scholarly journals Comparison of the Structure and Diversity of Root-Associated and Soil Microbial Communities Between Acacia Plantations and Native Tropical Mountain Forests

2021 ◽  
Vol 12 ◽  
Author(s):  
Kozue Sawada ◽  
Shinichi Watanabe ◽  
Ho Lam Nguyen ◽  
Soh Sugihara ◽  
Mayuko Seki ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Soil Types ◽  
Community Structures ◽  
Tree Roots ◽  
Exchangeable Al ◽  
Native Tree ◽  
Sustainable Productivity ◽  
Acacia Tree

Deforestation of native tropical forests has occurred extensively over several decades. The plantation of fast-growing trees, such as Acacia spp., is expanding rapidly in tropical regions, which can contribute to conserve the remaining native tropical forests. To better understand belowground biogeochemical cycles and the sustainable productivity of acacia plantations, we assessed the effects of vegetation (acacia plantations vs. native forests) and soil types (Oxisols vs. Ultisols) on soil properties, including the diversity and community structures of bacteria- and fungi-colonizing surface and subsurface roots and soil in the Central Highlands of Vietnam. The results in surface soil showed that pH was significantly higher in acacia than in native for Oxisols but not for Ultisols, while exchangeable Al was significantly lower in acacia than in native for Ultisols but not for Oxisols. Bacterial alpha diversity (especially within phylum Chloroflexi) was higher in acacia than in native only for Oxisols but not for Ultisols, which was the same statistical result as soil pH but not exchangeable Al. These results suggest that soil pH, but not exchangeable Al, can be the critical factor to determine bacterial diversity. Acacia tree roots supported greater proportions of copiotrophic bacteria, which may support lower contents of soil inorganic N, compared with native tree roots for both Oxisols and Ultisols. Acacia tree roots also supported greater proportions of plant pathogenic Mycoleptodiscus sp. but appeared to reduce the abundances and diversity of beneficial ECM fungi compared with native tree roots regardless of soil types. Such changes in fungal community structures may threaten the sustainable productivity of acacia plantations in the future.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

scholarly journals Distribution of soil nutrients and erodibility factor under different soil types in an erosion region of Southeast China

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11630
Author(s):  
Man Liu ◽  
Guilin Han
Keyword(s):  
Soil Erosion ◽  
Soil Nutrients ◽  
Soil Ph ◽  
Major Elements ◽  
Soil Types ◽  
Soil Erodibility ◽  
Soil Evolution ◽  
Southeast China ◽  
Red Soils ◽  
K Factor

Background Soil erosion can affect the distribution of soil nutrients, which restricts soil productivity. However, it is still a challenge to understand the response of soil nutrients to erosion under different soil types. Methods The distribution of soil nutrients, including soil organic carbon (SOC), soil organic nitrogen (SON), and soil major elements (expressed as Al2O3, CaO, Fe2O3, K2O, Na2O, MgO, TiO2, and SiO2), were analyzed in the profiles from yellow soils, red soils, and lateritic red soils in an erosion region of Southeast China. Soil erodibility K factor calculated on the Erosion Productivity Impact Calculator (EPIC) model was used to indicate erosion risk of surface soils (0∼30 cm depth). The relationships between these soil properties were explored by Spearman’s rank correlation analysis, further to determine the factors that affected the distribution of SOC, SON, and soil major elements under different soil types. Results The K factors in the red soils were significantly lower than those in the yellow soils and significantly higher than those in the lateritic red soils. The SON concentrations in the deep layer of the yellow soils were twice larger than those in the red soils and lateritic red soils, while the SOC concentrations between them were not significantly different. The concentrations of most major elements, except Al2O3 and SiO2, in the yellow soils, were significantly larger than those in the red soils and lateritic red soils. Moreover, the concentrations of major metal elements positively correlated with silt proportions and SiO2 concentrations positively correlated with sand proportions at the 0∼80 cm depth in the yellow soils. Soil major elements depended on both soil evolution and soil erosion in the surface layer of yellow soils. In the yellow soils below the 80 cm depth, soil pH positively correlated with K2O, Na2O, and CaO concentrations, while negatively correlated with Fe2O3 concentrations, which was controlled by the processes of soil evolution. The concentrations of soil major elements did not significantly correlate with soil pH or particle distribution in the red soils and lateritic red soils, likely associated with intricate factors. Conclusions These results suggest that soil nutrients and soil erodibility K factor in the yellow soils were higher than those in the lateritic red soils and red soils. The distribution of soil nutrients is controlled by soil erosion and soil evolution in the erosion region of Southeast China.

scholarly journals Crop Response to Soil Acidity Factors in Ultisols and Oxisols in Puerto Rico. XII. Tomatoes

