Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels

Grassland ecosystems form 30-40% of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage. Their productivity is closely related to soil microbial communities, yet the role of viruses within these critical ecosystems is currently undercharacterised and in particular, our knowledge of soil RNA viruses is significantly limited. Here, we applied viromics to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities therefore likely have the ability to influence soil ecosystems across multiple trophic levels. Our study represents an important step towards the characterisation of terrestrial RNA viral communities and the intricate interactions with their hosts, which will provide a more holistic view of the biology of economically and ecologically important terrestrial ecosystems.

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Ozone affects plant, insect, and soil microbial communities: A threat to terrestrial ecosystems and biodiversity

Science Advances ◽

10.1126/sciadv.abc1176 ◽

2020 ◽

Vol 6 (33) ◽

pp. eabc1176 ◽

Cited By ~ 10

Author(s):

Evgenios Agathokleous ◽

Zhaozhong Feng ◽

Elina Oksanen ◽

Pierre Sicard ◽

Qi Wang ◽

...

Keyword(s):

Plant Competition ◽

Root Exudation ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Terrestrial Ecosystems ◽

Insect Communities ◽

Soil Microbial ◽

Plant Soil ◽

Equatorial Africa ◽

Insect Interactions

Elevated tropospheric ozone concentrations induce adverse effects in plants. We reviewed how ozone affects (i) the composition and diversity of plant communities by affecting key physiological traits; (ii) foliar chemistry and the emission of volatiles, thereby affecting plant-plant competition, plant-insect interactions, and the composition of insect communities; and (iii) plant-soil-microbe interactions and the composition of soil communities by disrupting plant litterfall and altering root exudation, soil enzymatic activities, decomposition, and nutrient cycling. The community composition of soil microbes is consequently changed, and alpha diversity is often reduced. The effects depend on the environment and vary across space and time. We suggest that Atlantic islands in the Northern Hemisphere, the Mediterranean Basin, equatorial Africa, Ethiopia, the Indian coastline, the Himalayan region, southern Asia, and Japan have high endemic richness at high ozone risk by 2100.

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Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau

Microbial Ecology ◽

10.1007/s00248-017-1098-4 ◽

2017 ◽

Vol 75 (4) ◽

pp. 1009-1023 ◽

Cited By ~ 7

Author(s):

Jun Zeng ◽

Ju-Pei Shen ◽

Jun-Tao Wang ◽

Hang-Wei Hu ◽

Cui-Jing Zhang ◽

...

Keyword(s):

Tibetan Plateau ◽

Microbial Communities ◽

Climate Warming ◽

Soil Microbial Communities ◽

Alpine Grassland ◽

The Tibetan Plateau ◽

Soil Microbial ◽

Grassland Ecosystems

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Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

Biogeosciences ◽

10.5194/bg-11-3339-2014 ◽

2014 ◽

Vol 11 (12) ◽

pp. 3339-3352 ◽

Cited By ~ 23

Author(s):

A. S. Wieczorek ◽

S. A. Hetz ◽

S. Kolb

Keyword(s):

Carbon Dioxide ◽

Agricultural Soil ◽

Soil Microbial Communities ◽

Terrestrial Ecosystems ◽

Ecological Niches ◽

Acid Fermentation ◽

Fermentation Products ◽

Anoxic Conditions ◽

Chitin Degradation ◽

Soil Microbial

Abstract. Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N′-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

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Plant And Soil Microbial Communities Regulate Soil Respiration In Response To Precipitation And Land Use In An Inner Mongolian Grassland

10.21203/rs.3.rs-1070086/v1 ◽

2021 ◽

Author(s):

Chi Zhang ◽

Chao Song ◽

Donghui Wang ◽

Wenkuan Qin ◽

Biao Zhu ◽

...

Keyword(s):

Land Use ◽

Soil Respiration ◽

Microbial Communities ◽

Precipitation Amount ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Altered Precipitation ◽

Grassland Ecosystems ◽

Mongolian Grassland

Abstract Purpose: Changes in precipitation amount and land use are expected to greatly impact soil respiration (Rs) of grassland ecosystems. However, little is known about whether they can interactively impact Rs and how plant and soil microbial communities regulate the response of Rs. Methods: Here, we investigated the impacts of altered precipitation amount (–50%, ambient and +50%) and land-use regime (fencing, mowing and grazing) on Rs with a field experiment in the Inner Mongolian grassland.Results: We found that altered precipitation amount impacted Rs and its components across the 3-year study period, while land-use regime alone or its interaction with precipitation amount impacted them in certain years. In addition, changed soil microclimate, especially soil moisture, under altered precipitation amount and land-use regime can impact the components of Rs either directly or indirectly via influencing plant and soil microbial communities.Conclusions: Integrating changing precipitation amount and land-use regime within experiment can produce more accurate insights into grassland Rs, and chronically shifted plant and soil microbial communities under these changes may result in distinct long-term impacts on Rs.

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Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2105124118 ◽

2021 ◽

Vol 118 (32) ◽

pp. e2105124118

Author(s):

Sungeun Lee ◽

Ella T. Sieradzki ◽

Alexa M. Nicolas ◽

Robin L. Walker ◽

Mary K. Firestone ◽

...

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Stable Isotope Probing ◽

Trophic Levels ◽

Methylotrophic Bacteria ◽

Metagenomic Sequencing ◽

Atmospheric Methane ◽

Diverse Range ◽

Soil Microbial ◽

Predatory Bacteria

The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil–atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH4-fueled microbial food networks.

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Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm (Elaeis guineensis) via High-Throughput Sequencing

Biology ◽

10.3390/biology9120424 ◽

2020 ◽

Vol 9 (12) ◽

pp. 424

Author(s):

Yit Kheng Goh ◽

Muhammad Zarul Hanifah Md Zoqratt ◽

You Keng Goh ◽

Qasim Ayub ◽

Adeline Su Yien Ting

Keyword(s):

Oil Palm ◽

High Throughput Sequencing ◽

Elaeis Guineensis ◽

Disease Incidence ◽

Soil Microbial Communities ◽

Disease Suppression ◽

Soil Microbiome ◽

Physical Parameters ◽

Soil Microbial ◽

Coastal Soils

Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.

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Increasing aridity reduces soil microbial diversity and abundance in global drylands

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1516684112 ◽

2015 ◽

Vol 112 (51) ◽

pp. 15684-15689 ◽

Cited By ~ 269

Author(s):

Fernando T. Maestre ◽

Manuel Delgado-Baquerizo ◽

Thomas C. Jeffries ◽

David J. Eldridge ◽

Victoria Ochoa ◽

...

Keyword(s):

Climate Change ◽

Soil Bacteria ◽

Soil Microbial Communities ◽

Terrestrial Ecosystems ◽

Soil Microbial Diversity ◽

Change Models ◽

Soil Microbial ◽

Soil Bacteria And Fungi ◽

Abundance And Diversity ◽

Bacteria And Fungi

Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

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