scholarly journals Soil Microbial Biomass and Community Composition Relates to Poplar Genotypes and Environmental Conditions

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 262 ◽  
Author(s):  
Leszek Karliński ◽  
Sabine Ravnskov ◽  
Maria Rudawska
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Depth ◽  
Abiotic Factors ◽  
Soil Conditions ◽  
Main Role ◽  
Site Factors ◽  
Host Genotype ◽  
The Impact

Poplars, known for their diversity, are trees that can develop symbiotic relationships with several groups of microorganisms. The genetic diversity of poplars and different abiotic factors influence the properties of the soil and may shape microbial communities. Our study aimed to analyse the impact of poplar genotype on the biomass and community composition of the microbiome of four poplar genotypes grown under different soil conditions and soil depths. Of the three study sites, established in the mid-1990s, one was near a copper smelter, whereas the two others were situated in unpolluted regions, but were differentiated according to the physicochemical traits of the soil. The whole-cell fatty acid analysis was used to determine the biomass and proportions of gram-positive, gram-negative and actinobacteria, arbuscular fungi (AMF), other soil fungi, and protozoa in the whole microbial community in the soil. The results showed that the biomass of microorganisms and their contributions to the community of organisms in the soil close to poplar roots were determined by both factors: the tree-host genotype and the soil environment. However, each group of microorganisms was influenced by these factors to a different degree. In general, the site effect played the main role in shaping the microbial biomass (excluding actinobacteria), whereas tree genotype determined the proportions of the fungal and bacterial groups in the microbial communities and the proportion of AMF in the fungal community. Bacterial biomass was influenced more by site factors, whereas fungal biomass more by tree genotype. With increasing soil depth, a decrease in the biomass of all microorganisms was observed; however, the proportions of the different microorganisms within the soil profile were the result of interactions between the host genotype and soil conditions. Despite the predominant impact of soil conditions, our results showed the important role of poplar genotype in shaping microorganism communities in the soil.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

scholarly journals Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2954
Author(s):  
Luiz Leonardo Saldanha ◽  
Pierre-Marie Allard ◽  
Adlin Afzan ◽  
Fernanda Pereira de Souza Rosa de Melo ◽  
Laurence Marcourt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native Species ◽  
Abiotic Factors ◽  
Soil Nutrient ◽  
Brazilian Savanna ◽  
Soil Conditions ◽  
Native Plant ◽  
Specialized Metabolism ◽  
Temperature Radiation ◽  
The Impact

Environmental conditions influence specialized plant metabolism. However, many studies aiming to understand these modulations have been conducted with model plants and/or under controlled conditions, thus not reflecting the complex interaction between plants and environment. To fully grasp these interactions, we investigated the specialized metabolism and genetic diversity of a native plant in its natural environment. We chose Myrcia bella due to its medicinal interest and occurrence in Brazilian savanna regions with diverse climate and soil conditions. An LC-HRMS-based metabolomics approach was applied to analyze 271 samples harvested across seven regions during the dry and rainy season. Genetic diversity was assessed in a subset of 40 samples using amplified fragment length polymorphism. Meteorological factors including rainfall, temperature, radiation, humidity, and soil nutrient and mineral composition were recorded in each region and correlated with chemical variation through multivariate analysis (MVDA). Marker compounds were selected using a statistically informed molecular network and annotated by dereplication against an in silico database of natural products. The integrated results evidenced different chemotypes, with variation in flavonoid and tannin content mainly linked to soil conditions. Different levels of genetic diversity and distance of populations were found to be correlated with the identified chemotypes. These observations and the proposed analytical workflow contribute to the global understanding of the impact of abiotic factors and genotype on the accumulation of given metabolites and, therefore, could be valuable to guide further medicinal exploration of native species.

scholarly journals Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential

2015 ◽  
Vol 9 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Shyamalina Haldar ◽  
Sanghamitra Sengupta
Keyword(s):  
Developmental Stages ◽  
Biological Activities ◽  
Abiotic Factors ◽  
Environmental Parameters ◽  
Host Genotype ◽  
Nature Restoration ◽  
Microbiological Techniques ◽  
Microbe Interactions ◽  
Structural Principles ◽  
The Impact

