Shifting prokaryotic communities along a soil formation chronosequence and across soil horizons in a South Taiga ecosystem

Иванова, Е. А.; Pershina, Elizaveta; Shapkin, Vasilii; Kichko, Arina; Аксенова, Т. С.; Kimeklis, Anastasiia K.; Gladkov, Grigory; Zverev, Aleksei; Vasilyeva, Nadezda; Andronov, Evgeny; Abakumov, Evgeny

doi:10.1016/j.pedobi.2020.150650

Cited by 9 publications

(4 citation statements)

References 40 publications

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“…This phylum is one of the major ones in our dataset, but in comparison with previous data on soil microbiome composition ( Janssen, 2006 ; Jones et al, 2009 ), its relatable abundance was quite low. At the first sight this is consistent with the fact that its representatives are usually linked to acidic environments ( Belova et al, 2018 ; Ivanova et al., 2020b ), while soils from our dataset are alkaline. However, acidobacteria are gram negative and very sensitive to drought ( Barnard, Osborne & Firestone, 2013 ; Chodak et al, 2015 ; Zhou et al, 2016 ), so another explanation of low relative abundance of acidobacteria, in our dataset can be connected to the season of sample collection (summer) or microbiome alterations during sample transportation.…”

Section: Discussionsupporting

confidence: 90%

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Kimeklis

Gladkov

Zverev

et al. 2021

PeerJ

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Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.

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Section: Discussionsupporting

confidence: 90%

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Kimeklis

Gladkov

Zverev

et al. 2021

PeerJ

Self Cite

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“…This distribution is explained by the slow accumulation of organic matter and vertical migration of organic matter, iron and silt particles being the dominating soil-forming process in cold, humid conditions. The distribution of different groups of microorganisms (archaea, bacteria, and fungi) generally followed this pattern with the local reduction in the number of microorganisms gene copies from the surface to deep horizons [ 78 , 79 ]. The distribution of the fungal biomass in the natural Podzol generally followed the bimodal distribution of SOC with the highest number of the ITS rRNA gene copies of fungi and the highest fungi/prokaryotes ratio observed in the O horizon.…”

Section: Discussionmentioning

confidence: 99%

Urbanization Affects Soil Microbiome Profile Distribution in the Russian Arctic Region

Korneykova

Vasenev

Никитин

et al. 2021

IJERPH

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Urbanization in the Arctic results in considerable and still poorly known environmental consequences. The effect of urbanization on soil microbiome—an ecosystem component highly sensitive to anthropogenic disturbance—remains overlooked for the Arctic region. The research compared chemical and microbial properties of the natural Podzol soils and urban soils of Murmansk—the largest Arctic city. Particular attention was given to the profile distribution, which is almost completely ignored by most microbial studies. Soil microbiome was investigated by the quantitative indicators based on fluorescence microscopy (microbial biomass) and PCR real-time methods (amount of rRNA genes copies of archaea, bacteria, and fungi). The principal changes in urban soils’ properties compared to the natural references included a shift in pH and an increase in C and nutrients’ contents, especially remarkable for the subsoil. The numbers of rRNA genes copies of archaea, bacteria, and fungi in urban topsoils (106–1010, 109–1010, and 107–109, respectively) were lower than in Podzol; however, the opposite pattern was shown for the subsoil. Similarly, the total microbial biomass in urban topsoils (0.55–0.75 mg g−1) was lower compared to the 1.02 mg g−1 in Podzols, while urban subsoil microbial biomass was 2–2.5 times higher than in the natural conditions. Both for urban and natural soils and throughout the profiles, fungi were dominated by mycelium forms; however, the ratios of mycelium–spores were lower, and the amount of thin mycelium was higher in urban soils than in natural Podzols. Urbanization in the Arctic altered soil morphological and chemical properties and created a new niche for microbial development in urban subsoils; its contribution to biodiversity and nutrient cycling promises to become increasingly important under projected climate change.

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“…Representatives of the latter group are typical inhabitants of arid soils of warm latitudes [35]; their richness also often positively correlated with the reaction of the soil solution in the region of neutral or alkaline pH [36,37] characteristic for samples of native mountain grassland soil (Table 1). Representatives of the Subgroup_2, on the contrary, were associated with more acidic soils [38], which may explain the increase in their richness in the soil under larch. Thus, in microbiomes, we can observe a clear trend towards acidification of the microbiome and its approximation to podzolic soils.…”

Section: Plos Onementioning

confidence: 94%

“…It is also worth noting that the studied soils demonstrate some tendency of "podzolization" by shifts in physic-chemical properties, expressed, in addition to pH changes, in the presence of silica powdering in the upper layer, as well as a tendency towards eluvial-illuvial differentiation of the soil layer by the amount of organic matter and bases (Table 1). The diversity pattern observed in the soil under larch show a sharp decrease in biodiversity in the 5-10 cm layer, which may also indirectly indicate the beginning of the podzol-forming process: when studying the chronosequences of podzolic soils, the manifestation of this process was accompanied by a significant decrease in taxonomic and phylogenetic diversity in the eluvial layer [38].…”

Section: Plos Onementioning

confidence: 97%

The shifts in the structure of the prokaryotic community of mountain-grassland soil under the influence of artificial larch plantations

et al. 2022

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Creation of artificial forest plantations on a global scale is one of the ways to mitigate the negative effects of climate change on ecosystems, at the same time providing soil protection from erosion, regulation of the hydrological regime and carbon sequestration in soils of different natural and climatic zones. However, the change of the dominant plant community cause significant ecosystem changes, reflecting at the structure and functioning of the soil microbial complex as well. The shifts in prokaryotic community of the meadow soil resulting from the conversion of the native meadow (further grassland) phytocenosis to the artificial forest plantations was investigated with the use of NGS sequencing technology and metabarcoding approach–amplicon sequencing of V4 region of 16 S rRNA (performed on Illumina Miseq platform). The identified shifts in taxonomic structure and diversity may be the result of changes in the physic-chemical conditions of soils and, on the other hand, may serve as indicators of such changes. Cultivation of larch led to an increase in the diversity of the prokaryotic community and its stratification by depth. The acidifying effect of larch manifested itself in an increase in the proportion and diversity of acidobacteria, in the abundance of oligotrophic microorganisms of phyla Chloroflexi, Firmicutes, and a simultaneous comparative decrease in the bacteria of Verrucomicrobia phylum, alphaproteobacteria of or. Rhizobiales and Burkholderiales. The absence of clearly expressed dominants in the prokaryotic community, as well as a significant increase in alpha-diversity indices, compared with the control plot of native mountain-meadow soil under grassland vegetation, suggests a transitional nature of the soil ecosystem of artificial forest plantations.

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Shifting prokaryotic communities along a soil formation chronosequence and across soil horizons in a South Taiga ecosystem

Cited by 9 publications

References 40 publications

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Urbanization Affects Soil Microbiome Profile Distribution in the Russian Arctic Region

The shifts in the structure of the prokaryotic community of mountain-grassland soil under the influence of artificial larch plantations

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