Microorganisms In Permafrost Research Articles

Carbon‐cycling microorganisms in permafrost and their responses to a warming climate: A review

AbstractGlobal climate warming is accelerating permafrost degradation. The large amounts of soil organic matter in permafrost‐affected soils are prone to increased microbial decomposition in a warming climate. Along with permafrost degradation, changes to the soil microbiome play a crucial role in enhancing our understanding and in predicting the feedback of permafrost carbon. In this article, we review the current state of knowledge of carbon‐cycling microbial ecology in permafrost regions. Microbiomes in degrading permafrost exhibit variations across spatial and temporal scales. Among the short‐term, rapid degradation scenarios, thermokarst lakes have distinct biogeochemical conditions promoting emission of greenhouse gases. Additionally, extreme climatic events can trigger drastic changes in microbial consortia and activity. Notably, environmental conditions appear to exert a dominant influence on microbial assembly in permafrost ecosystems. Furthermore, as the global climate is closely connected to various permafrost regions, it will be crucial to extend our understanding beyond local scales, for example by conducting comparative and integrative studies between Arctic permafrost and alpine permafrost on the Qinghai–Tibet Plateau at global and continental scales. These comparative studies will enhance our understanding of microbial functioning in degrading permafrost ecosystems and help inform effective strategies for managing and mitigating the impacts of climate change on permafrost regions.

Permafrost thawing exhibits a greater influence on bacterial richness and community structure than permafrost age in Arctic permafrost soils

Abstract. Global warming accelerates permafrost thawing and changes its microbial community structure, but little is known about how microorganisms in permafrost with different ages respond to thawing. Herein, we disentangled the relative importance of permafrost age (young, medium-aged, old, and ancient, spanning from 50 to 5000 years) and thawing status (active, transitional, and permanently frozen) in shaping bacterial community structure using HiSeq sequencing of the 16S rRNA gene. Our results revealed significant influences of both permafrost thawing and age on bacterial richness. The bacterial richness was significantly higher in the young and thawed permafrost, and the richness increase was mainly observed in Firmicutes, Actinobacteria, Chloroflexi, Deltaproteobacteria, and Alphaproteobacteria. Permafrost thawing led to a gradual change in bacterial community structure and increased contribution of determinism. Permutational analysis of variance demonstrated that thawing significantly changed bacterial community structure at all soil ages, but the community convergence due to permafrost thawing was not observed. Structural equation modeling revealed that permafrost thawing exhibited a greater influence on both bacterial richness and community structure than permafrost age. Our results indicate that microorganisms in permafrost with different ages respond differently to thawing, which eventually leads to distinct bacterial community compositions and different organic carbon decomposition processes in Arctic permafrost.

Free Iron and Iron-Reducing Microorganisms in Permafrost and Permafrost-Affected Soils of Northeastern Siberia

An agreement between the content of amorphous (oxalate-extractable) iron and morphochromatic features of gley attests to the modern activity of gleyzation processes in tundra soils of the Kolyma Lowland, especially within lower parts of gentle and steep slopes. A suprapermafrost reduced gley horizon thawing out in the warmest years is considered a relic of the warmer and wetter stage of soil formation. An integrated analysis of data on the contents of mobile iron and annotated metagenomes indicates that microorganisms affiliated with the Proteobacteria phylum capable of iron reduction predominate in sediments formed under hydromorphic conditions and in modern mineral soil. In laboratory experiments, the process of microbial iron reduction was more active at 5°C than at 20°C. Therefore, it can be assumed that the majority of cultivated communities of iron-reducing bacteria have been adapted to low Arctic temperatures. Under conditions of climate warming and an increase in precipitation, permafrost temperature, and thickness of the seasonally thawed layer, iron reduction processes in the soils rich in the total iron will play an even greater role and create favorable redox conditions for the formation of methane, one of the most important greenhouse gases.

Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria.

Permafrost accounts for 27% of all soil ecosystems and harbors diverse microbial communities. Our understanding of microorganisms in permafrost, their activities and adaptations, remains limited. Using five subzero-growing (cryophilic) permafrost bacteria, we examined features of cold adaptation through comparative genomic analyses with mesophilic relatives. The cryophiles possess genes associated with cold adaptation, including cold shock proteins, RNA helicases, and oxidative stress and carotenoid synthesis enzymes. Higher abundances of genes associated with compatible solutes were observed, important for osmoregulation in permafrost brine veins. Most cryophiles in our study have higher transposase copy numbers than mesophiles. We investigated amino acid (AA) modifications in the cryophiles favoring increased protein flexibility at cold temperatures. Although overall there were few differences with the mesophiles, we found evidence of cold adaptation, with significant differences in proline, serine, glycine and aromaticity, in several cryophiles. The use of cold/hot AA ratios of >1, used in previous studies to indicate cold adaptation, was found to be inadequate on its own. Comparing the average of all cryophiles to all mesophiles, we found that overall cryophiles had a higher ratio of cold adapted proteins for serine (more serine), and to a lesser extent, proline and acidic residues (fewer prolines/acidic residues).

