scholarly journals Soil microbial community composition in a paddy field with different fertilization managements

2021 ◽  
pp. 1-11
Author(s):  
Limin Wang ◽  
Dongfeng Huang

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

2020 ◽  
Author(s):  
Markus Haber ◽  
Dalit Roth Rosenberg ◽  
Maya Lalzar ◽  
Ilia Burgsdorf ◽  
Kumar Saurav ◽  
...  

AbstractMarine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. We studied temporal and spatial patterns of the microbial community structure and activity along a coast to offshore transect from the Israeli coast of the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of two consecutive years. The ultra-oligotrophic status of the South Eastern Mediterranean Sea was reflected in the microbial community composition that was dominated by oligotrophic microbial groups such as SAR11 throughout the year, even at the most coastal station sampled. Seasons affected microbial communities much more than distance from shore explaining about half of the observed variability in the microbial community, compared to only about 6% that was explained by station. However, the most coastal site differed significantly in community structure and activity from the three further offshore stations in early winter and summer, but not in spring. Our data on the microbial community composition and its seasonality from a transect into the South Eastern Levantine basin support the notion that the EMS behaves similar to open gyres rather than an inland sea.


2021 ◽  
Vol 13 (8) ◽  
pp. 4111
Author(s):  
Fen Hou ◽  
Junjie Du ◽  
Ye Yuan ◽  
Xihui Wu ◽  
Sai Zhao

Aged refuse is widely considered to have certain soil fertility. 16S rRNA amplicon sequencing is used to investigate the microbial community of aged refuse. The aged refuse is found to contain higher soil fertility elements (total nitrogen, total phosphorus, total potassium, etc.) and higher concentrations of heavy metals (Pb, Cd, Zn, and Hg). Taxonomy based on operational taxonomic units (OTUs) shows that Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes are the main bacterial phyla in the two soils and there is a palpable difference in the microbial community composition between the two groups of samples. The genera Paramaledivibacter, Limnochorda, Marinobacter, Pseudaminobacter, Kocuria, Bdellovibrio, Halomonas, Gillisia, and Membranicola are enriched in the aged refuse. Functional predictive analysis shows that both the control soil and aged refuse have a high abundance of “carbohydrate metabolism” and “amino acid metabolism”, and show differences in the abundance of several metabolism pathways, such as “xenobiotics biodegradation and metabolism” and “lipid metabolism”. Aged refuse and undisturbed soil show significant differences in alpha diversity and microbial community composition. Multiple environmental factors (Hg, TN, Cr, Cd, etc.) significantly impact microorganisms’ abundance (Marinobacter, Halomonas, Blastococcus, etc.). Our study provides valuable knowledge for the ecological restoration of closed landfills.


Water ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 3300
Author(s):  
Alexis N. Neff ◽  
Dean M. DeNicola ◽  
Chris Maltman

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.


2018 ◽  
Vol 117 ◽  
pp. 164-174 ◽  
Author(s):  
Maaike van Agtmaal ◽  
Angela L. Straathof ◽  
Aad Termorshuizen ◽  
Bart Lievens ◽  
Ellis Hoffland ◽  
...  

2021 ◽  
Vol 12 ◽  
Author(s):  
Lucas Fillinger ◽  
Kerstin Hürkamp ◽  
Christine Stumpp ◽  
Nina Weber ◽  
Dominik Forster ◽  
...  

Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.


2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams

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.


2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu

<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>


2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang

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.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.


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