scholarly journals Insights into the Variations of Hao-Dependent Nitrifying and Nir-Dependent Denitrifying Microbial Communities in Ammonium-Graduated Lake Environments

2019 ◽  
Vol 9 (16) ◽  
pp. 3229
Author(s):  
Zhao ◽  
Chen ◽  
Qu ◽  
Jin ◽  
Zheng ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Spatial Scales ◽  
Biogeochemical Cycles ◽  
Nitrifying Bacteria ◽  
Microbial Populations ◽  
High Nitrogen ◽  
Hydroxylamine Oxidoreductase ◽  
Nitrosomonas Oligotropha

Biological nitrification and denitrification play significant roles in nitrogen-associated biogeochemical cycles. However, our understanding of the spatial scales at which microbial communities act and vary is limited. We used gene-specific metagenomic PCR to explore changes in nitrifying and denitrifying microbial communities within pristine lake and its branches, where the ammonium and dissolved organic carbon (DOC) concentrations form a gradient. The biomarkers hydroxylamine oxidoreductase and nitrite reductase genes indicated that strong relationships exist between the diversities and community structures of denitrifiers and ammonium gradients. It showed that the Nitrosomonas oligotropha cluster dominates the nitrifying bacteria in low-nutrition environments, while a new Nitrosomonas ureae cluster accounted for nearly 80% of the nitrifying bacteria in high-nitrogen environments. The distribution and diversity of nirS/K-dependent denitrifiers in the various habitats were similar, but predominantly affiliated with unknown clusters. Moreover, the abundance of all the hao genes dramatically outnumbered that of nir genes. The relative abundance of hao was clearly higher during eutrophication (13.60%) than during oligotrophy (5.23%), whereas that of nirS showed opposite tendencies. Overall, this study provides valuable comparative insights into the shifts in nitrifying and denitrifying microbial populations in lake environments with ammonium gradients, suggesting that unique dominant denitrifiers probably play an important role in the nitrogen cycle.

scholarly journals Impact of Pesticides on Microbial Diversity and Enzymes in Soil

2019 ◽  
pp. 1-16 ◽  
Author(s):  
T. L. Ataikiru ◽  
G. S. C. Okpokwasili ◽  
P. O. Okerentugba
Keyword(s):  
Enzyme Activity ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Soil Quality ◽  
Enzyme Activities ◽  
Heterotrophic Bacteria ◽  
Field Application ◽  
Nitrifying Bacteria ◽  
Microbial Populations ◽  
Microbial Counts

Introduction: The presence of pesticides in soils could result in alterations in microbial activities (enzyme activities, microbial populations), soil physical and chemical properties. Research gap/Challenges: Insufficient literatures on extensive monitoring of soil quality through enzyme activity, during pesticides application. Existing literatures concerning analysis of effect of pesticide application on soil enzyme activity are not comprehensive with respect to number of soil enzymes analysed. Aim/Objective: The study was conducted to investigate the effect of carbofuran and paraquat on soil biochemical characteristics on certain soils in the Niger Delta region of Nigeria. Methodology: These pesticides were applied at recommended doses, their effects on soil organic carbon, enzymes activity and microbial populations were assessed using standard methods. The enzymes monitored were amylase, invertase, protease, urease, phosphatase and dehydrogenase. Microbial counts were carried out for total heterotrophic bacteria, fungi, actinomycetes, nitrifying bacteria and phosphate solubilizers using the spread plate method. Results: There were variations in the different enzyme activities in carbofuran – and paraquat - treated soil during this research. Dehydrogenase activity increased in treated soils. Also, urease activity was lower compared to other enzyme activities. As the study progressed, variations in values of soil organic carbon were observed.  There was a gradual increase in microbial counts and can be traceable to their ability to temporarily mineralize and use the pesticides as carbon and energy source. The soil organic carbon, enzymes and microbial counts values were significantly different at P=0.05. Conclusion: This research revealed that the pesticides cause temporal impact on microbial populations and enzyme activities, associated with the pesticide type at recommended field application rates. A change in numbers, activity and diversity of soil microorganisms may act as indicators of soil fertility and reflect the soil quality.

scholarly journals Spatial Variability of Abyssal Nitrifying Microbes in the North-Eastern Clarion-Clipperton Zone

