scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

scholarly journals Apple Root stocks and Pre-plant Soil Treatments Alter Soil Microbial Community Composition in a New York Orchard

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1128C-1128
Author(s):  
Shengrui Yao ◽  
Ian A. Merwin ◽  
Janice E. Thies
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Growth And Yield ◽  
Soil Microbial ◽  
Plant Soil ◽  
Soil Microbial Community Composition

Apple (Malu ×domestica) replant disease (ARD) is a soil-borne disease syndrome of complex etiology that occurs worldwide when establishing new orchards in old fruit-growing sites. Methyl bromide (MB) has been an effective soil fumigant to control ARD, but safer alternatives to MB are needed. We evaluated soil microbial communities, tree growth, and fruit yield for three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and five clonal rootstocks (M7, M26, CG6210, CG30, and G16), in an apple replant site at Ithaca, N.Y. Molecular fingerprinting (PCR-DGGE) techniques were used to study soil microbial community composition of root-zone soil of the different soil treatments and rootstocks. Tree caliper, shoot growth, and yield were measured annually from 2002–04. Among the five rootstocks we compared, trees on CG6210 had the most growth and yield, while trees on M26 had the least growth and yield. Soil treatments altered soil microbial communities during the year after pre-plant treatments, and each treatment was associated with distinct microbial groups in hierarchical cluster analyses. However, those differences among fungal and bacterial communities diminished during the second year after planting, and soil fungal communities equilibrated faster than bacterial communities. Pre-plant soil treatments altered bulk-soil microbial community composition, but those shifts in soil microbial communities had no obvious correlation with tree performance. Rootstock genotypes were the dominant factor in tree performance after 3 years of observations, and different rootstocks were associated with characteristic bacterial, pseudomonad, fungal, and oomycetes communities in root-zone soil.

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

2018 ◽  
Author(s):  
Alex Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

AbstractPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form endospores differed among taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results since its removal did not significantly alter the microbial community composition. These results extend the findings of a previous study that showed permafrost age and ice content largely control microbial community diversity and cell abundances.ImportanceThe study of permafrost transcends the study of climate change and exobiology. Permafrost soils store more than half earth’s soil carbon despite covering ∽15% of the land area (Tarnocai et al 2009). This permafrost carbon is rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. Permafrost is also an analog for frozen extraterrestrial environments and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive permafrost we can focus efforts searching for evidence of life on cryogenic cosmic bodies. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains across geologic timescales.

Surviving onshore soil microbial communities differ among the Qing-Tibetan lakes with different salinity

2019 ◽  
Vol 95 (11) ◽  
Author(s):  
Jianrong Huang ◽  
Jian Yang ◽  
Hongchen Jiang ◽  
Geng Wu ◽  
Zhanling Xie ◽  
...  
Keyword(s):  
Microbial Community ◽  
Tibetan Plateau ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Positive Correlation ◽  
Soil Microbial ◽  
Lake Waters

ABSTRACT Little is known about the onshore microbial contribution to the microbial communities in nearby lakes and its response to salinity. In this study, transplanting experiments were established by caging onshore soils with dialysis bags followed by in situ 50-day incubation in nearby lakes with different salinity on the Qinghai-Tibetan Plateau. At the end of the experiment, geochemical and microbial analyses were performed on the original soils, caged soils and lake waters and sediments at the incubation sites. The results showed that the salinity increased significantly (P < 0.05) in the caged soils and such salinity increases showed significant (P < 0.05) positive correlation with the salinity of the studied lakes. The microbial community composition and predicted functions in the caged soils were significantly (P < 0.05) changed in comparison with their corresponding original soils, and such variation could be mainly explained by the succession of members of the Proteobacteria, Bacteroidetes and Actinobacteria from the original soils to their corresponding caged soils. The onshore microbial contribution appeared to be limited (up to 11.2% for sediment and negligible for water, respectively) to nearby lake microbial communities. Nevertheless, the survival of onshore soil microbial communities was mainly limited by the salinity of the receiving lakes.

Microbial community composition seasonality and drift over years in small freshwater ecosystems

2021 ◽  
Author(s):  
Ludwig Jardillier ◽  
Gwendoline David ◽  
Philippe Deschamps ◽  
Paola Bertolino ◽  
David Moreira ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Temporal Patterns ◽  
Freshwater Ecosystems ◽  
Temperate Climate ◽  
Environmental Selection ◽  
Over Time

&lt;p&gt;Small freshwater ecosystems are highly diverse, widely distributed, may be identified as major actors in greenhouse gas fluxes and are potential stocks of freshwater for human usages. In principle, they are more sensitive to environmental disturbance than large aquatic ecosystems because their small volumes provide low buffering capacity. However, little is yet known about their microbial biodiversity and function and how it is structured over time. Yet, understanding the structuring of microbial primary producers, predators, parasites and degraders in these ecosystems is essential to appreciate and model their functioning in the next decades. We investigated the spatial distribution and temporal dynamics of microorganisms of the three domains of life (bacteria, archaea, microbial eukaryotes) at the intra- (seasonal) and inter-annual (pluri-annual) scale in five small freshwater ecosystems. We focused on four ponds and a brook located in northwestern France under temperate climate that we studied for eight years (2011-2019) at seasonal frequency. Microbial diversity was assessed through Illumina MiSeq sequencing of 16S and 18S rDNA amplicons. Several abiotic parameters (physical and chemical) were measured&lt;em&gt; in situ&lt;/em&gt; and in the laboratory to characterise the environmental conditions. Multivariate statistical analyses were conducted to identify temporal patterns and link them to environment changes. Microbial communities differed among the ecosystems despite their spatial proximity, likely due to differences in local environmental conditions. Microbial eukaryotic and prokaryotic communities exhibited seasonal temporal patterns and a shift in composition over the years. Microbial communities experienced a strong turnover at the seasonal scale leading to a low fraction (&lt; 2%) of recurrent taxa. In each ecosystem, the measured physico-chemical parameters slightly influenced the microbial community variance over time. These results suggest that biotic interactions but also dormancy, immigration and genetic evolution superimpose to environmental selection through time. Understanding their interplay will be essential to explain microbial community composition change in these ecosystems.&lt;span&gt;&amp;#160;&lt;/span&gt;&lt;/p&gt;

scholarly journals Slope Aspect Affects The Soil Microbial Communities In Karst Tiankeng Negative Landforms

2021 ◽  
Author(s):  
Cong Jiang ◽  
Wei Shui ◽  
Su-Feng Zhu ◽  
Jie Feng
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Large Scale ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Slope Aspect ◽  
Soil Conditions ◽  
Metagenomic Sequencing ◽  
Soil Microbial

Abstract Background: Karst tiankeng is a large-scale negative surface terrain, and slope aspect affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated. Methods: In this study, metagenomic sequencing technology was used to analyzed the soil microbial communities and metabolic function on the shady and sunny slopes of karst tiankeng. Results: The Shannon-Wiener diversity of microbial communities on shady slopes was significantly higher than that on shady slopes. Shady and sunny slopes have similar microbial community composition, but there are differences in abundance. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOM and pH). Conclusions: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.

scholarly journals Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

2015 ◽  
Vol 12 (13) ◽  
pp. 10359-10387 ◽  
Author(s):  
W. Y. Dong ◽  
X. Y. Zhang ◽  
X. Y. Liu ◽  
X. L. Fu ◽  
F. S. Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Chinese Fir ◽  
Subtropical China ◽  
Nitrogen And Phosphorus ◽  
Soil Microbial ◽  
Nutrient Additions

Abstract. Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

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