1969 ◽  
Vol 69 (3) ◽  
pp. 357-365
Author(s):  
Edmundo Rivera ◽  
José Rodríguez ◽  
Fernando Abruña
Keyword(s):  
Puerto Rico ◽  
Cation Exchange ◽  
Soil Ph ◽  
Cation Exchange Capacity ◽  
Soil Acidity ◽  
Exchange Capacity ◽  
Crop Response ◽  
Exchangeable Al

The effect of acidity factors of two Ultisols and one Oxisol on yield and foliar composition of tomatoes was determined. Yields were not markedly reduced by acidity in the Ultisols until pH dropped to around 4.6 with 45% Al saturation of the cation exchange capacity (CEC), and no yield was produced at about pH 4.1 and 80% Al saturation. In the Oxisol, tomato yields dropped steadily from 39.7 t/ha, when there was no exchangeable AI, to 17.5 t/ha at the highest level of acidity, pH 4.4 and 43% AI saturation. In all soils, yields were closely correlated with soil pH, exchangeable Al and Ca and Al/Ca.

scholarly journals Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Silvia Pajares ◽  
Julio Campo ◽  
Brendan J. M. Bohannan ◽  
Jorge D. Etchevers
Keyword(s):  
Tropical Forest ◽  
Tropical Forests ◽  
Soil Microbial Communities ◽  
Soil Heterogeneity ◽  
N Deposition ◽  
Seasonally Dry Tropical Forest ◽  
Content Type ◽  
Soil Microbial ◽  
Seasonally Dry ◽  
Rainfall Seasonality

ABSTRACTSeveral studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirKandnirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances.Actinobacteria,Proteobacteria,Firmicutes, andAcidobacteriawere the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCEUnderstanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.

scholarly journals Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

2019 ◽  
Vol 20 (9) ◽  
pp. 2125 ◽  
Author(s):  
Muhammad Imran Ghani ◽  
Ahmad Ali ◽  
Muhammad Jawaad Atif ◽  
Muhammad Ali ◽  
Bakht Amin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Soil Microbiome ◽  
Plant Residues ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Community Structures ◽  
Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

scholarly journals Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Silvia Garaycochea ◽  
Héctor Romero ◽  
Elena Beyhaut ◽  
Andrew L Neal ◽  
Nora Altier
Keyword(s):  
Soil Microbial Communities ◽  
Nutrient Status ◽  
Parent Material ◽  
Water Holding Capacity ◽  
Soil Types ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Principal Coordinates ◽  
Natural Grasslands ◽  
Water Holding

ABSTRACT Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

Temporal variation in soil acidity

Soil Research ◽  
1997 ◽  
Vol 35 (5) ◽  
pp. 1115 ◽  
Author(s):  
M. K. Conyers ◽  
N. C. Uren ◽  
K. R. Helyar ◽  
G. J. Poile ◽  
B. R. Cullis
Keyword(s):  
Temporal Variation ◽  
Soil Ph ◽  
Soil Acidity ◽  
Soil Depth ◽  
Weather Conditions ◽  
Climatic Conditions ◽  
Variable Response ◽  
Related Factors ◽  
Exchangeable Al ◽  
Eastern Australia

Seasonal variation in the response of crops and pastures to limestone application has been observed on acidic soils in south-eastern Australia. Our hypothesis was that temporal variation in soil acidity related factors may contribute to this variable response. Soils from 4 annual pasture sites were sampled at least monthly for 3 years during 1988–1990 to monitor changes in pH(CaCl2) and in concentrations of exchangeable aluminium (Al) and manganese (Mn). The sites received no fertiliser or cultivation and therefore allowed for the estimation of natural temporal variation. Temporal variation in soil pH during a year ranged from 0 to 0·45 pH units depending on the site, soil depth, and the weather conditions. The larger changes in soil pH were associated with more extreme climatic conditions than normal, e.g. following the break of season after a hot, dry summer (autumn 1988) or during periods of above-average rainfall in autumn and early spring (1990). Temporal variation in pH was less than the spatial variability at the sites but greater than the long-term net acidification rate reported for the region. Temporal variation in the concentration of exchangeable Al ranged from 0 to 0·4 cmol(+)/kg during a year and varied primarily with the inverse of pH. Variations in the concentration of exchangeable Mn ranged from 0·05 to 0·35 cmol(+)/kg during a year. The concentration of exchangeable Mn increased over summer to an extent dependent on the drying of the soil. At the 2 sites with duplex profiles, maxima in the concentration of exchangeable Mn also occurred in spring, particularly in the warm wet spring of 1990. Soil tests for soil acidity therefore represent guides to probable risks of toxicity, as pH and the concentrations of exchangeable Al and Mn may change between soil sampling, sowing, and the period of crop or annual pasture growth. Such variations will alter the responsiveness of crops and pastures to lime.

