scholarly journals Spatial-temporal dynamics of N-cycle functional genes in a temperate Atlantic estuary (Douro, Portugal)

2020 ◽  
Vol 84 ◽  
pp. 205-216
Author(s):  
P Salgado ◽  
A Machado ◽  
AA Bordalo
Keyword(s):  
Microbial Communities ◽  
Temporal Dynamics ◽  
Inorganic Nitrogen ◽  
Functional Genes ◽  
Estuarine Ecosystem ◽  
Monthly Basis ◽  
N Cycle ◽  
Low Salinity ◽  
Key Factor ◽  
Nitrogen Nutrients

Understanding the spatial and seasonal dynamics of nitrogen (N)-cycle microbial communities is pivotal for the knowledge of N biogeochemistry. The present study addressed the spatial-temporal variability of nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, and nosZI) key genes, as well as of non-denitrifying nitrous oxide (N2O) reducers (nosZII), coupled with key environmental variables, in an estuarine ecosystem (Douro, NW Portugal). Samples were collected on a monthly basis over 1 yr, key physical-chemical parameters were measured, and specific functional gene abundances were assayed. The results revealed a clear seasonality for nirS, nosZII, and bacterial and archaeal amoA abundance, with an increase during the winter/spring seasons. This period was especially characterized by high levels of dissolved oxygen, low temperature, low salinity, and increased turbidity. Indeed, turbidity emerged as the key factor controlling the distribution of nirS, nosZII bacterial, and archaeal amoA abundance. In contrast, the abundance of nosZI increased during the summer, while nirK abundance was enhanced from the fall to late spring. Additionally, the availability of dissolved inorganic nitrogen nutrients had no commensurable effect on N-cycle functional genes. This study of the annual variation of N-cycle functional genes in a temperate Atlantic estuary provides a major contribution to the understanding of how environmental factors potentially influence the distribution and abundance of N-cycle microbial communities.

scholarly journals Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Ezequiel Santillan ◽  
Florentin Constancias ◽  
Stefan Wuertz
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Community Assembly ◽  
Temporal Dynamics ◽  
Functional Gene ◽  
Functional Genes ◽  
Rrna Gene ◽  
Α Diversity ◽  
Press Disturbance ◽  
Joint Evaluation

ABSTRACT Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance. IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Construction of a Ginseng Root-Meristem Sensor and a Sensing Kinetics Study on the Main Nitrogen Nutrients

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 681
Author(s):  
Shiang Wang ◽  
Dingqiang Lu ◽  
Guangchang Pang
Keyword(s):  
Limit Of Detection ◽  
Inorganic Nitrogen ◽  
Equilibrium Analysis ◽  
Ginseng Root ◽  
Continuous Cropping ◽  
Sodium Glutamate ◽  
Sensor Sensitivity ◽  
Group A ◽  
Hardy Weinberg Equilibrium ◽  
Nitrogen Nutrients

Severe continuous cropping obstacles exist in ginseng cultivation. In order to assess these obstacles, a “sandwich” ginseng root tissue sensor was developed for the kinetic determination of five nitrogen nutrients. The results showed that the sensing parameters of the sensor reached an ultrasensitive level (limit of detection up to 5.451 × 10−24 mol/L) for the five nitrogen nutrients, and exhibited good stability and reproducibility. In the order of two-, four-, and six-year-old ginseng plants, the sensitivity to inorganic nitrogen nutrients (sodium nitrate and urea) showed an upward trend following an initial decline (the interconnected allosteric constant Ka values acted as the parameter). The fluctuations in sensor sensitivity to organic nitrogen nutrients, specifically nucleotides (disodium inosinate and disodium guanylate), were relatively small. The sensor sensitivity of two-, four-, and six-year-old ginseng plants to sodium glutamate was 9.277 × 10−19 mol/L, 6.980 × 10−21 mol/L, and 5.451 × 10−24 mol/L, respectively. Based on the survival rate of the seedlings and mortality rate of the ginseng in each age group, a Hardy–Weinberg equilibrium analysis was carried out. The results showed that the sensing ability of the root system to sodium glutamate may be an important factor affecting its survival under continuous cropping obstacles with increasing age.

scholarly journals Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions

2018 ◽  
Vol 9 ◽  
Author(s):  
Kadiya Calderón ◽  
Laurent Philippot ◽  
Florian Bizouard ◽  
Marie-Christine Breuil ◽  
David Bru ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
N Cycle ◽  
Soil Microbial

scholarly journals Life on leaves : uncovering temporal dynamics in Arabidopsis' leaf microbiota

2021 ◽  
Author(s):  
Juliana Almario ◽  
Maryam Mahmoudi ◽  
Samuel Kroll ◽  
Matthew Agler ◽  
Aleksandra Placzek ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Photosynthetic Activity ◽  
Temporal Dynamics ◽  
Growing Season ◽  
High Turnover ◽  
Microbial Network ◽  
Stabilization Phase ◽  
Time Patterns ◽  
Microbe Interactions ◽  
Compositional Changes

Leaves are primarily responsible for the plant′s photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plant′s lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plant′s growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plant′s growing season. Despite a high turnover in these communities, we identified 19 "core" taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network "hubs" and "hubs" alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.

scholarly journals Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data

2019 ◽  
Vol 3 ◽  
Author(s):  
Shruthi Magesh ◽  
Viktor Jonsson ◽  
Johan Bengtsson-Palme
Keyword(s):  
Microbial Communities ◽  
Point Mutations ◽  
Software Tool ◽  
Metagenomic Data ◽  
Data Sets ◽  
Resistance Mutations ◽  
Shotgun Metagenomics ◽  
Key Factor ◽  
Detection Of Mutations ◽  
And Function

Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. Bioinformatic methods for metagenomic analysis have generally been poor at accounting for this fact, resulting in a somewhat limited picture of important aspects of microbial communities. Here, we address this problem by providing a software tool called Mumame, which can distinguish between wildtype and mutated sequences in shotgun metagenomic data and quantify their relative abundances. We demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets. We also identified that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. Mumame is freely available online (http://microbiology.se/software/mumame).

scholarly journals Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

2020 ◽  
Author(s):  
Haitao Wang ◽  
Micha Weil ◽  
Dominik Zak ◽  
Diana Münch ◽  
Anke Günther ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Community Composition ◽  
Structural Equation ◽  
Structural Equation Models ◽  
Temporal Dynamics ◽  
Salt Water ◽  
Microbial Community Composition ◽  
Gas Emissions

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

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