Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Jonathan R Gaiero ◽  
Micaela Tosi ◽  
Elizabeth Bent ◽  
Gustavo Boitt ◽  
Kamini Khosla ◽  
...  
Keyword(s):  
New Zealand ◽  
Acid Phosphatase ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Organic Phosphorus ◽  
Mineral Soil ◽  
Soil Microbial Communities ◽  
Organic P ◽  
Fungal Community Composition ◽  
Soil Microbial

ABSTRACT The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

scholarly journals Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

scholarly journals Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

2016 ◽  
Vol 82 (22) ◽  
pp. 6518-6530 ◽  
Author(s):  
Grace Pold ◽  
Andrew F. Billings ◽  
Jeff L. Blanchard ◽  
Daniel B. Burkhardt ◽  
Serita D. Frey ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Carbon ◽  
Carbon Cycling ◽  
Temperate Forest ◽  
Mineral Soil ◽  
Soil Microbial Communities ◽  
Organic Horizon ◽  
Soil Microbial ◽  
Carbohydrate Degradation

ABSTRACTAs Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated withActinobacteriain all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.IMPORTANCEThe massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.

scholarly journals An invasive plant rapidly increased the similarity of soil fungal pathogen communities

2020 ◽  
Author(s):  
Meiling Wang ◽  
Xuefei Tang ◽  
Xiaoqiu Sun ◽  
Bingbing Jia ◽  
Hao Xu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Invasive Plants ◽  
Fungal Pathogen ◽  
High Throughput Sequencing ◽  
Invasive Plant ◽  
Soil Microbial Communities ◽  
Plant Invasions ◽  
Alternanthera Philoxeroides ◽  
Native Plant ◽  
Soil Microbial

Abstract Background and Aims Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities (the biotic homogenization hypothesis), but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A. sessilis on soil fungal communities, and their feedback effects on plants and a foliar beetle. Methods We conducted a plant–soil feedback (PSF) experiment and a laboratory bioassay to examine PSFs associated with the native and invasive plants and a beetle feeding on them. We also characterized the soil fungal community using high-throughput sequencing. Key Results We found locally differentiated soil fungal pathogen assemblages associated with high densities of the native plant A. sessilis but little variation in those associated with the invasive congener A. philoxeroides, regardless of plant density. In contrast, arbuscular mycorrhizal fungal assemblages associated with high densities of the invasive plant were more variable. Soil biota decreased plant shoot mass but their effect was weak for the invasive plant growing in native plant-conditioned soils. PSFs increased the larval biomass of a beetle reared on leaves of the native plant only. Moreover, PSFs on plant shoot and root mass and beetle mass were predicted by different pathogen taxa in a plant species-specific manner. Conclusion Our results suggest that plant invasions can rapidly increase the similarity of soil pathogen assemblages even at low plant densities, leading to taxonomically and functionally homogeneous soil communities that may limit negative soil effects on invasive plants.

scholarly journals An Examination of Soil Microbial Communities and Litter Decomposition in Five Urban Land Uses in Metropolitan Milwaukee, WI, U.S.

2016 ◽  
Vol 42 (1) ◽  
Author(s):  
Keith Turnquist ◽  
Les Werner ◽  
Brian Sloss
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
C:N Ratio ◽  
Soil Microbial Communities ◽  
Urban Land ◽  
Land Uses ◽  
Fungal Community Composition ◽  
Soil Microbial ◽  
Physical And Chemical

The process of urbanization may alter the ability of microorganisms to supply nutrients to plants. However, both the composition and structure of soil biological communities, and the extent of variation within these communities, is not clear in urban areas. Therefore, baseline information regarding the impact of urban land management practices on soil microbial communities is essential to improving individuals’ ability to manage urban soils and the plants they support. This study examined soil microbial communities over five urban land uses with different degrees of urbanization in metropolitan Milwaukee, Wisconsin, U.S. The objectives were to 1) determine if differences exist in bacterial and fungal community composition, biological activity, and the soil physical and chemical environment across five urban land uses, and 2) determine if differences in the bacterial and fungal compositions compare to differences in the soil’s physical and chemical characteristics. Bulk density, soil organic matter, pH, magnesium, sodium, total nitrogen, and C:N ratio displayed significant differences between streets and forests. Microbial biomass did not differ between land uses, and the differences in bacterial and fungal community composition reflect only a small portion of the total microbial pool. The decomposition of transposed leaf litter showed significant decline in C:N ratio over time, but no statistical differences between land use were observed. The results display a highly redundant microbial assemblage, and suggest that in locations with adequate levels of soil carbon and where parent material and soil forming processes are homogeneous, urbanization and landscape management have less impact on soil microbiology than expected.

scholarly journals The activity and functions of subarctic soil microbial communities vary across vegetation types

2021 ◽  
Author(s):  
Sirja Viitamaki ◽  
Igor S Pessi ◽  
Anna-Maria Virkkala ◽  
Pekka Niittynen ◽  
Julia Kemppinen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Vegetation Type ◽  
Mineral Soil ◽  
Soil Layer ◽  
Soil Microbial Communities ◽  
High Latitudes ◽  
Vegetation Types ◽  
Soil Microbial ◽  
Carbon And Nitrogen Content ◽  
Plant Polymer

Global warming changes the activity of soil microbial communities in high latitudes, which might result in higher greenhouse gas emissions. However, these microbial processes involved in GHG production and consumption are not thoroughly understood. We analyzed 116 soil metatranscriptomes from 73 tundra sites and investigated how bacterial and archaeal communities and their functions vary horizontally (i.e. vegetation type) and vertically (i.e. topsoil organic and mineral layers) during the summer season, in soil types that differed in pH, moisture, soil organic matter (SOM), carbon and nitrogen content. Active microbial communities were significantly different in the organic and mineral soil layers. Additionally, the communities differed significantly between the different vegetation types both in the organic and mineral layers. Various plant polymer degraders were particularly active in shrub-dominated ecosystems with high SOM and low pH, whereas less known mixotrophic groups such as Chloroflexi were active in graminoid-dominated soil with lower SOM and higher pH. Additionally, we detected transcripts of alphaproteobacterial methanothrophs, which potentially moderate methane release from tundra soils in deeper soil layer. Our results provide new insights into the diversity and activity of microbial communities of the high-latitudes under climate change.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration

2020 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Yeast Genus ◽  
Soil Microbial ◽  
Physicochemical Factors ◽  
Permanent Loss ◽  
Relative Abundances ◽  
Bacteria And Fungi

Abstract Background: Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on the physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the communities and their correlation with environmental factors, and compare community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa.Results: The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. Conclusion: The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

scholarly journals Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah I. Leichty ◽  
Christopher P. Kasanke ◽  
Sheryl L. Bell ◽  
Kirsten S. Hofmockel
Keyword(s):  
Microbial Communities ◽  
Soil Texture ◽  
Sandy Loam ◽  
Soil Microbial Communities ◽  
Cropping System ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Soil Microbial ◽  
Total Community ◽  
Rna And Dna

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

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