A COMPARISON OF LIME REQUIREMENT METHODS FOR ACID CANADIAN SOILS

1977 ◽  
Vol 57 (3) ◽  
pp. 361-370 ◽  
Author(s):  
M. D. WEBBER ◽  
DIANE CORNEAU ◽  
P. B. HOYT ◽  
M. NYBORG
Keyword(s):  
British Columbia ◽  
Organic Matter ◽  
Soil Ph ◽  
Acid Soils ◽  
Toxic Level ◽  
Laboratory Methods ◽  
Exchangeable Al ◽  
Canadian Soils ◽  
Highly Correlated ◽  
Diagnostic Index

Several laboratory methods for estimating lime requirements of acid soils were compared using 24 soils from Alberta and northeastern British Columbia and 15 from elsewhere in Canada. The Peech, Schofield, Woodruff and SMP (Shoemaker et al. 1971) buffer methods were equally well correlated with lime requirements for raising soil pH to 5.5 or 6, which in turn were highly correlated with the amounts of soluble and exchangeable Al and organic matter in the soils. The SMP buffer method is recommended for use as the diagnostic index of lime requirement to achieve pH 5.5 or 6 because of its speed and simplicity. A refinement is suggested for Alberta and northeastern B.C. soils on the basis that lime need not be added to achieve pH 5.5 but should be added to reduce Al below the toxic level for sensitive crops. The lime requirements to reduce Al in those soils were highly correlated with the amounts of 0.02 M CaCl2-soluble Al they contained and it is recommended that the 0.02 M CaCl2-soluble AI be used as the diagnostic index of lime requirement. Lime requirements related to SMP (pH) and 0.02 M CaCl2-soluble Al are presented.

Long-term acidification of a Brazilian Acrisol as affected by no till cropping systems and nitrogen fertiliser

Soil Research ◽  
2008 ◽  
Vol 46 (1) ◽  
pp. 17 ◽  
Author(s):  
F. C. B. Vieira ◽  
C. Bayer ◽  
J. Mielniczuk ◽  
J. Zanatta ◽  
C. A. Bissani
Keyword(s):  
Soil Ph ◽  
Soil Acidification ◽  
Plant Material ◽  
Cropping Systems ◽  
Maize Yield ◽  
Mineral N ◽  
No Till ◽  
Leguminous Species ◽  
Exchangeable Al ◽  
C Cycle

Cropping systems and N fertilisation affect soil acidification mainly due to the removal of alkaline plant material from the field and nitrate leaching. The study evaluated the acidification of a subtropical soil under no till cropping systems with different C and N addition rates for 19 years. The contributions of leguminous and non-leguminous crops (fallow/maize, black oat/maize, black oat + vetch/maize, black oat + vetch/maize + cowpea, lablab + maize, pigeon pea + maize, and digitaria) and mineral N fertiliser (0 and 180 kg N/ha.year as urea) to total acidification were estimated. Cropping systems and N fertilisation significantly affected soil pH, which ranged from 4.3 to 5.1. The presence of leguminous species and mineral N promoted greater decreases in soil pH and net soil acidification, which resulted in increases in exchangeable Al content and Al saturation. Black oat + vetch/maize with N fertilisation promoted the highest soil net acidification rate (2.65 kmol H+/ha.year), while digitaria had the lowest (1.07 kmol H+/ha.year). Leguminous species and N fertilisation increased soil acidification through changes in the C cycle associated with the removal of alkaline plant material by grains. Leguminous-based cropping systems promoted higher maize yields than those comprising essentially gramineous species, indicating an opportunity for a reduction in N fertiliser rates. With N application, however, maize yield did not differ among cropping systems, despite differences in soil pH and exchangeable Al.

scholarly journals Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba

2020 ◽  
Vol 4 (2) ◽  
pp. 142-155 ◽  
Author(s):  
L. Mangeot-Peter ◽  
T. J. Tschaplinski ◽  
N. L. Engle ◽  
C. Veneault-Fourrey ◽  
F. Martin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mycorrhizal Fungi ◽  
Root Colonization ◽  
Soil Microbial Communities ◽  
Populus Tremula ◽  
Soil Microbiome ◽  
Gas Chromatography Mass Spectrometry ◽  
Natural Soil ◽  
Tree Roots ◽  
Natural Variations

Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × alba clone 717-1B4) in natural soil taken from a poplar stand under the same tree over two consecutive years and grew them in a greenhouse. We analyzed the soil and root microbiomes by high throughput Illumina MiSeq sequencing of fungal rDNA internal transcribed spacer and bacterial 16S rRNA amplicons and we characterized the root metabolome by gas chromatography-mass spectrometry. Soil and root microbial communities significantly shifted over the 2 years. A modification of the balance between endophytes, saprophytes, and mycorrhizal fungi occurred in the roots as well as a replacement of some dominant operational taxonomic units by others. These modifications were correlated with a significant alteration of the levels of about 10% of primary and secondary metabolites, suggesting that natural fluctuations in soil microbial communities can have a profound impact on tree root metabolism and physiology. Tree roots functioning may thus be indirectly strongly affected by the effects of future extreme climatic variations on the soil microbiome.

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