2021 ◽  
Vol 8 ◽  
Author(s):  
Anita L. Hollingsworth ◽  
Daniel O. B. Jones ◽  
C. Robert Young
Keyword(s):  
Organic Carbon ◽  
Spatial Variability ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Biogeochemical Cycles ◽  
Rrna Gene ◽  
Seafloor Topography ◽  
Ammonia Oxidizing Archaea ◽  
The North ◽  
Polymetallic Nodules

Abyssal microbes drive biogeochemical cycles, regulate fluxes of energy and contribute to organic carbon production and remineralization. Therefore, characterizing the spatial variability of benthic microbes is important for understanding their roles in benthic environments and for conducting baseline assessments of areas of the seabed that might be targeted by commercial mining activities. Yet, detailed assessments of the spatial distributions of benthic microbial communities in these regions are still incomplete, and these efforts have not yet considered the influence of seafloor topography and heterogeneity on microbial distributions across a range of scales. In this study, we investigated the composition and spatial variability of benthic microbial assemblages found in sediments and polymetallic nodules collected from the Clarion Clipperton Zone (CCZ) in the equatorial Pacific (4000–4300 m water depth). We used 16S rRNA gene sequences to characterize these communities. The upper 20 cm of abyssal sediments harbored diverse and distinctive microbial communities in both sediments and their associated polymetallic nodules, with high similarity across topographical areas of the seabed. Assemblage composition differed vertically through the sediment, by habitat and across small to mesoscales. Potential carbon-fixing microbes formed more than 25% relative abundance of sediment assemblages, which were dominated by ammonia-oxidizing Archaea Nitrosopumilus. Non-photosynthetic Cyanobacteria were more frequent in the deeper sediment layers and nodules. Sediment communities had a higher abundance of taxa involved in nitrogen cycling, such as Nitrosopumilus, Nitrospina, Nitrospira, AqS1 (Nitrosococcaceae), and methanogens wb1-A12 (NC10 phylum). In contrast, nodules were more enriched in Alphaproteobacteria, Gammaproteobacteria, Planctomycetes, Acidobacteria, Bacteroidetes, Nanoarchaeaeota, and Calditrichaeota. Microbes related to potential metal-cycling (Magnetospiraceae and Kiloniellaceae), organic carbon remineralization (Woeseia), and sulfur-oxidizing Thiohalorhabdaceae were also more enriched in nodules. Our results indicate that benthic microbial community composition is driven by sediment profile depth and seafloor heterogeneity at small and mesoscales. The most abundant microbial taxa within the sediments were nitrifying and putative carbon-fixing microbes, and may have key ecological roles in mediating biogeochemical cycles in this habitat.

scholarly journals A gene co-association network regulating gut microbial communities in a Duroc pig population

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Reverter ◽  
Maria Ballester ◽  
Pamela A. Alexandre ◽  
Emilio Mármol-Sánchez ◽  
Antoni Dalmau ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Candidate Genes ◽  
Relative Abundance ◽  
Association Studies ◽  
Single Gene ◽  
Host Genome ◽  
Genome Wide Association Studies ◽  
Vaccine Response ◽  
Microbiome Composition ◽  
Host Genetic

Abstract Background Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical “single-gene-single-trait” approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP–P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. Conclusions Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits.

scholarly journals Multicellular and unicellular responses of microbial biofilms to stress

2020 ◽  
Vol 401 (12) ◽  
pp. 1365-1374
Author(s):  
Daniel K.H. Rode ◽  
Praveen K. Singh ◽  
Knut Drescher
Keyword(s):  
Microbial Communities ◽  
Stress Responses ◽  
Spatial Scales ◽  
Organizational Level ◽  
Internal Stresses ◽  
Microbial Life ◽  
Microbial Biofilms ◽  
Applied Stresses

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.

