scholarly journals The effect of organic fertilizers on the taxonomic composition of microbial communities in agro-soddy-podzolic soils of the middle taiga

2020 ◽  
Author(s):  
Ya. V. Puhalsky ◽  
S. I. Loskutov ◽  
E. M. Lapteva ◽  
Yu. A. Vinogradova ◽  
V. A. Kovaleva ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Taxonomic Composition ◽  
Organic Fertilizers ◽  
Middle Taiga ◽  
Podzolic Soils

The taxonomic composition of prokaryotes of agro-soddy podzolic soils of the middle taiga and the patterns of its change with the application of various doses of organic fertilizers were studied.

scholarly journals Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Chengyuan Tao ◽  
Rong Li ◽  
Wu Xiong ◽  
Zongzhuan Shen ◽  
Shanshan Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Pathogens ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Plant Diseases ◽  
Disease Suppression ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Soil Microbial ◽  
Bioorganic Fertilizer

Abstract Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

scholarly journals Is soil management system really important? comparison of microbial community diversity and structure in soils managed under organic and conventional regimes with some view on soil properties

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256969
Author(s):  
Kamila Rachwał ◽  
Klaudia Gustaw ◽  
Waldemar Kazimierczak ◽  
Adam Waśko
Keyword(s):  
Microbial Communities ◽  
Soil Microorganisms ◽  
Cropping Systems ◽  
Chemical Properties ◽  
Soil Management ◽  
Community Diversity ◽  
Organic Fertilizers ◽  
Management Regime ◽  
Abundance And Diversity ◽  
Physical And Chemical

The fertility and productive value of soil are closely related to the physical and chemical properties of the soil as well as its biological activity. This activity is related to the intensity of microbially catalysed processes of transformation of organic and mineral substances contained in the soil. These processes are closely correlated with the abundance and biodiversity of soil microorganisms, especially bacteria, and the activity of enzymes produced by them. In this article we have compared some physicochemical properties of soil derived from conventional and organic farms and microbial communities inhabiting these ecosystems. We aim to investigate whether the soil management regime affects the abundance and diversity of these environments in terms of bacteria. Some differences in microbial communities were observed, but the rhizosphere of plants from organic and conventional soils does not harbour separate microbiomes. Albeit, the method of fertilization influences the diversity of soil microorganisms. A greater diversity of bacteria was observed in soils from farms where organic fertilizers were applied. Soil pH and activity of some soil enzymes were also shown to differ between organic and conventional soil cropping systems.

scholarly journals Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3246 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Sofie E. Voerman ◽  
Jenna M. Lang ◽  
John J. Stachowicz ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Communities ◽  
Zostera Marina ◽  
Sulfur Metabolism ◽  
Model Organism ◽  
Environmental Parameters ◽  
Taxonomic Composition ◽  
Point Of View ◽  
Sample Type ◽  
Significant Finding ◽  
Taxonomic Groups

Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.

Clearer than mud? Using environmental DNA to track historical shifts in lake communities.

2021 ◽  
Author(s):  
John Pearman ◽  
Laura Biessy ◽  
Georgia Thomson-Laing ◽  
Lizette Reyes ◽  
Claire Shepherd ◽  
...  
Keyword(s):  
New Zealand ◽  
Microbial Communities ◽  
Environmental History ◽  
Environmental Changes ◽  
Environmental Dna ◽  
Taxonomic Composition ◽  
Molecular Methods ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Dna And Rna

<p>A continuous record of environmental history is stored in lake sediments providing an avenue to explore current and historical lake communities. Traditionally paleolimnological methods have focussed on macroscopic indicators (e.g. pollen, chronomids, diatoms) to investigate environmental changes but the application of environmental DNA techniques has enabled the investigation of microbial communities and other soft bodied organisms through time. The ‘Our lakes’ health; past, present, future (Lakes380)’ project aims to combined traditional and molecular methods to explore shifts in biological communities over the last 1,000 years (pre-human arrival in New Zealand). Sediments cores have been collected from a wide diversity of lakes across New Zealand and 16S rRNA gene metabarcoding approaches of both DNA and RNA applied to reveal how microbial community changes across time and especially in response to the arrival of humans and associated changes to the landscape and lake environments. We further investigate the changes in inferred metabolic potential of the microbial communities as the taxonomic composition of the lake differs over time. Finally, we combine these novel molecular methods with hyperspectral scanning and pollen data to increase the knowledge of changes in lake communities and identifying the timing of changes in lake health. The combination of methodologies provides a greater understanding of the environmental history of lake systems and will help to inform management decisions relating to the restoration and protection of lake health.</p>

Bio-Organic Fertilizers Manipulate Abundance Patterns of Rhizosphere Soil Microbial Community Structure To Improve Tomato Productivity