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration.

scholarly journals Microbiomes and Pathogen Survival in Crop Residues, an Ecotone Between Plant and Soil

2019 ◽  
Vol 3 (4) ◽  
pp. 246-255 ◽  
Author(s):  
Lydie Kerdraon ◽  
Valérie Laval ◽  
Frédéric Suffert
Keyword(s):  
Disease Management ◽  
Microbial Communities ◽  
Plant Pathogens ◽  
Crop Residues ◽  
Abiotic Factors ◽  
Plant Diseases ◽  
Negative Contribution ◽  
Positive Effects ◽  
Fungal Plant Pathogens ◽  
The Impact

The negative contribution of crop residues as a source of inoculum for plant diseases is well established. However, microbial ecologists have long reported positive effects of residues on the stability of agrosystems and conservation tillage practices have become increasingly widespread. Most studies have suggested that large microbial communities should be taken into account in plant disease management, but we know little about their ecological interaction with pathogens in the crop residue compartment. This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connected residue microbiome with the survival of residue-borne fungal plant pathogens, thus combining knowledge in microbial ecology and epidemiology, two disciplines still not sufficiently connected. We provide an overview of the impact of residues on cereal disease epidemics and how dynamic interactions between microbial communities of nonburied residues during their degradation, along with soil and multitude of abiotic factors, can contribute to innovative disease management strategies, including next-generation microbiome-based biocontrol strategies. Starting from the classical but still relevant view of crop residues as a source of pathogen inoculum, we first consider possibilities for limiting the amount of residues on the soil surface to reduce the pathogen pressure. We then describe residues as a transient half-plant/half-soil compartment constituting a key fully fledged microbial ecosystem: in other words, an ecotone which deserves special attention. We focus on microbial communities, the changes in these communities over time and the factors influencing them. Finally, we discuss how the interactions between the microbial communities and the pathogens present on residues could be used: identification of keystone taxa and beneficial assemblages, then preservation of these taxa by adapted agronomic practices or development of synthetic communities, rather than the introduction of a single exogenous biocontrol species designed as a treatment product. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Biochar affects the structure rather than the total biomass of microbial communities in temperate soils

2013 ◽  
Vol 22 (4) ◽  
pp. 404-423 ◽  
Author(s):  
Elena Anders ◽  
Andrea Watzinger ◽  
Franziska Rempt ◽  
Barbara Kitzler ◽  
Bernhard Wimmer ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Field Experiments ◽  
Soil Microbial Communities ◽  
Greenhouse Experiment ◽  
Soil Conditions ◽  
Total Biomass ◽  
Soil Microbial ◽  
Temperate Soils

Biochar application is a promising strategy for sequestering carbon in agricultural soils and for improving degraded soils. Nonetheless, contradictory and unsettled issues remain. This study investigates whether biochar influences the soil microbial biomass and community structure using phospholipid fatty acid (PLFA) analysis. We monitored the effects of four different types of biochar on the soil microbial communities in three temperate soils of Austria over several months. A greenhouse experiment and two field experiments were conducted. The biochar application did not significantly increase or decrease the microbial biomass. Only the addition of vineyard pruning biochar pyrolysed at 400°C caused microbial biomass to increase in the greenhouse experiment. The biochar treatments however caused shifts in microbial communities (visualized by principal component analysis). We concluded that the shifts in the microbial community structure are an indirect rather than a direct effect and depend on soil conditions and nutrient status.

scholarly journals Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott A. Klasek ◽  
Marcus T. Brock ◽  
Hilary G. Morrison ◽  
Cynthia Weinig ◽  
Loïs Maignien
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Host Genotype ◽  
Rhizosphere Community ◽  
Scale Variation

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Microbial cenosis of typical chernozem at the biological and intensive agrarian systems

2016 ◽  
Vol 1 (90) ◽  
pp. 58-63
Author(s):  
Yu.P. Borko ◽  
M.V. Patyka ◽  
O.Yu. Kolodyazhni
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Sugar Beet ◽  
Microbial Communities ◽  
Trophic Relationships ◽  
Typical Chernozem ◽  
Ecological Index ◽  
Microbial Identification ◽  
The Impact ◽  
Agrarian Systems

