Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

Pershina, E. V.; Valkonen, Jari P. T.; Kurki, Päivi; Иванова, Е. А.; Чирак, Е. Л.; Korvigo, Ilia; Проворов, Н. А.; Andronov, E. E.

doi:10.1371/journal.pone.0145072

Cited by 85 publications

(44 citation statements)

References 44 publications

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“…Microbial cell counts ranged from 2.3 10 7 to 4.7 10 7 cells gdw -1 and were consistent with previous studies from Arctic and sub-Arctic permafrost (1) (14) (15) (64) (65), but were one to two orders of magnitude lower than is commonly observed in temperate soils (66) (67) (68). Among the three age categories the intermediate had the highest number of live, dead, and total cells and the highest proportion of live cells.…”

Section: Discussionsupporting

confidence: 89%

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Burkert

Douglas

Waldrop

et al. 2018

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29Permafrost hosts a community of microorganisms that survive and reproduce for 30 millennia despite extreme environmental conditions such as water stress, subzero 31 temperatures, high salinity, and low nutrient availability. Many studies focused on 32 permafrost microbial community composition use DNA-based methods such as 33 metagenomic and 16S rRNA gene sequencing. However, these methods do not 34 distinguish between active, dead, and dormant cells. This is of particular concern in 35 ancient permafrost where constant subzero temperatures preserve DNA from dead 36 organisms and dormancy may be a common survival strategy. To circumvent this 37 we applied: (i) live/dead differential staining coupled with microscopy, (ii) 38 endospore enrichment, and (iii) selective depletion of DNA from dead cells to 39 permafrost microbial communities across a Pleistocene permafrost chronosequence 40 (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from 41 live, dead, and dormant cells revealed how communities differ between these pools 42 and how they change over geologic time. We found clear evidence that cells capable 43 of forming endospores are not necessarily dormant and that the propensity to form 44 endospores differed among taxa. Specifically, Bacilli are more likely to form 45 endospores in response to long-term stressors associated with permafrost 46 environmental conditions than members of Clostridia, which are more likely to 47 content largely control microbial community diversity and cell abundances. 52 53 IMPORTANCE 54 The study of permafrost transcends the study of climate change and 55 exobiology. Permafrost soils store more than half earth's soil carbon despite 56 covering ~15% of the land area (Tarnocai et al 2009). This permafrost carbon is 57 rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015) . 58 Understanding microbial communities in permafrost will contribute to the 59 knowledge base necessary to understand the rates and forms of permafrost C and N 60 cycling post thaw. Permafrost is also an analog for frozen extraterrestrial 61 environments and evidence of viable organisms in ancient permafrost is of interest 62 to those searching for potential life on distant worlds. If we can identify strategies 63 microbial communities utilize to survive permafrost we can focus efforts searching 64 for evidence of life on cryogenic cosmic bodies. Our work is significant because it 65 contributes to an understanding of how microbial life adapts and survives in the 66 extreme environmental conditions in permafrost terrains across geologic timescales. 67 68 drastically alter estimates of diversity and abundance. Furthermore, because many 75 communities host dormant cells, DNA-based approaches may not represent active 76 members. In temperate soils, up to 40% of DNA is from dead or compromised cells (3). 77In permafrost, the amount of 'relic' DNA may be even higher because frozen conditions 78 preserve DNA from dead cells. In non-permafrost environments, multi-omic approac...

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Section: Discussionsupporting

confidence: 89%

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Burkert

Douglas

Waldrop

et al. 2018

Preprint

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“…The effect of 10 and 20 years of continuous organic farming versus conventional farming practices on agricultural soil health was studied [111], reporting a stimulation of soil ecosystem functioning under organic management which was driven by the alteration of the soil microbial composition rather than by changes in species richness. A lack of long-term impact of organic amendments on soil microbial alpha-diversity, in the presence of significant shifts in soil microbial community structure, was observed by other authors [82,112].…”

Section: Beneficial Effects Of Organic Amendmentssupporting

confidence: 50%

“…Aiming to facilitate this somewhat overwhelming task, the use of molecular and, particularly, "omics" methods and techniques is currently being increasingly promoted. Nevertheless, many of these molecular biology tools still have many technical limitations and constraints, which points out the need to be very cautious when drawing conclusions about the responses of soil microbial communities to the application of agricultural practices, including, of course, the application of organic amendments [81,82].…”

Section: Beneficial Effects Of Organic Amendmentsmentioning

confidence: 99%

“…Positive effects on soil biological properties following the application of organic amendments were substantially evidenced in many studies. A great deal of investigations on the use of organic amendments [41,49,50,82,[95][96][97][98][99][100][101][102][103][104][105] reported increases in soil microbial activity and biomass, as well as changes in microbial community composition (with potential concomitant effects on soil functioning) and, to a lesser extent, in microbial diversity. In this sense, a 10-year field experiment was conducted [106] to study the effects of replacing a mineral nitrogen fertilizer by an organic amendment (fermented pig manure), at different substitution ratios (0, 25, 50, 75, and 100%), on agricultural soil properties.…”

Section: Beneficial Effects Of Organic Amendmentsmentioning

confidence: 99%

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Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture

2019

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The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.

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“…The highest abundance of Firmicutes was observed in the MS1-and S2-amended soils. These bacteria thrive in soil with high C availability [50] and are well-known to degrade several complex organic materials [51,52]. Similarly, Wu and He [53] explained that Firmicutes can play a role in lignin depolymerization.…”

Section: Discussionmentioning

confidence: 99%

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

et al. 2018

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Crop residue and animal manure as a soil amendment have been recognized as a feasible agricultural practice owing to its contribution in improving the soil fertility (SF). The primary advantages of this practice are determined by the activities of soil microorganisms. However, goat manure (M), sugarcane straw (S), and goat manure plus straw (MS) amendments influence soil bacteria, their activities, and SF in clay-loam soil remains undefinable. Therefore, this study distinguished the efficacy of M, MS, and S amendment on soil enzyme activities and the availability of nutrients, including various bacterial populations in clay-loamy soil with respect to two different phases (50 and 100 days). In order to analyze the bacterial structure and their activities, we employed high-throughput sequencing (HTS) and soil enzyme activity (SEA) tests. Soil amended with M and MS not only significantly enhanced nutrient availability, including C, P, and N, soil pH, as well as SEA for C and N cycles in both phases. Additionally, the increase in nutrient availability was greater in M-and MS-amended soils in the second phase (100 days) compared to the M-and S-amended soils in the first phase (50 days). Moreover, plant growth promoting and lignocellulose degrading bacterial genera were enhanced under M-and MS-amended soil compared to S-amended soil in both phases. Distance-based redundancy analysis (dbRDA) showed that soil pH, carbon-nitrogen ratio (C:N), and nitrates (NO 3 − )were inducing the fewest changes, while total nitrogen (TN), total carbon (TC), available nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), and ammonium (NH 4 + )were the main operators in terms of change in bacterial populations. In general, we observed that M and MS are better amendment sources as compared to S amendment in order to enhance the SF in the clay-loamy soil in both phases, but greater fertility was exhibited in the second phase.

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Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

Cited by 85 publications

References 44 publications

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Potential Benefits and Risks for Soil Health Derived From the Use of Organic Amendments in Agriculture

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

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