and P stocks, and longitude and elevation were positive drivers for soil C, N, and P stocks. Overall, Litchi plantations are the only type of plantation that obtained enhanced C storage in 0–100 cm soils and diverse N concentrations among soil layers during the conversion from secondary forests to plantations over ultisols.

scholarly journals Dark gray podzolized soils of the Chyzhykiv ridge: problems of degradation and protection

2019 ◽  
Vol 53 ◽  
pp. 85-96
Author(s):  
Volodymyr Haskevych ◽  
Nadiya Lemeha ◽  
Anastasiya Vishchur
Keyword(s):  
Soil Aggregates ◽  
Humus Content ◽  
Soil Layer ◽  
Research Area ◽  
Soil Protection ◽  
Anthropogenic Pressure ◽  
Degradation Processes ◽  
Erosion Processes ◽  
General Physical ◽  
Very High

The results of the research of degradation of dark gray podzolized soils (Luvis Greyzemic Phaeozems) of the Chyzhykiv ridge are presented. The causes and consequences of this dangerous natural and anthropogenic phenomenon are analyzed. It has been established that the intensive agricultural use of soils caused the activation of water erosion processes, the development of physical degradation processes, which lead to soil compaction, deterioration of their general physical properties, and loss of humus. Degradation processes lead to a decrease in soil fertility and unprofitability of agriculture, worsen the ecological state of the environment. In the study of degradation processes and their consequences in dark gray podzolized soils, the following methods were used: comparative-geographical, comparative-profile, catena method, analytical, statistical. Soil field explorations were carried out after the growing season. The most dangerous among the degradation processes are erosion degradation, which leads to a decrease in the capacity of the soil profile and deterioration of the soil agrophysical properties. The results of the studies demonstrated that the capacity of the profile of poorly eroded soils decreased on average by 14.5 cm compared to the standard, in medium-eroded – by 28.3 cm, in highly-eroded – by 50.8 cm. Soils underwent erosion from low to very high (crisis) degree. Degradation processes of anthropogenic genesis caused a deterioration of the structural and aggregate state of the soils, which is manifested in a decrease in the content of agronomically valuable soil aggregates and the dominance of the sloping fraction. According to the research results, the content of agronomically valuable aggregates with a size of 10–0.25 mm in the arable soil layer is 18.65–33.86 %, which indicates a high and very high (crisis) level of degradation. Soils also undergo degradation due to re-compaction, which is manifested in an increase in the density of the structure and a decrease in the overall porosity of the soil. Long anthropogenic pressure on soils and erosion degradation processes have led to a decrease in humus content. In particular, in poorly eroded soils the humus content is 2.03 %, in medium-eroded soils – 1.45 %, in highly eroded – 1.06 %, which is 16.9–64.6 % less than the standard. Measures are proposed to minimize the degradation of the dark gray podzolized soils of the Chyzhykiv ridge, which consist in the application of anti-erosion measures and soil-protective methods of soil processing, conservation of heavily degraded lands. The introduction of basic and crisis monitoring of the state of soils in the research area is recommended. Key words: the Chyzhykiv ridge, dark gray podzolized soils, erosion, degradation, soil protection.

scholarly journals Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato 

2020 ◽  
Author(s):  
Zhiyuan Gao ◽  
Yaya Hu ◽  
Meikun Han ◽  
Junjie Xu ◽  
Xue Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Sweet Potatoes ◽  
Potato Varieties ◽  
Soil Bacterial Community Structure

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, cause certain economic losses. Bacteria of Rhizospheric soil are the richest and are associated with obstacles to continuous cropping. However, few studies on how continuous sweet potato cropping affects the rhizospheric soil bacterial community structure. In the study, Illumina Miseq method was used to explore rhizosphere soil bacterial community structure changes with different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, to provide theoretical guidance for prevention and treatment of sweet potatoes continuous cropping obstacles. Results: After continuous cropping two years, the results showed that (1) the dominant bacterial phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. The relative abundance of rhizospheric soil bacteria of two sweet potato varieties changed significantly. (2) The richness and diversity indexes of bacteria in Xushu18 rhizospheric soil were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis result indicated that soil pH was correlated significantly with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively associated with Planctomycetes and Acidobacteria, but negatively associated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping, the bacterial community structure and physicochemical properties of sweet potato rhizospheric soil were unbalanced, and the changes from different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for developing new microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

scholarly journals Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato

2020 ◽  
Author(s):  
Zhiyuan Gao ◽  
Yaya Hu ◽  
Meikun Han ◽  
Junjie Xu ◽  
Xue Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Potato Industry ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Potato Varieties

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, restrict the sustainable development of sweet potato industry. Bacteria are the most abundant in rhizospheric soil and have a certain relationship with continuous cropping obstacles. However, there are few reports on how continuous cropping affected the bacterial community structure in the rhizospheric soil of sweet potato. In this study, high-throughput sequencing technique was used to explore the changes of rhizospheric soil bacterial community structure of different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, so as to provide a theoretical basis for the prevention and control of sweet potato continuous cropping obstacles.Results: After two years of continuous cropping, the results showed that (1) the dominant bacteria phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. Significant changes in the relative abundance of rhizospheric soil bacteria were observed for two sweet potato varieties. (2) Bacterial richness and diversity indexes of rhizospheric soil from Xushu18 were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis showed that soil pH was significantly correlated with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively correlated with Planctomycetes and Acidobacteria, and negatively correlated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping of sweet potato, the bacterial community structure and physicochemical properties in the rhizospheric soil were unbalanced, and the changes of different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for the development of special microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

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