Quantitative characteristics of microorganisms in permafrost at different depths and their relation to soil physicochemical properties

Quantitative characteristics of microorganisms in permafrost at different depths and their relation to soil physicochemical properties

The structural bases of long-term anabiosis in non-spore-forming bacteria

Peculiarities of the structural organization in non-spore-forming bacteria associated with long-term anabiosis were revealed both in laboratory cultures and in natural populations isolated from 1–3-Myr-old Eastern Siberian permafrost and tundra soil. Different advanced methods were used, including (a) high-resolution electron microscopy; (b) simulation of in situ conditions in the laboratory by varying the composition of growth medium and cultivation conditions; (c) low-temperature fractionation to isolate and concentrate microbial cells from natural soils; (d) comparative morphological analysis of microbial cells in model cultures and natural soils (in situ). Under laboratory conditions, the intense formation of resting cells by representatives of various taxa of eubacteria and halophilic archaea occurred in 2–9-month-old cultures grown in carbon-, nitrogen-, or phosphorus-limited media, in starved cell suspensions in the presence of sodium silicate, or on soil agar. Among resting cells, we revealed cystlike forms having a complicated structure and common features. These included a thick capsule; a thickened and multiprofile cell wall; the presence of large intramembrane particles on PF- and EF-fracture surfaces; fine-grained or lumpy cytoplasm; and a condensed nucleoid. The general morphological properties, ultrastructural organization, physiological features of cystlike cells, and their ability to germinate under the appropriate conditions suggest the existence of constitutive dormancy in non-spore-forming bacteria. It was found that the majority of microorganisms in permafrost and tundra soil are cystlike cells, very similar to those in laboratory cultures. Anabiotic (resting) cystlike cells are responsible for the survival of non-spore-formers in extreme Earth habitats and may be regarded as possible analogs of extraterrestrial forms of microbial life.

Methane generation in permafrost sediments.

Discovery of viable microorganisms in permafrost [1–4] raised the problem of their metabolic status. It is uncertain whether or not the microorganisms stored in permafrost sediments remain metabolically active. The use of radioactively labeled compounds is one of a few methods of detection of metabolic processes in permafrost sediments. It was shown [5] that microbial lipids could be synthesized in permafrost sediments.

Exobiological aspects of mass transfer in microzones of permafrost deposits

The possibility of long-term survival of viable microorganisms in permafrost on other plants and on asteroids is inferred from physical and chemical conditions in dispersed frozen systems. An important factor for long-term survival of microorganisms in dispersed systems at temperatures below 0°C is the transfer of unfrozen liquid water and ions. Our experimental data show that mass exchange in frozen rocks is greatest in microzones with low ice content and high chemical potential gradients. Ion diffusion coefficients there are greater that 10 −10 m 2/s. These microzones are localized close to ice inclusions (schlierens, lenses, veins). Material with high ice content, on the other hand, is characterized by very low transfer coefficients (ion diffusion less than 10 −16 m 2/s). The occurrence of highly permeable microzones in permafrost supports the hypothesis that mass transfer there could result in exchange of liquid water and ions between living cells and the habitat, permitting metabolism. Highly permeable microzones in frozen rocks are the areas in permafrost most likely to support viable microorganisms in the active state on Earth, on cold planets, and on asteroids.

Evidence for Longevity of Seeds and Microorganisms in Permafrost

The problem of whether seeds and microorganisms are able to remain viable in permanently frozen ground during a very long span of years was recently considered by Porsild et al. who germinated Lupinus arcticus seeds from fossil rodent burrows in permanently frozen silt deposited in a placer mining area in the Yukon Territory. Based on the geology of the locality, Porsild et al. estimated the age of the seeds to be at least 10,000 years. Moreover, in that and in previous papers Porsild suggests that seeds of Rorippa barbareaefolia, Descurainia sophioides, and Senecio congestus may be able to survive in permanently frozen silt as these species apparently are restricted to freshly disturbed soil within the placer mining districts. Discussing in general the problems of dating viable seeds in old deposits Godwin questions the dating of the Lupinus arcticus seeds because of the indirect method applied. In view of these studies and the investigations made by Odum on the presence and age of viable seeds in Danish soils, Ester Creek placer mine west of Fairbanks, Alaska, was visited 16 to 19 July 1968. Some observations on the vegetation on the exposed silt and disturbed soil were made and soil samples were taken for further examination .... The contents of microorganisms in the soil samples were examined by using the dilution plate technique: 10 g of each sample were mixed with 90 ml of sterile water and placed on a shaking table for 20 minutes. Serial dilutions were made, and 0.1 ml of each of 10**-1, 10**-2, 10**-3 and 10**-4 suspensions were plated on Bengal Rose-, Sabouraud-, Cook-, and V-8-agar. Besides 1 ml of each suspension was added to test tubes with NIB. After one week of incubation at 4°C, 24°C, and 37°C the colonies were counted and the different strains isolated on slants with V-8-agar. The sample from the top soil showed c 10**3 fungi per g soil at 24° C, representing the following genera, known from similar localities: Cladosporium herbarum, Mortierella sp., Mucor circinelloides, Penicillium spp., Trichoderma viride, and unidentified, sterile imperfects and phycomycetes. ... Only a few investigations have been carried out to find living microorganisms in permanently frozen soil, and generally only the upper layers have been studied, because of the difficulties of sampling through permafrost. However Becker and Volkmannlo recovered 8 bacteria at 20 to 60 feet below the surface in permanently frozen soil near Fairbanks. Boyd and Boyd also studied permafrost soils from Barrow, Alaska, near Bison Lagoon, and found living bacteria at 8 to 15 feet. The distribution of Descurainia sophioides within the placer mine area and its extremely high frequency on the exposed muck does strongly support Porsild's theory. However, the fact that the seeds of the species are lacking in the investigated samples may lead to the alternative possibility that the ecology of the species is rather specific. Which factor or combination of factors is responsible for the germination and growth of the species on that particular substratum, ... cannot be determined without field experiments at the locality and further analyses; the high water content of the silt may appear to be a factor of importance. The investigation does not prove that viable seeds of Descurainia sophioides, Rorippa barbareaefolia, Senecio congestus or any other species are not present in permanently frozen soil; the negative result of the investigation, however, indicates that on this locality it is not very likely that they are present. ...