2021 ◽  
Author(s):  
Bintao Li ◽  
Luodi Guo ◽  
Haoming Wang ◽  
Yulong Li ◽  
Hangxian Lai ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Microbial Communities ◽  
Crop Yields ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Growth Stages ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Abstract Background Bio-organic fertilizers has been shown to improve crop yields, partially because of the effects on the structure and function in resident soil microbiome. Purpose and methods Whereas, it is unknown if such improvements have been facilitated by the particular action of microbial inoculants, or the compost substrate. To understand the ecological mechanisms to increase crop productivity by bio-organic fertilizers, we conducted a pot experiment tracking soil physicochemical factors and extracellular enzyme activity over two growth stages and variations of soil microbial communities caused by fertilization practices as below: Bacillus subtilis CY1 inoculation, swine compost, and bio-organic fertilizer. Results Results showed that different fertilization measures, especially bio-organic fertilizers, increased soil nutrients, enzyme activity, and the diversity of microbial communities. For quantifying the “effect size” of microbiota manipulation, we discoverd that, respectively, 19.94% and 48.99% of variation in the bacterial and fungal communities could be interpreted using tested fertilization practices. Fertilization-sensitive microbes showed taxonomy diversity and gave responses as guilds of taxa to specific treatments. The microbes exhibited medium to high degree of co-occurrence in the network and could be recruited, directly or indirectly, by B. subtilis CY1, suggesting that bio-organic fertilizer may allow manipulation of influential community members.Conclusion Together we demonstrated that the increase in tomato productivity by bio-organic fertilizer was caused by the synergistic effect of organic fertilizer and beneficial microorganisms, thus providing novel insights into the soil microbiome manipulation strategies of biologically-enhanced organic fertilizers.

scholarly journals Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
John I. Miller ◽  
Stephen Techtmann ◽  
Dominique Joyner ◽  
Nagissa Mahmoudi ◽  
Julian Fortney ◽  
...  
Keyword(s):  
Decision Making ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Taxonomic Composition ◽  
Hydrocarbon Biodegradation ◽  
Decision Making Process ◽  
Degrading Bacteria ◽  
Vital Component ◽  
Marine Microbial Communities ◽  
Marine Basins

ABSTRACT The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins. IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.

scholarly journals Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems

2009 ◽  
Vol 75 (15) ◽  
pp. 4993-5000 ◽  
Author(s):  
Brigitte Hai ◽  
Ndeye Hélène Diallo ◽  
Saidou Sall ◽  
Felix Haesler ◽  
Kristina Schauss ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycle ◽  
Plant Development ◽  
Water Availability ◽  
Management Practices ◽  
Ammonia Oxidation ◽  
Organic Fertilizers ◽  
Ammonia Oxidizing Bacteria ◽  
Development Stages ◽  
The Impact

ABSTRACT The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.

Micromycetes in podzolic and bog-podzolic soils in the middle taiga subzone of northeastern European Russia

2014 ◽  
Vol 47 (10) ◽  
pp. 1027-1032 ◽  
Author(s):  
F. M. Khabibullina ◽  
E. G. Kuznetsova ◽  
I. Z. Vaseneva
Keyword(s):  
European Russia ◽  
Middle Taiga ◽  
Podzolic Soils ◽  
Middle Taiga Subzone

scholarly journals Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples

2020 ◽  
Author(s):  
Michael Baumgartner ◽  
Katia R Pfrunder-Cardozo ◽  
Alex R Hall
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Nutrient Status ◽  
Taxonomic Composition ◽  
Colonization Resistance ◽  
Abiotic Conditions ◽  
E Coli ◽  
And Function

AbstractBiological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status). Here, we used a gut microcosm system to disentangle some of the drivers of susceptibility to invasion in microbial communities sampled from humans. We found resident microbial communities inhibited an invading E. coli strain, compared to community-free control treatments, sometimes excluding the invader completely (colonization resistance). These effects were stronger at later time points, coinciding with shifts in microbial community composition and nutrient availability. By separating these two components (microbial community and abiotic environment), we found taxonomic composition played a crucial role in suppressing invasion, but this depended critically on local abiotic conditions (adapted communities were more suppressive in nutrient-depleted conditions). This helps predict when resident communities will be most susceptible to invasion, with implications for optimizing treatments based around microbiota management.

scholarly journals Meadows and pastures in the agricultural landscapes of the Karelian province of the Middle Taiga zone of the North-West of Russia

2021 ◽  
Vol 901 (1) ◽  
pp. 012037
Author(s):  
I A Trofimov ◽  
L S Trofimova ◽  
E P Yakovleva ◽  
D M Teberdiev ◽  
A A Kutuzova ◽  
...  
Keyword(s):  
Agricultural Land ◽  
Arable Land ◽  
Agricultural Landscapes ◽  
Middle Taiga ◽  
Leningrad Region ◽  
Taiga Zone ◽  
North West ◽  
Podzolic Soils ◽  
The North ◽  
Mixed Grass

Abstract In order to take into account the territorial differences of natural and economic conditions, to identify biological and ecological patterns, the agro-landscape and ecological zoning of natural forage lands (NFL) of the North-Western natural and economic region of the Russian Federation has been developed. The Karelian province occupies 23% of the area in the north of the Leningrad region, bordering Karelia and Finland. The Karelian province is located in the western part of the Middle Taiga zone, which is characterized by Eastern European Middle Taiga plains. Most of the area of the province (65%) is covered by forests. Agricultural land occupies only 4% of the total area of the province. Including arable land – 2%, hayfields and pastures – 1% each. The territory of the province is significantly moistened and swampy. Swamps occupy 11% of the area, under water – about 11%. Shrubs occupy 3% of the area of the province, other land – about 6%. The structure of NFL is dominated (53%) by normally moistened dry-grass grasslands on sod-podzolic soils. Fine-grained sweet-scented and finegrained grasslands with a large participation of various grasses are common. The yield of hay is 9–13 c/ha, feed is 70 c/ha. Grass-mixed grass and grass-sedge-mixed grass lowland and swampy meadows on swamp-podzolic soils occupy 44%. Grass stands with the dominance of the sod pike are common. Swampy depressions are occupied by large-seeded grass stands. The yield of hay is 10–15 c/ha, feed is 9–11 c/ha. The ecological state of the province’s landscapes is satisfactory-tense.

Sign in / Sign up

Export Citation Format

Share Document