Soil organic carbon and microbial communities respond to vineyard management

2015 ◽  
Vol 31 (4) ◽  
pp. 528-533 ◽  
Author(s):  
F. Zehetner ◽  
I. Djukic ◽  
R. Hofmann ◽  
L. Kühnen ◽  
G. Rampazzo-Todorovic ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Microbial Communities ◽  
Vineyard Management

scholarly journals Iron-bound organic carbon in forest soils: quantification and characterization

2016 ◽  
Vol 13 (16) ◽  
pp. 4777-4788 ◽  
Author(s):  
Qian Zhao ◽  
Simon R. Poulson ◽  
Daniel Obrist ◽  
Samira Sumaila ◽  
James J. Dynes ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Spatial Variability ◽  
Forest Soils ◽  
The United States ◽  
Biogeochemical Cycles ◽  
Mean Annual Temperature ◽  
Aliphatic Carbon ◽  
A Site ◽  
The Impact ◽  
X Ray Absorption

Abstract. Iron oxide minerals play an important role in stabilizing organic carbon (OC) and regulating the biogeochemical cycles of OC on the earth surface. To predict the fate of OC, it is essential to understand the amount, spatial variability, and characteristics of Fe-bound OC in natural soils. In this study, we investigated the concentrations and characteristics of Fe-bound OC in soils collected from 14 forests in the United States and determined the impact of ecogeographical variables and soil physicochemical properties on the association of OC and Fe minerals. On average, Fe-bound OC contributed 37.8 % of total OC (TOC) in forest soils. Atomic ratios of OC : Fe ranged from 0.56 to 17.7, with values of 1–10 for most samples, and the ratios indicate the importance of both sorptive and incorporative interactions. The fraction of Fe-bound OC in TOC (fFe-OC) was not related to the concentration of reactive Fe, which suggests that the importance of association with Fe in OC accumulation was not governed by the concentration of reactive Fe. Concentrations of Fe-bound OC and fFe-OC increased with latitude and reached peak values at a site with a mean annual temperature of 6.6 °C. Attenuated total reflectance–Fourier transform infrared spectroscopy (ATR-FTIR) and near-edge X-ray absorption fine structure (NEXAFS) analyses revealed that Fe-bound OC was less aliphatic than non-Fe-bound OC. Fe-bound OC also was more enriched in 13C compared to the non-Fe-bound OC, but C ∕ N ratios did not differ substantially. In summary, 13C-enriched OC with less aliphatic carbon and more carboxylic carbon was associated with Fe minerals in the soils, with values of fFe-OC being controlled by both sorptive and incorporative associations between Fe and OC. Overall, this study demonstrates that Fe oxides play an important role in regulating the biogeochemical cycles of C in forest soils and uncovers the governing factors for the spatial variability and characteristics of Fe-bound OC.

scholarly journals Do soil bacterial communities respond differently to abrupt or gradual additions of copper?

2018 ◽  
Vol 95 (1) ◽  
Author(s):  
Michael McTee ◽  
Lorinda Bullington ◽  
Matthias C Rillig ◽  
Philip W Ramsey
Keyword(s):  
Heavy Metals ◽  
Soil Respiration ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Diversity Indices ◽  
Microbial Populations ◽  
Metal Concentrations ◽  
Soil Bacterial Communities ◽  
Bacterial Richness

ABSTRACTMany experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

scholarly journals Forest defoliator outbreaks alter nutrient cycling in northern waters

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Samuel G. Woodman ◽  
Sacha Khoury ◽  
Ronald E. Fournier ◽  
Erik J. S. Emilson ◽  
John M. Gunn ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Water Chemistry ◽  
Inorganic Nitrogen ◽  
Biogeochemical Cycles ◽  
Dissolved Inorganic Nitrogen ◽  
Insect Outbreaks ◽  
Receiving Waters ◽  
North Temperate Lakes ◽  
Lake Waters ◽  
Terrestrial Biomass

AbstractInsect defoliators alter biogeochemical cycles from land into receiving waters by consuming terrestrial biomass and releasing biolabile frass. Here, we related insect outbreaks to water chemistry across 12 boreal lake catchments over 32-years. We report, on average, 27% lower dissolved organic carbon (DOC) and 112% higher dissolved inorganic nitrogen (DIN) concentrations in lake waters when defoliators covered entire catchments and reduced leaf area. DOC reductions reached 32% when deciduous stands dominated. Within-year changes in DOC from insect outbreaks exceeded 86% of between-year trends across a larger dataset of 266 boreal and north temperate lakes from 1990 to 2016. Similarly, within-year increases in DIN from insect outbreaks exceeded local, between-year changes in DIN by 12-times, on average. As insect defoliator outbreaks occur at least every 5 years across a wider 439,661 km2 boreal ecozone of Ontario, we suggest they are an underappreciated driver of biogeochemical cycles in forest catchments of this region.

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