The results of investigations on studying of the impact of agromeasures at the functioning of microbial communities in chernozem typical has been shown. The aim of article was a comparative analysis of the functioning of bacterial and fungal microbiota in sugar beet rhizosphere at the application of biological and intensive (industrial) agrarian systems during culture ontogenesis. We applied a microbial (identification of microorganism’s number and their qualitative composition), ecological (ecological index calculation), biochemical (estimation of the microbial biomass and metabolic coefficient) and statistical (establishing the results probability) research methods is to achieve of this purpose. The application of agromeasures are significant impact on microbial communities in chernozem typical in sugar beet rhizosphere during ontogeny and are caused the change of trophic relationships and different direction of microbial processes in soil has been established. The phase of plant development is also had a significant impact on the activity of soil microorganisms functioning. The number of root exudates is increased and plant debrises are accumulated in the soil during sugar beet ontogeny. It is promotes to the growth of numbers, biomass and diversity of microbial communities’ in chernozem typical and consequently intensification of soil organic matter transformation. Thus the application of biological agrarian system compared to intensive is helped to optimization of soil microbial complex. It is accompanied the increasing of the number, diversity and content of microbial biomass and growth of microbial groups resistance. This helps to enhance of microbial transformation of organic matter and improve of soil trophic metabolic profile. The use of intensive agrarian system are involved the reducing of the number, diversity and biomass of microorganisms, that accompanied by a simplification of trophic relationships and deregulation of plant-microbe systems.

scholarly journals The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

2020 ◽  
Author(s):  
Jingjie Hao ◽  
Yen Ning Chai ◽  
Raziel A. Ordóñez ◽  
Emily E. Wright ◽  
Sotirios Archontoulis ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Depth ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.

scholarly journals Whole-soil warming decreases abundance and modifies the community structure of microorganisms in the subsoil but not in surface soil

SOIL ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 477-494
Author(s):  
Cyrill U. Zosso ◽  
Nicholas O. E. Ofiti ◽  
Jennifer L. Soong ◽  
Emily F. Solly ◽  
Margaret S. Torn ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Community Composition ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Community Response ◽  
Similar Response

Abstract. The microbial community composition in subsoils remains understudied, and it is largely unknown whether subsoil microorganisms show a similar response to global warming as microorganisms at the soil surface do. Since microorganisms are the key drivers of soil organic carbon decomposition, this knowledge gap causes uncertainty in the predictions of future carbon cycling in the subsoil carbon pool (> 50 % of the soil organic carbon stocks are below 30 cm soil depth). In the Blodgett Forest field warming experiment (California, USA) we investigated how +4 ∘C warming in the whole-soil profile to 100 cm soil depth for 4.5 years has affected the abundance and community structure of microorganisms. We used proxies for bulk microbial biomass carbon (MBC) and functional microbial groups based on lipid biomarkers, such as phospholipid fatty acids (PLFAs) and branched glycerol dialkyl glycerol tetraethers (brGDGTs). With depth, the microbial biomass decreased and the community composition changed. Our results show that the concentration of PLFAs decreased with warming in the subsoil (below 30 cm) by 28 % but was not affected in the topsoil. Phospholipid fatty acid concentrations changed in concert with soil organic carbon. The microbial community response to warming was depth dependent. The relative abundance of Actinobacteria increased in warmed subsoil, and Gram+ bacteria in subsoils adapted their cell membrane structure to warming-induced stress, as indicated by the ratio of anteiso to iso branched PLFAs. Our results show for the first time that subsoil microorganisms can be more affected by warming compared to topsoil microorganisms. These microbial responses could be explained by the observed decrease in subsoil organic carbon concentrations in the warmed plots. A decrease in microbial abundance in warmed subsoils might reduce the magnitude of the respiration response over time. The shift in the subsoil microbial community towards more Actinobacteria might disproportionately enhance the degradation of previously stable subsoil carbon, as this group is able to metabolize complex carbon sources.

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